Stitching fails on test dataset.

[vbrow29]

Hi,

I am deploying the PairwiseStitching module on my HPC system. To test the latest version of BigStitcher-Spark, I am running the latest version on the test dataset (N5+XML, unaligned).
Previous version (0.0.2) of BigStitcher handles this data fine and generates the correlation for all overlapping views, but I am seeing only r=0 for all tile pairs with the latest version (0.1.0) [61c4424].

I also observe this error in the log file for both versions:

2025-03-13 16:31:59,193 [task-result-getter-1] WARN [TaskSetManager]: Lost task 209.0 in stage 0.0 (TID 209) (10.110.100.15 executor 9): java.lang.NullPointerException
	at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineOrSplitBy(Group.java:234)
	at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineBy(Group.java:172)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.pickBrightest(GroupedViewAggregator.java:119)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.aggregate(GroupedViewAggregator.java:102)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator.aggregate(GroupedViewAggregator.java:396)
	at net.preibisch.stitcher.algorithm.globalopt.TransformationTools.computeStitching(TransformationTools.java:277)
	at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.lambda$call$c9354d04$1(SparkPairwiseStitching.java:202)
	at org.apache.spark.api.java.JavaPairRDD$.$anonfun$toScalaFunction$1(JavaPairRDD.scala:1070)
	at scala.collection.Iterator$$anon$10.next(Iterator.scala:461)
	at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:224)
	at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:302)
	at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1597)
	at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1524)
	at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1588)
	at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1389)
	at org.apache.spark.storage.BlockManager.getOrElseUpdateRDDBlock(BlockManager.scala:1343)
	at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:379)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:329)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:93)
	at org.apache.spark.TaskContext.runTaskWithListeners(TaskContext.scala:166)
	at org.apache.spark.scheduler.Task.run(Task.scala:141)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:620)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally(SparkErrorUtils.scala:64)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally$(SparkErrorUtils.scala:61)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:94)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:623)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)

I also attached an image showing the diff between the log for my old version (0.0.2) and the latest.

[StephanPreibisch]

Thanks so much, I'll look into it!

[StephanPreibisch]

So, that's weird, for me it works with the current version, running it locally using Spark (see below). Could you please confirm that this works for you too? Because if so it is most likely related to some deployment issue, i.e. the Spark environment you run it on @vbrow29:

(base) preibischs@preibischs-lm5 BigStitcher-Spark % ./stitching -x '/Users/preibischs/Downloads/Stitching_N5_XML/dataset.xml' --minR 0.8 --localSparkBindAddress
[-x, /Users/preibischs/Downloads/Stitching_N5_XML/dataset.xml, --minR, 0.8, --localSparkBindAddress]
xml: file:/Users/preibischs/Downloads/Stitching_N5_XML/dataset.xml
Compression 'org.janelia.saalfeldlab.n5.blosc.BloscCompression' could not be registered
The following ViewIds will be processed: 
[0,0] [0,1] [0,2] [0,3] [0,4] [0,5] [0,6] [0,7] [0,8] [0,9] [0,10] [0,11] [0,12] [0,13] [0,14] [0,15] [0,16] [0,17] 
(Sat Mar 15 10:22:24 EDT 2025): Downsampling used for stitching: (2, 2, 1)
(Sat Mar 15 10:22:24 EDT 2025): Finding pairs to compute overlap ... 
Sat Mar 15 10:22:24 EDT 2025: Removed 4 non-overlapping view-pairs for computing.
(Sat Mar 15 10:22:24 EDT 2025): For the following pairs pairwise stitching will be computed:
	0-5, 0-11, 0-17 <=> 0-4, 0-10, 0-16
	0-5, 0-11, 0-17 <=> 0-3, 0-9, 0-15
	0-5, 0-11, 0-17 <=> 0-2, 0-8, 0-14
	0-5, 0-11, 0-17 <=> 0-1, 0-7, 0-13
	0-5, 0-11, 0-17 <=> 0-0, 0-6, 0-12
	0-4, 0-10, 0-16 <=> 0-3, 0-9, 0-15
	0-4, 0-10, 0-16 <=> 0-2, 0-8, 0-14
	0-4, 0-10, 0-16 <=> 0-1, 0-7, 0-13
	0-4, 0-10, 0-16 <=> 0-0, 0-6, 0-12
	0-3, 0-9, 0-15 <=> 0-2, 0-8, 0-14
	0-3, 0-9, 0-15 <=> 0-1, 0-7, 0-13
	0-3, 0-9, 0-15 <=> 0-0, 0-6, 0-12
	0-2, 0-8, 0-14 <=> 0-1, 0-7, 0-13
	0-2, 0-8, 0-14 <=> 0-0, 0-6, 0-12
	0-1, 0-7, 0-13 <=> 0-0, 0-6, 0-12
(Sat Mar 15 10:22:24 EDT 2025): In total: 15 pair(s).
Using Spark's default log4j profile: org/apache/spark/log4j2-defaults.properties
25/03/15 10:22:24 INFO SparkContext: Running Spark version 3.3.2
25/03/15 10:22:24 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/03/15 10:22:24 INFO ResourceUtils: ==============================================================
25/03/15 10:22:24 INFO ResourceUtils: No custom resources configured for spark.driver.
25/03/15 10:22:24 INFO ResourceUtils: ==============================================================
25/03/15 10:22:24 INFO SparkContext: Submitted application: SparkPairwiseStitching
25/03/15 10:22:24 INFO ResourceProfile: Default ResourceProfile created, executor resources: Map(cores -> name: cores, amount: 1, script: , vendor: , memory -> name: memory, amount: 1024, script: , vendor: , offHeap -> name: offHeap, amount: 0, script: , vendor: ), task resources: Map(cpus -> name: cpus, amount: 1.0)
25/03/15 10:22:24 INFO ResourceProfile: Limiting resource is cpu
25/03/15 10:22:24 INFO ResourceProfileManager: Added ResourceProfile id: 0
25/03/15 10:22:24 INFO SecurityManager: Changing view acls to: preibischs
25/03/15 10:22:24 INFO SecurityManager: Changing modify acls to: preibischs
25/03/15 10:22:24 INFO SecurityManager: Changing view acls groups to: 
25/03/15 10:22:24 INFO SecurityManager: Changing modify acls groups to: 
25/03/15 10:22:24 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(preibischs); groups with view permissions: Set(); users  with modify permissions: Set(preibischs); groups with modify permissions: Set()
25/03/15 10:22:24 INFO Utils: Successfully started service 'sparkDriver' on port 52051.
25/03/15 10:22:24 INFO SparkEnv: Registering MapOutputTracker
25/03/15 10:22:24 INFO SparkEnv: Registering BlockManagerMaster
25/03/15 10:22:24 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/03/15 10:22:24 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/03/15 10:22:24 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
25/03/15 10:22:24 INFO DiskBlockManager: Created local directory at /private/var/folders/b0/sgyw0d9918vfjl96c5dlc3fw0000gp/T/blockmgr-1a7a171f-cd56-409d-84aa-e941e8fcaf92
25/03/15 10:22:24 INFO MemoryStore: MemoryStore started with capacity 8.4 GiB
25/03/15 10:22:24 INFO SparkEnv: Registering OutputCommitCoordinator
25/03/15 10:22:24 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/03/15 10:22:24 INFO Executor: Starting executor ID driver on host 208.91.197.27
25/03/15 10:22:24 INFO Executor: Starting executor with user classpath (userClassPathFirst = false): ''
25/03/15 10:22:24 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 52052.
25/03/15 10:22:24 INFO NettyBlockTransferService: Server created on 208.91.197.27:52052
25/03/15 10:22:24 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/03/15 10:22:24 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 208.91.197.27, 52052, None)
25/03/15 10:22:24 INFO BlockManagerMasterEndpoint: Registering block manager 208.91.197.27:52052 with 8.4 GiB RAM, BlockManagerId(driver, 208.91.197.27, 52052, None)
25/03/15 10:22:24 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 208.91.197.27, 52052, None)
25/03/15 10:22:24 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 208.91.197.27, 52052, None)
Sat Mar 15 10:22:25 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-1, 0-7, 0-13: No shift found.
Sat Mar 15 10:22:25 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-0, 0-6, 0-12: No shift found.
Sat Mar 15 10:22:26 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-3, 0-9, 0-15: r=0.9589934808169884
Sat Mar 15 10:22:26 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-2, 0-8, 0-14: r=0.955800435940482
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-0, 0-6, 0-12: r=0.9290416526134466
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-1, 0-7, 0-13: No shift found.
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-1, 0-7, 0-13: r=0.9363659295585218
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-0, 0-6, 0-12: r=0.9793178941211977
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-1, 0-7, 0-13: r=0.9679939385326735
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-4, 0-10, 0-16: r=0.9723565991315614
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-2, 0-8, 0-14: r=0.9623363667060237
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-3, 0-9, 0-15: r=0.9730414262207491
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-0, 0-6, 0-12: No shift found.
Sat Mar 15 10:22:27 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-2, 0-8, 0-14: r=0.9777585663957139
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-1, 0-7, 0-13 <> 0-0, 0-6, 0-12: r=0.9801891737880244

Collecting results

Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-0, 0-6, 0-12: No shift found, skipping pair.
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-4, 0-10, 0-16: r=0.9723565991315614
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-3, 0-9, 0-15: r=0.9589934808169884
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-2, 0-8, 0-14: r=0.9777585663957139
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-2, 0-8, 0-14: r=0.9623363667060237
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-1, 0-7, 0-13: r=0.9679939385326735
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-1, 0-7, 0-13: No shift found, skipping pair.
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-0, 0-6, 0-12: r=0.9793178941211977
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-3, 0-9, 0-15: r=0.9730414262207491
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-0, 0-6, 0-12: No shift found, skipping pair.
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-1, 0-7, 0-13 <> 0-0, 0-6, 0-12: r=0.9801891737880244
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-2, 0-8, 0-14: r=0.955800435940482
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-0, 0-6, 0-12: r=0.9290416526134466
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-1, 0-7, 0-13: r=0.9363659295585218
Sat Mar 15 10:22:28 EDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-1, 0-7, 0-13: No shift found, skipping pair.
Sat Mar 15 10:22:28 EDT 2025: Remaining pairs: 11
Sat Mar 15 10:22:28 EDT 2025: Applying filter minR=0.8
Sat Mar 15 10:22:28 EDT 2025: Applying filter maxR=1.0
Sat Mar 15 10:22:28 EDT 2025: Remaining pairs after applying filters: 11
Saving resulting XML ... 
Saving interest points multi-threaded ... 
Saving PSFs multi-threaded ... 
(Sat Mar 15 10:22:28 EDT 2025): Saved xml 'file:/Users/preibischs/Downloads/Stitching_N5_XML/dataset.xml'.

[StephanPreibisch]

Actually, @nvladimus experienced almost the same issue deploying on google cloud:

25/03/14 09:31:12 WARN TaskSetManager: Lost task 9.0 in stage 1.0 (TID 11) (10.172.0.25 executor 0): java.lang.NullPointerException: Cannot invoke "Object.getClass()" because "e" is null
        at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineOrSplitBy(Group.java:234)
        at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineBy(Group.java:172)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.pickBrightest(GroupedViewAggregator.java:119)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.aggregate(GroupedViewAggregator.java:102)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator.aggregate(GroupedViewAggregator.java:396)
        at net.preibisch.stitcher.algorithm.globalopt.TransformationTools.computeStitching(TransformationTools.java:277)
        at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.lambda$call$c9354d04$1(SparkPairwiseStitching.java:202)
        at org.apache.spark.api.java.JavaPairRDD$.$anonfun$toScalaFunction$1(JavaPairRDD.scala:1070)
        at scala.collection.Iterator$$anon$9.next(Iterator.scala:584)
        at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:224)
        at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:302)
        at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1602)
        at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1529)
        at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1593)
        at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1394)
        at org.apache.spark.storage.BlockManager.getOrElseUpdateRDDBlock(BlockManager.scala:1348)
        at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:379)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:329)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:93)
        at org.apache.spark.TaskContext.runTaskWithListeners(TaskContext.scala:166)
        at org.apache.spark.scheduler.Task.run(Task.scala:141)
        at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:620)
        at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally(SparkErrorUtils.scala:64)
        at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally$(SparkErrorUtils.scala:61)
        at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:96)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:623)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:840)

This is confusing ... must be some dependency stuff, argh

[StephanPreibisch]

The NullPointerException points to the XML not being loaded properly (the attributes map in Group.java:234 seems to be null).

I changed the code so it will output the properties of each ViewId that potentially causes the error, to make sure the loading of the XML works. Can you please run this newest version and let me know what happens @vbrow29 @nvladimus ? Sorry, this will be slow since I cannot re-produce the issue (yet) ...

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=7
ViewDescription=tpId=0 setupId=7
ViewSetup=BasicViewSetup{name='7', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=13
ViewDescription=tpId=0 setupId=13
ViewSetup=BasicViewSetup{name='13', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=6
ViewDescription=tpId=0 setupId=6
ViewSetup=BasicViewSetup{name='6', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=12
ViewDescription=tpId=0 setupId=12
ViewSetup=BasicViewSetup{name='12', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Sat Mar 15 10:43:23 EDT 2025: Compute pairwise: 0-1, 0-7, 0-13 <> 0-0, 0-6, 0-12: r=0.9801891737880244

[StephanPreibisch]

I just ran it succesfully on Google Cloud ... I think what happened is that a previous multiview-reconstruction (5.25 and/or 5.2.6) had a build issue where annotations somehow didn't work, so it is likely that this also affected the attribute loading. So please try to make a clean build from the current version of the main branch by typing mvn clean package -U before making the fatjar. Then it should hopefully just work.

Just in case, my built of the fatjar is available here for download: https://drive.google.com/file/d/1jRlImbLc4fv09nbLeb-ZIDDRc9EkJ11Q/view?usp=sharing

[nvladimus]

Hi, @StephanPreibisch ,
Thanks for looking into this! I pulled form github main, did a clean build with mvn clean package -U then mvn clean package -P fatjar, and launched stitching by:

gcloud dataproc batches submit spark --region=europe-west6 --jars=gs://bigstitcher-test-example1/BigStitcher-Spark-0.1.0-SNAPSHOT.jar --class=net.preibisch.bigstitcher.spark.SparkPairwiseStitching -- -x gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml --channelId 0 

Still got the same error:

WARNING: No runtime version specified. Using the default runtime version. It is recommended to select a specific major.minor runtime version in production, as the default runtime version may change at any time.
Using the default container image
Waiting for container log creation
PYSPARK_PYTHON=/opt/dataproc/conda/bin/python
Generating /home/spark/.pip/pip.conf
Configuring index-url as 'https://europe-python.pkg.dev/artifact-registry-python-cache/virtual-python/simple/'
JAVA_HOME=/usr/lib/jvm/temurin-17-jdk-amd64
SPARK_EXTRA_CLASSPATH=
:: loading settings :: file = /etc/spark/conf/ivysettings.xml
[-x, gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml, --channelId, 0]
xml: gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml
Compression 'org.janelia.saalfeldlab.n5.blosc.BloscCompression' could not be registered
Parsing selected angle ids ... all
Parsing selected channel ids ... [0]
Parsing selected illumination ids ... all
Parsing selected tile ids ... all
Parsing selected timepoint ids ... all
The following ViewIds will be processed: 
[0,0] [0,1] [0,2] [0,3] [0,4] [0,5] 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
(Mon Mar 17 10:00:09 UTC 2025): Downsampling used for stitching: (2, 2, 1)
(Mon Mar 17 10:00:09 UTC 2025): Finding pairs to compute overlap ... 
Mon Mar 17 10:00:09 UTC 2025: Removed 4 non-overlapping view-pairs for computing.
(Mon Mar 17 10:00:09 UTC 2025): For the following pairs pairwise stitching will be computed:
        0-5 <=> 0-4
        0-5 <=> 0-3
        0-5 <=> 0-2
        0-5 <=> 0-1
        0-5 <=> 0-0
        0-4 <=> 0-3
        0-4 <=> 0-2
        0-4 <=> 0-1
        0-4 <=> 0-0
        0-3 <=> 0-2
        0-3 <=> 0-1
        0-3 <=> 0-0
        0-2 <=> 0-1
       0-2 <=> 0-0
        0-1 <=> 0-0
(Mon Mar 17 10:00:09 UTC 2025): In total: 15 pair(s).
25/03/17 10:00:12 WARN MetricsConfig: Cannot locate configuration: tried hadoop-metrics2-google-hadoop-file-system.properties,hadoop-metrics2.properties
25/03/17 10:00:12 INFO MetricsSystemImpl: Scheduled Metric snapshot period at 10 second(s).
25/03/17 10:00:12 INFO MetricsSystemImpl: google-hadoop-file-system metrics system started
25/03/17 10:00:31 WARN TaskSetManager: Lost task 10.0 in stage 1.0 (TID 12) (10.172.0.27 executor 1): java.lang.NullPointerException: Cannot invoke "Object.getClass()" because "e" is null
        at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineOrSplitBy(Group.java:234)
        at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineBy(Group.java:172)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.pickBrightest(GroupedViewAggregator.java:119)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.aggregate(GroupedViewAggregator.java:102)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator.aggregate(GroupedViewAggregator.java:396)
        at net.preibisch.stitcher.algorithm.globalopt.TransformationTools.computeStitching(TransformationTools.java:277)
        at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.lambda$call$c9354d04$1(SparkPairwiseStitching.java:247)
        at org.apache.spark.api.java.JavaPairRDD$.$anonfun$toScalaFunction$1(JavaPairRDD.scala:1070)
        at scala.collection.Iterator$$anon$9.next(Iterator.scala:584)
        at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:224)
        at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:302)
        at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1602)
        at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1529)
        at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1593)
        at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1394)
        at org.apache.spark.storage.BlockManager.getOrElseUpdateRDDBlock(BlockManager.scala:1348)
        at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:379)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:329)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:93)
        at org.apache.spark.TaskContext.runTaskWithListeners(TaskContext.scala:166)
        at org.apache.spark.scheduler.Task.run(Task.scala:141)
        at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:620)
        at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally(SparkErrorUtils.scala:64)
        at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally$(SparkErrorUtils.scala:61)
        at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:96)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:623)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:840)


Collecting results

Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-4 <> 0-2: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-4 <> 0-1: No shift found, skipping pair.
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-4 <> 0-0: No shift found, skipping pair.
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-3 <> 0-2: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-3 <> 0-1: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-3 <> 0-0: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-5 <> 0-4: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-2 <> 0-1: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-5 <> 0-3: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-2 <> 0-0: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-5 <> 0-2: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-1 <> 0-0: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-5 <> 0-1: No shift found, skipping pair.
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-5 <> 0-0: No shift found, skipping pair.
Mon Mar 17 10:00:35 UTC 2025: Compute pairwise: 0-4 <> 0-3: r=0.0
Mon Mar 17 10:00:35 UTC 2025: Remaining pairs: 11
Mon Mar 17 10:00:35 UTC 2025: Applying filter minR=0.3
Mon Mar 17 10:00:35 UTC 2025: Applying filter maxR=1.0
Mon Mar 17 10:00:35 UTC 2025: Remaining pairs after applying filters: 0
Saving resulting XML ... 
gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml
Saving interest points multi-threaded ... 
Saving PSFs multi-threaded ... 
(Mon Mar 17 10:00:37 UTC 2025): Saved xml 'gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml'.
Batch [4631...200a] finished.
metadata:
  '@type': type.googleapis.com/google.cloud.dataproc.v1.BatchOperationMetadata
  batch: projects/bigstitcheruzh/locations/europe-west6/batches/4631...200a
  batchUuid: 1e33...984
  createTime: '2025-03-17T09:58:56.907870Z'
  description: Batch
  labels:
    goog-dataproc-batch-id: 46312...200a
    goog-dataproc-batch-uuid: 1e33...984
    goog-dataproc-drz-resource-uuid: batch-1...f984
    goog-dataproc-location: europe-west6
  operationType: BATCH
  warnings:
  - No runtime version specified. Using the default runtime version. It is recommended
    to select a specific major.minor runtime version in production, as the default
    runtime version may change at any time.

This was on google cloud...

[nvladimus]

Unfortunately stitching locally also didn't work for me, with the following error:

Exception in thread "main" java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x4da69805) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x4da69805
        at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
        at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
        at org.apache.spark.storage.BlockManagerMasterEndpoint.<init>(BlockManagerMasterEndpoint.scala:114)
        at org.apache.spark.SparkEnv$.$anonfun$create$9(SparkEnv.scala:353)
        at org.apache.spark.SparkEnv$.registerOrLookupEndpoint$1(SparkEnv.scala:290)
        at org.apache.spark.SparkEnv$.create(SparkEnv.scala:339)
        at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:194)
        at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:279)
        at org.apache.spark.SparkContext.<init>(SparkContext.scala:464)
        at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:58)
        at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.call(SparkPairwiseStitching.java:189)
        at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.call(SparkPairwiseStitching.java:72)
        at picocli.CommandLine.executeUserObject(CommandLine.java:2045)
        at picocli.CommandLine.access$1500(CommandLine.java:148)
        at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2465)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2457)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2419)
        at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2277)
        at picocli.CommandLine$RunLast.execute(CommandLine.java:2421)
        at picocli.CommandLine.execute(CommandLine.java:2174)
        at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.main(SparkPairwiseStitching.java:398)

I will send the full log by email if that's OK (not sure which log info may be sensitive).

[StephanPreibisch]

@nvladimus, 2 things:

• for the cloud: please try my fatjar that I put online for download above
• for local: which java version are you using locally? Please use Zulu JDK 8 + FX … it looks like you use Java21, which has issues with the Spark version we are using.

[vbrow29]

Hi Stephan, thanks for looking into this.

Here are my logs for running the latest version on my cluster (just pulled today):

Mon Mar 17 11:11:08 PDT 2025 [b001.grid.gs.washington.edu] running /net/beliveau/vol1/home/vbrow/spark-3.5.1-bin-hadoop3/bin/spark-submit --deploy-mode client --master spark://10.110.100.15:7077 --conf spark.executor.extraJavaOptions=-Dnative.libpath.jhdf5=/net/beliveau/vol1/project/VB_ImageProcessing/BigStitcher-Spark/libjhdf5.so --verbose --conf spark.default.parallelism=210 --conf spark.driver.cores=1 --conf spark.executor.instances=2 --conf spark.executor.cores=5 --conf spark.executor.memory=75g --class net.preibisch.bigstitcher.spark.SparkPairwiseStitching /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar -x /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3 --channelId 0 --minR 0.7
Using properties file: /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/logs/spark/20250317_111004/conf/spark-defaults.conf
Adding default property: spark.storage.blockManagerHeartBeatMs=30000
Adding default property: spark.driver.maxResultSize=0
Adding default property: spark.kryoserializer.buffer.max=1024m
Adding default property: spark.rpc.askTimeout=300s
Adding default property: spark.driver.memory=14g
Adding default property: spark.submit.deployMode=cluster
Adding default property: spark.rpc.retry.wait=30s
Adding default property: spark.core.connection.ack.wait.timeout=600s
Parsed arguments:
  master                  spark://10.110.100.15:7077
  remote                  null
  deployMode              client
  executorMemory          75g
  executorCores           5
  totalExecutorCores      null
  propertiesFile          /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/logs/spark/20250317_111004/conf/spark-defaults.conf
  driverMemory            14g
  driverCores             1
  driverExtraClassPath    null
  driverExtraLibraryPath  null
  driverExtraJavaOptions  null
  supervise               false
  queue                   null
  numExecutors            2
  files                   null
  pyFiles                 null
  archives                null
  mainClass               net.preibisch.bigstitcher.spark.SparkPairwiseStitching
  primaryResource         file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar
  name                    net.preibisch.bigstitcher.spark.SparkPairwiseStitching
  childArgs               [-x /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3 --channelId 0 --minR 0.7]
  jars                    null
  packages                null
  packagesExclusions      null
  repositories            null
  verbose                 true

Spark properties used, including those specified through
 --conf and those from the properties file /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/logs/spark/20250317_111004/conf/spark-defaults.conf:
  (spark.core.connection.ack.wait.timeout,600s)
  (spark.default.parallelism,210)
  (spark.driver.cores,1)
  (spark.driver.maxResultSize,0)
  (spark.driver.memory,14g)
  (spark.executor.cores,5)
  (spark.executor.extraJavaOptions,-Dnative.libpath.jhdf5=/net/beliveau/vol1/project/VB_ImageProcessing/BigStitcher-Spark/libjhdf5.so)
  (spark.executor.instances,2)
  (spark.executor.memory,75g)
  (spark.kryoserializer.buffer.max,1024m)
  (spark.rpc.askTimeout,300s)
  (spark.rpc.retry.wait,30s)
  (spark.storage.blockManagerHeartBeatMs,30000)
  (spark.submit.deployMode,cluster)

    
2025-03-17 11:11:10,936 [main] WARN [SparkConf]: The configuration key 'spark.rpc.retry.wait' has been deprecated as of Spark 2.2.0 and may be removed in the future. Not used anymore
2025-03-17 11:11:11,012 [main] WARN [SparkConf]: The configuration key 'spark.rpc.retry.wait' has been deprecated as of Spark 2.2.0 and may be removed in the future. Not used anymore
Main class:
net.preibisch.bigstitcher.spark.SparkPairwiseStitching
Arguments:
-x
/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3
--channelId
0
--minR
0.7
Spark config:
(spark.app.name,net.preibisch.bigstitcher.spark.SparkPairwiseStitching)
(spark.app.submitTime,1742235071201)
(spark.core.connection.ack.wait.timeout,600s)
(spark.default.parallelism,210)
(spark.driver.cores,1)
(spark.driver.maxResultSize,0)
(spark.driver.memory,14g)
(spark.executor.cores,5)
(spark.executor.extraJavaOptions,-Dnative.libpath.jhdf5=/net/beliveau/vol1/project/VB_ImageProcessing/BigStitcher-Spark/libjhdf5.so)
(spark.executor.instances,2)
(spark.executor.memory,75g)
(spark.jars,file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar)
(spark.kryoserializer.buffer.max,1024m)
(spark.master,spark://10.110.100.15:7077)
(spark.rpc.askTimeout,300s)
(spark.rpc.retry.wait,30s)
(spark.storage.blockManagerHeartBeatMs,30000)
(spark.submit.deployMode,client)
(spark.submit.pyFiles,)
Classpath elements:
file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar


[-x, /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3, --channelId, 0, --minR, 0.7]
xml: file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3
Parsing selected angle ids ... all
Parsing selected channel ids ... [0]
Parsing selected illumination ids ... all
Parsing selected tile ids ... all
Parsing selected timepoint ids ... all
The following ViewIds will be processed: 
[0,0] [0,1] [0,2] [0,3] [0,4] [0,5] 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
(Mon Mar 17 11:11:14 PDT 2025): Downsampling used for stitching: (2, 2, 1)
(Mon Mar 17 11:11:14 PDT 2025): Finding pairs to compute overlap ... 
Mon Mar 17 11:11:14 PDT 2025: Removed 4 non-overlapping view-pairs for computing.
(Mon Mar 17 11:11:14 PDT 2025): For the following pairs pairwise stitching will be computed:
	0-5 <=> 0-4
	0-5 <=> 0-3
	0-5 <=> 0-2
	0-5 <=> 0-1
	0-5 <=> 0-0
	0-4 <=> 0-3
	0-4 <=> 0-2
	0-4 <=> 0-1
	0-4 <=> 0-0
	0-3 <=> 0-2
	0-3 <=> 0-1
	0-3 <=> 0-0
	0-2 <=> 0-1
	0-2 <=> 0-0
	0-1 <=> 0-0
(Mon Mar 17 11:11:14 PDT 2025): In total: 15 pair(s).
2025-03-17 11:11:14,344 [main] WARN [SparkConf]: The configuration key 'spark.rpc.retry.wait' has been deprecated as of Spark 2.2.0 and may be removed in the future. Not used anymore
2025-03-17 11:11:14,381 [main] INFO [SparkContext]: Running Spark version 3.5.1
2025-03-17 11:11:14,381 [main] INFO [SparkContext]: OS info Linux, 5.15.0-119-generic, amd64
2025-03-17 11:11:14,382 [main] INFO [SparkContext]: Java version 1.8.0_422-422
2025-03-17 11:11:14,463 [main] WARN [NativeCodeLoader]: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2025-03-17 11:11:14,595 [main] INFO [ResourceUtils]: ==============================================================
2025-03-17 11:11:14,596 [main] INFO [ResourceUtils]: No custom resources configured for spark.driver.
2025-03-17 11:11:14,596 [main] INFO [ResourceUtils]: ==============================================================
2025-03-17 11:11:14,597 [main] INFO [SparkContext]: Submitted application: SparkPairwiseStitching
2025-03-17 11:11:14,628 [main] INFO [ResourceProfile]: Default ResourceProfile created, executor resources: Map(cores -> name: cores, amount: 5, script: , vendor: , memory -> name: memory, amount: 76800, script: , vendor: , offHeap -> name: offHeap, amount: 0, script: , vendor: ), task resources: Map(cpus -> name: cpus, amount: 1.0)
2025-03-17 11:11:14,647 [main] INFO [ResourceProfile]: Limiting resource is cpus at 5 tasks per executor
2025-03-17 11:11:14,649 [main] INFO [ResourceProfileManager]: Added ResourceProfile id: 0
2025-03-17 11:11:14,797 [main] INFO [SecurityManager]: Changing view acls to: vbrow
2025-03-17 11:11:14,797 [main] INFO [SecurityManager]: Changing modify acls to: vbrow
2025-03-17 11:11:14,798 [main] INFO [SecurityManager]: Changing view acls groups to: 
2025-03-17 11:11:14,798 [main] INFO [SecurityManager]: Changing modify acls groups to: 
2025-03-17 11:11:14,798 [main] INFO [SecurityManager]: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: vbrow; groups with view permissions: EMPTY; users with modify permissions: vbrow; groups with modify permissions: EMPTY
2025-03-17 11:11:15,118 [main] INFO [Utils]: Successfully started service 'sparkDriver' on port 36781.
2025-03-17 11:11:15,179 [main] INFO [SparkEnv]: Registering MapOutputTracker
2025-03-17 11:11:15,237 [main] INFO [SparkEnv]: Registering BlockManagerMaster
2025-03-17 11:11:15,275 [main] INFO [SparkEnv]: Registering BlockManagerMasterHeartbeat
2025-03-17 11:11:15,371 [main] INFO [SparkEnv]: Registering OutputCommitCoordinator
2025-03-17 11:11:15,607 [main] INFO [JettyUtils]: Start Jetty 0.0.0.0:4040 for SparkUI
2025-03-17 11:11:15,710 [main] INFO [Utils]: Successfully started service 'SparkUI' on port 4040.
2025-03-17 11:11:15,778 [main] INFO [SparkContext]: Added JAR file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar at spark://b001.grid.gs.washington.edu:36781/jars/BigStitcher-Spark-0.1.0-SNAPSHOT.jar with timestamp 1742235074372
2025-03-17 11:11:16,010 [appclient-register-master-threadpool-0] INFO [StandaloneAppClient$ClientEndpoint]: Connecting to master spark://10.110.100.15:7077...
2025-03-17 11:11:16,117 [netty-rpc-connection-0] INFO [TransportClientFactory]: Successfully created connection to /10.110.100.15:7077 after 44 ms (0 ms spent in bootstraps)
2025-03-17 11:11:16,369 [main] INFO [Utils]: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 37733.
2025-03-17 11:11:16,369 [main] INFO [NettyBlockTransferService]: Server created on b001.grid.gs.washington.edu:37733
2025-03-17 11:11:16,406 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/0 on worker-20250317111042-10.110.100.15-34063 (10.110.100.15:34063) with 5 core(s)
2025-03-17 11:11:16,409 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/1 on worker-20250317111042-10.110.100.15-34063 (10.110.100.15:34063) with 5 core(s)
2025-03-17 11:11:16,412 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/2 on worker-20250317111041-10.110.100.15-42351 (10.110.100.15:42351) with 5 core(s)
2025-03-17 11:11:16,414 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/3 on worker-20250317111041-10.110.100.15-42351 (10.110.100.15:42351) with 5 core(s)
2025-03-17 11:11:16,417 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/4 on worker-20250317111041-10.110.100.15-45461 (10.110.100.15:45461) with 5 core(s)
2025-03-17 11:11:16,420 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/5 on worker-20250317111041-10.110.100.15-45461 (10.110.100.15:45461) with 5 core(s)
2025-03-17 11:11:16,422 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/6 on worker-20250317111041-10.110.100.15-39417 (10.110.100.15:39417) with 5 core(s)
2025-03-17 11:11:16,425 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/7 on worker-20250317111041-10.110.100.15-39417 (10.110.100.15:39417) with 5 core(s)
2025-03-17 11:11:16,428 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/8 on worker-20250317111041-10.110.100.15-33765 (10.110.100.15:33765) with 5 core(s)
2025-03-17 11:11:16,430 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/9 on worker-20250317111041-10.110.100.15-33765 (10.110.100.15:33765) with 5 core(s)
2025-03-17 11:11:16,432 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/10 on worker-20250317111041-10.110.100.15-35945 (10.110.100.15:35945) with 5 core(s)
2025-03-17 11:11:16,433 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/11 on worker-20250317111041-10.110.100.15-35945 (10.110.100.15:35945) with 5 core(s)
2025-03-17 11:11:16,436 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/12 on worker-20250317111042-10.110.100.15-45873 (10.110.100.15:45873) with 5 core(s)
2025-03-17 11:11:16,439 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111116-0000/13 on worker-20250317111042-10.110.100.15-45873 (10.110.100.15:45873) with 5 core(s)
2025-03-17 11:11:16,585 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/0 is now RUNNING
2025-03-17 11:11:16,586 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/1 is now RUNNING
2025-03-17 11:11:16,604 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/9 is now RUNNING
2025-03-17 11:11:16,614 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/8 is now RUNNING
2025-03-17 11:11:16,616 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/5 is now RUNNING
2025-03-17 11:11:16,618 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/4 is now RUNNING
2025-03-17 11:11:16,621 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/6 is now RUNNING
2025-03-17 11:11:16,623 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/7 is now RUNNING
2025-03-17 11:11:16,625 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/3 is now RUNNING
2025-03-17 11:11:16,627 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/2 is now RUNNING
2025-03-17 11:11:16,628 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/12 is now RUNNING
2025-03-17 11:11:16,632 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/13 is now RUNNING
2025-03-17 11:11:16,634 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/11 is now RUNNING
2025-03-17 11:11:16,641 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111116-0000/10 is now RUNNING
2025-03-17 11:11:17,855 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Adding task set 0.0 with 210 tasks resource profile 0
2025-03-17 11:11:24,879 [task-result-getter-1] INFO [TaskSchedulerImpl]: Removed TaskSet 0.0, whose tasks have all completed, from pool 
2025-03-17 11:11:24,934 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Adding task set 1.0 with 15 tasks resource profile 0
2025-03-17 11:11:27,555 [task-result-getter-2] WARN [TaskSetManager]: Lost task 12.0 in stage 1.0 (TID 220) (10.110.100.15 executor 7): java.lang.NullPointerException
	at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineOrSplitBy(Group.java:234)
	at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineBy(Group.java:172)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.pickBrightest(GroupedViewAggregator.java:119)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.aggregate(GroupedViewAggregator.java:102)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator.aggregate(GroupedViewAggregator.java:396)
	at net.preibisch.stitcher.algorithm.globalopt.TransformationTools.computeStitching(TransformationTools.java:277)
	at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.lambda$call$c9354d04$1(SparkPairwiseStitching.java:247)
	at org.apache.spark.api.java.JavaPairRDD$.$anonfun$toScalaFunction$1(JavaPairRDD.scala:1070)
	at scala.collection.Iterator$$anon$10.next(Iterator.scala:461)
	at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:224)
	at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:302)
	at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1597)
	at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1524)
	at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1588)
	at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1389)
	at org.apache.spark.storage.BlockManager.getOrElseUpdateRDDBlock(BlockManager.scala:1343)
	at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:379)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:329)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:93)
	at org.apache.spark.TaskContext.runTaskWithListeners(TaskContext.scala:166)
	at org.apache.spark.scheduler.Task.run(Task.scala:141)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:620)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally(SparkErrorUtils.scala:64)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally$(SparkErrorUtils.scala:61)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:94)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:623)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)

2025-03-17 11:11:32,291 [task-result-getter-0] INFO [TaskSchedulerImpl]: Removed TaskSet 1.0, whose tasks have all completed, from pool 
2025-03-17 11:11:32,295 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Killing all running tasks in stage 1: Stage finished

Collecting results

2025-03-17 11:11:32,326 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Adding task set 3.0 with 15 tasks resource profile 0
2025-03-17 11:11:32,369 [task-result-getter-2] INFO [TaskSchedulerImpl]: Removed TaskSet 3.0, whose tasks have all completed, from pool 
2025-03-17 11:11:32,376 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Killing all running tasks in stage 3: Stage finished
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-5 <> 0-4: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-5 <> 0-0: No shift found, skipping pair.
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-3 <> 0-1: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-5 <> 0-1: No shift found, skipping pair.
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-3 <> 0-2: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-2 <> 0-0: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-2 <> 0-1: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-4 <> 0-1: No shift found, skipping pair.
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-4 <> 0-3: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-4 <> 0-0: No shift found, skipping pair.
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-5 <> 0-3: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-5 <> 0-2: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-1 <> 0-0: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-3 <> 0-0: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Compute pairwise: 0-4 <> 0-2: r=0.0
Mon Mar 17 11:11:32 PDT 2025: Remaining pairs: 11
Mon Mar 17 11:11:32 PDT 2025: Applying filter minR=0.7
Mon Mar 17 11:11:32 PDT 2025: Applying filter maxR=1.0
Mon Mar 17 11:11:32 PDT 2025: Remaining pairs after applying filters: 0
Saving resulting XML ... 
Saving interest points multi-threaded ... 
Saving PSFs multi-threaded ... 
(Mon Mar 17 11:11:32 PDT 2025): Saved xml 'file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3'.

And using the fatjar you uploaded:

Mon Mar 17 11:18:50 PDT 2025 [b001.grid.gs.washington.edu] running /net/beliveau/vol1/home/vbrow/spark-3.5.1-bin-hadoop3/bin/spark-submit --deploy-mode client --master spark://10.110.100.15:7077 --conf spark.executor.extraJavaOptions=-Dnative.libpath.jhdf5=/net/beliveau/vol1/project/VB_ImageProcessing/BigStitcher-Spark/libjhdf5.so --verbose --conf spark.default.parallelism=210 --conf spark.driver.cores=1 --conf spark.executor.instances=2 --conf spark.executor.cores=5 --conf spark.executor.memory=75g --class net.preibisch.bigstitcher.spark.SparkPairwiseStitching /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar -x /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3 --channelId 0 --minR 0.7
Using properties file: /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/logs/spark/20250317_111746/conf/spark-defaults.conf
Adding default property: spark.storage.blockManagerHeartBeatMs=30000
Adding default property: spark.driver.maxResultSize=0
Adding default property: spark.kryoserializer.buffer.max=1024m
Adding default property: spark.rpc.askTimeout=300s
Adding default property: spark.driver.memory=14g
Adding default property: spark.submit.deployMode=cluster
Adding default property: spark.rpc.retry.wait=30s
Adding default property: spark.core.connection.ack.wait.timeout=600s
Parsed arguments:
  master                  spark://10.110.100.15:7077
  remote                  null
  deployMode              client
  executorMemory          75g
  executorCores           5
  totalExecutorCores      null
  propertiesFile          /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/logs/spark/20250317_111746/conf/spark-defaults.conf
  driverMemory            14g
  driverCores             1
  driverExtraClassPath    null
  driverExtraLibraryPath  null
  driverExtraJavaOptions  null
  supervise               false
  queue                   null
  numExecutors            2
  files                   null
  pyFiles                 null
  archives                null
  mainClass               net.preibisch.bigstitcher.spark.SparkPairwiseStitching
  primaryResource         file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar
  name                    net.preibisch.bigstitcher.spark.SparkPairwiseStitching
  childArgs               [-x /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3 --channelId 0 --minR 0.7]
  jars                    null
  packages                null
  packagesExclusions      null
  repositories            null
  verbose                 true

Spark properties used, including those specified through
 --conf and those from the properties file /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/logs/spark/20250317_111746/conf/spark-defaults.conf:
  (spark.core.connection.ack.wait.timeout,600s)
  (spark.default.parallelism,210)
  (spark.driver.cores,1)
  (spark.driver.maxResultSize,0)
  (spark.driver.memory,14g)
  (spark.executor.cores,5)
  (spark.executor.extraJavaOptions,-Dnative.libpath.jhdf5=/net/beliveau/vol1/project/VB_ImageProcessing/BigStitcher-Spark/libjhdf5.so)
  (spark.executor.instances,2)
  (spark.executor.memory,75g)
  (spark.kryoserializer.buffer.max,1024m)
  (spark.rpc.askTimeout,300s)
  (spark.rpc.retry.wait,30s)
  (spark.storage.blockManagerHeartBeatMs,30000)
  (spark.submit.deployMode,cluster)

    
2025-03-17 11:18:53,186 [main] WARN [SparkConf]: The configuration key 'spark.rpc.retry.wait' has been deprecated as of Spark 2.2.0 and may be removed in the future. Not used anymore
2025-03-17 11:18:53,268 [main] WARN [SparkConf]: The configuration key 'spark.rpc.retry.wait' has been deprecated as of Spark 2.2.0 and may be removed in the future. Not used anymore
Main class:
net.preibisch.bigstitcher.spark.SparkPairwiseStitching
Arguments:
-x
/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3
--channelId
0
--minR
0.7
Spark config:
(spark.app.name,net.preibisch.bigstitcher.spark.SparkPairwiseStitching)
(spark.app.submitTime,1742235533443)
(spark.core.connection.ack.wait.timeout,600s)
(spark.default.parallelism,210)
(spark.driver.cores,1)
(spark.driver.maxResultSize,0)
(spark.driver.memory,14g)
(spark.executor.cores,5)
(spark.executor.extraJavaOptions,-Dnative.libpath.jhdf5=/net/beliveau/vol1/project/VB_ImageProcessing/BigStitcher-Spark/libjhdf5.so)
(spark.executor.instances,2)
(spark.executor.memory,75g)
(spark.jars,file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar)
(spark.kryoserializer.buffer.max,1024m)
(spark.master,spark://10.110.100.15:7077)
(spark.rpc.askTimeout,300s)
(spark.rpc.retry.wait,30s)
(spark.storage.blockManagerHeartBeatMs,30000)
(spark.submit.deployMode,client)
(spark.submit.pyFiles,)
Classpath elements:
file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar


[-x, /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3, --channelId, 0, --minR, 0.7]
xml: file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3
Parsing selected angle ids ... all
Parsing selected channel ids ... [0]
Parsing selected illumination ids ... all
Parsing selected tile ids ... all
Parsing selected timepoint ids ... all
The following ViewIds will be processed: 
[0,0] [0,1] [0,2] [0,3] [0,4] [0,5] 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
(Mon Mar 17 11:18:55 PDT 2025): Downsampling used for stitching: (2, 2, 1)
(Mon Mar 17 11:18:55 PDT 2025): Finding pairs to compute overlap ... 
Mon Mar 17 11:18:55 PDT 2025: Removed 4 non-overlapping view-pairs for computing.
(Mon Mar 17 11:18:55 PDT 2025): For the following pairs pairwise stitching will be computed:
	0-5 <=> 0-4
	0-5 <=> 0-3
	0-5 <=> 0-2
	0-5 <=> 0-1
	0-5 <=> 0-0
	0-4 <=> 0-3
	0-4 <=> 0-2
	0-4 <=> 0-1
	0-4 <=> 0-0
	0-3 <=> 0-2
	0-3 <=> 0-1
	0-3 <=> 0-0
	0-2 <=> 0-1
	0-2 <=> 0-0
	0-1 <=> 0-0
(Mon Mar 17 11:18:55 PDT 2025): In total: 15 pair(s).
2025-03-17 11:18:55,798 [main] WARN [SparkConf]: The configuration key 'spark.rpc.retry.wait' has been deprecated as of Spark 2.2.0 and may be removed in the future. Not used anymore
2025-03-17 11:18:55,849 [main] INFO [SparkContext]: Running Spark version 3.5.1
2025-03-17 11:18:55,849 [main] INFO [SparkContext]: OS info Linux, 5.15.0-119-generic, amd64
2025-03-17 11:18:55,850 [main] INFO [SparkContext]: Java version 1.8.0_422-422
2025-03-17 11:18:55,951 [main] WARN [NativeCodeLoader]: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
2025-03-17 11:18:56,087 [main] INFO [ResourceUtils]: ==============================================================
2025-03-17 11:18:56,087 [main] INFO [ResourceUtils]: No custom resources configured for spark.driver.
2025-03-17 11:18:56,088 [main] INFO [ResourceUtils]: ==============================================================
2025-03-17 11:18:56,088 [main] INFO [SparkContext]: Submitted application: SparkPairwiseStitching
2025-03-17 11:18:56,135 [main] INFO [ResourceProfile]: Default ResourceProfile created, executor resources: Map(cores -> name: cores, amount: 5, script: , vendor: , memory -> name: memory, amount: 76800, script: , vendor: , offHeap -> name: offHeap, amount: 0, script: , vendor: ), task resources: Map(cpus -> name: cpus, amount: 1.0)
2025-03-17 11:18:56,150 [main] INFO [ResourceProfile]: Limiting resource is cpus at 5 tasks per executor
2025-03-17 11:18:56,152 [main] INFO [ResourceProfileManager]: Added ResourceProfile id: 0
2025-03-17 11:18:56,318 [main] INFO [SecurityManager]: Changing view acls to: vbrow
2025-03-17 11:18:56,319 [main] INFO [SecurityManager]: Changing modify acls to: vbrow
2025-03-17 11:18:56,321 [main] INFO [SecurityManager]: Changing view acls groups to: 
2025-03-17 11:18:56,321 [main] INFO [SecurityManager]: Changing modify acls groups to: 
2025-03-17 11:18:56,322 [main] INFO [SecurityManager]: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: vbrow; groups with view permissions: EMPTY; users with modify permissions: vbrow; groups with modify permissions: EMPTY
2025-03-17 11:18:56,622 [main] INFO [Utils]: Successfully started service 'sparkDriver' on port 38307.
2025-03-17 11:18:56,664 [main] INFO [SparkEnv]: Registering MapOutputTracker
2025-03-17 11:18:56,704 [main] INFO [SparkEnv]: Registering BlockManagerMaster
2025-03-17 11:18:56,736 [main] INFO [SparkEnv]: Registering BlockManagerMasterHeartbeat
2025-03-17 11:18:56,793 [main] INFO [SparkEnv]: Registering OutputCommitCoordinator
2025-03-17 11:18:56,961 [main] INFO [JettyUtils]: Start Jetty 0.0.0.0:4040 for SparkUI
2025-03-17 11:18:57,040 [main] INFO [Utils]: Successfully started service 'SparkUI' on port 4040.
2025-03-17 11:18:57,092 [main] INFO [SparkContext]: Added JAR file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/BigStitcher-Spark/target/BigStitcher-Spark-0.1.0-SNAPSHOT.jar at spark://b001.grid.gs.washington.edu:38307/jars/BigStitcher-Spark-0.1.0-SNAPSHOT.jar with timestamp 1742235535834
2025-03-17 11:18:57,285 [appclient-register-master-threadpool-0] INFO [StandaloneAppClient$ClientEndpoint]: Connecting to master spark://10.110.100.15:7077...
2025-03-17 11:18:57,371 [netty-rpc-connection-0] INFO [TransportClientFactory]: Successfully created connection to /10.110.100.15:7077 after 39 ms (0 ms spent in bootstraps)
2025-03-17 11:18:57,589 [main] INFO [Utils]: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 32865.
2025-03-17 11:18:57,589 [main] INFO [NettyBlockTransferService]: Server created on b001.grid.gs.washington.edu:32865
2025-03-17 11:18:57,617 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/0 on worker-20250317111824-10.110.100.15-43119 (10.110.100.15:43119) with 5 core(s)
2025-03-17 11:18:57,619 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/1 on worker-20250317111824-10.110.100.15-43119 (10.110.100.15:43119) with 5 core(s)
2025-03-17 11:18:57,622 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/2 on worker-20250317111824-10.110.100.15-37041 (10.110.100.15:37041) with 5 core(s)
2025-03-17 11:18:57,624 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/3 on worker-20250317111824-10.110.100.15-37041 (10.110.100.15:37041) with 5 core(s)
2025-03-17 11:18:57,628 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/4 on worker-20250317111824-10.110.100.15-36825 (10.110.100.15:36825) with 5 core(s)
2025-03-17 11:18:57,631 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/5 on worker-20250317111824-10.110.100.15-36825 (10.110.100.15:36825) with 5 core(s)
2025-03-17 11:18:57,632 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/6 on worker-20250317111824-10.110.100.15-41111 (10.110.100.15:41111) with 5 core(s)
2025-03-17 11:18:57,636 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/7 on worker-20250317111824-10.110.100.15-41111 (10.110.100.15:41111) with 5 core(s)
2025-03-17 11:18:57,640 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/8 on worker-20250317111823-10.110.100.15-33055 (10.110.100.15:33055) with 5 core(s)
2025-03-17 11:18:57,642 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/9 on worker-20250317111823-10.110.100.15-33055 (10.110.100.15:33055) with 5 core(s)
2025-03-17 11:18:57,642 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/10 on worker-20250317111823-10.110.100.15-45891 (10.110.100.15:45891) with 5 core(s)
2025-03-17 11:18:57,643 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/11 on worker-20250317111823-10.110.100.15-45891 (10.110.100.15:45891) with 5 core(s)
2025-03-17 11:18:57,648 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/12 on worker-20250317111824-10.110.100.15-34377 (10.110.100.15:34377) with 5 core(s)
2025-03-17 11:18:57,651 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor added: app-20250317111857-0000/13 on worker-20250317111824-10.110.100.15-34377 (10.110.100.15:34377) with 5 core(s)
2025-03-17 11:18:57,764 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/1 is now RUNNING
2025-03-17 11:18:57,767 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/0 is now RUNNING
2025-03-17 11:18:57,769 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/5 is now RUNNING
2025-03-17 11:18:57,772 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/4 is now RUNNING
2025-03-17 11:18:57,777 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/7 is now RUNNING
2025-03-17 11:18:57,802 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/6 is now RUNNING
2025-03-17 11:18:57,806 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/8 is now RUNNING
2025-03-17 11:18:57,809 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/9 is now RUNNING
2025-03-17 11:18:57,812 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/3 is now RUNNING
2025-03-17 11:18:57,815 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/2 is now RUNNING
2025-03-17 11:18:57,818 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/11 is now RUNNING
2025-03-17 11:18:57,820 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/10 is now RUNNING
2025-03-17 11:18:57,822 [dispatcher-event-loop-0] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/12 is now RUNNING
2025-03-17 11:18:57,829 [dispatcher-event-loop-1] INFO [StandaloneAppClient$ClientEndpoint]: Executor updated: app-20250317111857-0000/13 is now RUNNING
2025-03-17 11:18:59,001 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Adding task set 0.0 with 210 tasks resource profile 0
2025-03-17 11:19:05,706 [task-result-getter-2] INFO [TaskSchedulerImpl]: Removed TaskSet 0.0, whose tasks have all completed, from pool 
2025-03-17 11:19:05,767 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Adding task set 1.0 with 15 tasks resource profile 0
2025-03-17 11:19:07,124 [task-result-getter-2] WARN [TaskSetManager]: Lost task 6.0 in stage 1.0 (TID 215) (10.110.100.15 executor 4): java.lang.NullPointerException
	at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineOrSplitBy(Group.java:234)
	at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineBy(Group.java:172)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.pickBrightest(GroupedViewAggregator.java:119)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.aggregate(GroupedViewAggregator.java:102)
	at net.preibisch.stitcher.algorithm.GroupedViewAggregator.aggregate(GroupedViewAggregator.java:396)
	at net.preibisch.stitcher.algorithm.globalopt.TransformationTools.computeStitching(TransformationTools.java:277)
	at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.lambda$call$c9354d04$1(SparkPairwiseStitching.java:247)
	at org.apache.spark.api.java.JavaPairRDD$.$anonfun$toScalaFunction$1(JavaPairRDD.scala:1070)
	at scala.collection.Iterator$$anon$10.next(Iterator.scala:461)
	at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:224)
	at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:302)
	at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1597)
	at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1524)
	at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1588)
	at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1389)
	at org.apache.spark.storage.BlockManager.getOrElseUpdateRDDBlock(BlockManager.scala:1343)
	at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:379)
	at org.apache.spark.rdd.RDD.iterator(RDD.scala:329)
	at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:93)
	at org.apache.spark.TaskContext.runTaskWithListeners(TaskContext.scala:166)
	at org.apache.spark.scheduler.Task.run(Task.scala:141)
	at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$4(Executor.scala:620)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally(SparkErrorUtils.scala:64)
	at org.apache.spark.util.SparkErrorUtils.tryWithSafeFinally$(SparkErrorUtils.scala:61)
	at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:94)
	at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:623)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:750)

2025-03-17 11:19:10,198 [task-result-getter-0] INFO [TaskSchedulerImpl]: Removed TaskSet 1.0, whose tasks have all completed, from pool 
2025-03-17 11:19:10,204 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Killing all running tasks in stage 1: Stage finished

Collecting results

2025-03-17 11:19:10,236 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Adding task set 3.0 with 15 tasks resource profile 0
2025-03-17 11:19:10,270 [task-result-getter-0] INFO [TaskSchedulerImpl]: Removed TaskSet 3.0, whose tasks have all completed, from pool 
2025-03-17 11:19:10,271 [dag-scheduler-event-loop] INFO [TaskSchedulerImpl]: Killing all running tasks in stage 3: Stage finished
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-5 <> 0-4: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-5 <> 0-0: No shift found, skipping pair.
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-3 <> 0-1: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-5 <> 0-1: No shift found, skipping pair.
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-3 <> 0-2: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-2 <> 0-0: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-2 <> 0-1: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-4 <> 0-1: No shift found, skipping pair.
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-4 <> 0-3: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-5 <> 0-3: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-4 <> 0-0: No shift found, skipping pair.
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-5 <> 0-2: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-1 <> 0-0: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-3 <> 0-0: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Compute pairwise: 0-4 <> 0-2: r=0.0
Mon Mar 17 11:19:10 PDT 2025: Remaining pairs: 11
Mon Mar 17 11:19:10 PDT 2025: Applying filter minR=0.7
Mon Mar 17 11:19:10 PDT 2025: Applying filter maxR=1.0
Mon Mar 17 11:19:10 PDT 2025: Remaining pairs after applying filters: 0
Saving resulting XML ... 
Saving interest points multi-threaded ... 
Saving PSFs multi-threaded ... 
(Mon Mar 17 11:19:10 PDT 2025): Saved xml 'file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3'.

I am using Java 8 (1.8.0_422-422) and Spark 3.5.1 on an SGE system.

Stitching locally seems to work with the fatjar you provided:

[-x, /net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3]
xml: file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3
The following ViewIds will be processed: 
[0,0] [0,1] [0,2] [0,3] [0,4] [0,5] [0,6] [0,7] [0,8] [0,9] [0,10] [0,11] [0,12] [0,13] [0,14] [0,15] [0,16] [0,17] 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=6
ViewDescription=tpId=0 setupId=6
ViewSetup=BasicViewSetup{name='6', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=7
ViewDescription=tpId=0 setupId=7
ViewSetup=BasicViewSetup{name='7', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=8
ViewDescription=tpId=0 setupId=8
ViewSetup=BasicViewSetup{name='8', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=9
ViewDescription=tpId=0 setupId=9
ViewSetup=BasicViewSetup{name='9', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=10
ViewDescription=tpId=0 setupId=10
ViewSetup=BasicViewSetup{name='10', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=11
ViewDescription=tpId=0 setupId=11
ViewSetup=BasicViewSetup{name='11', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=12
ViewDescription=tpId=0 setupId=12
ViewSetup=BasicViewSetup{name='12', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=13
ViewDescription=tpId=0 setupId=13
ViewSetup=BasicViewSetup{name='13', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=14
ViewDescription=tpId=0 setupId=14
ViewSetup=BasicViewSetup{name='14', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=15
ViewDescription=tpId=0 setupId=15
ViewSetup=BasicViewSetup{name='15', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=16
ViewDescription=tpId=0 setupId=16
ViewSetup=BasicViewSetup{name='16', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=17
ViewDescription=tpId=0 setupId=17
ViewSetup=BasicViewSetup{name='17', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
(Mon Mar 17 11:30:40 PDT 2025): Downsampling used for stitching: (2, 2, 1)
(Mon Mar 17 11:30:40 PDT 2025): Finding pairs to compute overlap ... 
Mon Mar 17 11:30:40 PDT 2025: Removed 4 non-overlapping view-pairs for computing.
(Mon Mar 17 11:30:40 PDT 2025): For the following pairs pairwise stitching will be computed:
        0-5, 0-11, 0-17 <=> 0-4, 0-10, 0-16
        0-5, 0-11, 0-17 <=> 0-3, 0-9, 0-15
        0-5, 0-11, 0-17 <=> 0-2, 0-8, 0-14
        0-5, 0-11, 0-17 <=> 0-1, 0-7, 0-13
        0-5, 0-11, 0-17 <=> 0-0, 0-6, 0-12
        0-4, 0-10, 0-16 <=> 0-3, 0-9, 0-15
        0-4, 0-10, 0-16 <=> 0-2, 0-8, 0-14
        0-4, 0-10, 0-16 <=> 0-1, 0-7, 0-13
        0-4, 0-10, 0-16 <=> 0-0, 0-6, 0-12
        0-3, 0-9, 0-15 <=> 0-2, 0-8, 0-14
        0-3, 0-9, 0-15 <=> 0-1, 0-7, 0-13
        0-3, 0-9, 0-15 <=> 0-0, 0-6, 0-12
        0-2, 0-8, 0-14 <=> 0-1, 0-7, 0-13
        0-2, 0-8, 0-14 <=> 0-0, 0-6, 0-12
        0-1, 0-7, 0-13 <=> 0-0, 0-6, 0-12
(Mon Mar 17 11:30:40 PDT 2025): In total: 15 pair(s).
Using Spark's default log4j profile: org/apache/spark/log4j2-defaults.properties
25/03/17 11:30:41 INFO SparkContext: Running Spark version 3.3.2
25/03/17 11:30:42 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
25/03/17 11:30:42 INFO ResourceUtils: ==============================================================
25/03/17 11:30:42 INFO ResourceUtils: No custom resources configured for spark.driver.
25/03/17 11:30:42 INFO ResourceUtils: ==============================================================
25/03/17 11:30:42 INFO SparkContext: Submitted application: SparkPairwiseStitching
25/03/17 11:30:42 INFO ResourceProfile: Default ResourceProfile created, executor resources: Map(cores -> name: cores, amount: 1, script: , vendor: , memory -> name: memory, amount: 1024, script: , vendor: , offHeap -> name: offHeap, amount: 0, script: , vendor: ), task resources: Map(cpus -> name: cpus, amount: 1.0)
25/03/17 11:30:42 INFO ResourceProfile: Limiting resource is cpu
25/03/17 11:30:42 INFO ResourceProfileManager: Added ResourceProfile id: 0
25/03/17 11:30:42 INFO SecurityManager: Changing view acls to: vbrow
25/03/17 11:30:42 INFO SecurityManager: Changing modify acls to: vbrow
25/03/17 11:30:42 INFO SecurityManager: Changing view acls groups to: 
25/03/17 11:30:42 INFO SecurityManager: Changing modify acls groups to: 
25/03/17 11:30:42 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(vbrow); groups with view permissions: Set(); users  with modify permissions: Set(vbrow); groups with modify permissions: Set()
25/03/17 11:30:42 INFO Utils: Successfully started service 'sparkDriver' on port 39039.
25/03/17 11:30:42 INFO SparkEnv: Registering MapOutputTracker
25/03/17 11:30:42 INFO SparkEnv: Registering BlockManagerMaster
25/03/17 11:30:42 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
25/03/17 11:30:42 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
25/03/17 11:30:42 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
25/03/17 11:30:42 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-bf8a8eee-a479-4f7e-9de1-fc3dcdfa0cb4
25/03/17 11:30:42 INFO MemoryStore: MemoryStore started with capacity 4.1 GiB
25/03/17 11:30:42 INFO SparkEnv: Registering OutputCommitCoordinator
25/03/17 11:30:43 INFO Utils: Successfully started service 'SparkUI' on port 4040.
25/03/17 11:30:43 INFO Executor: Starting executor ID driver on host s006.grid.gs.washington.edu
25/03/17 11:30:43 INFO Executor: Starting executor with user classpath (userClassPathFirst = false): ''
25/03/17 11:30:43 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 35473.
25/03/17 11:30:43 INFO NettyBlockTransferService: Server created on s006.grid.gs.washington.edu:35473
25/03/17 11:30:43 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
25/03/17 11:30:43 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, s006.grid.gs.washington.edu, 35473, None)
25/03/17 11:30:43 INFO BlockManagerMasterEndpoint: Registering block manager s006.grid.gs.washington.edu:35473 with 4.1 GiB RAM, BlockManagerId(driver, s006.grid.gs.washington.edu, 35473, None)
25/03/17 11:30:43 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, s006.grid.gs.washington.edu, 35473, None)
25/03/17 11:30:43 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, s006.grid.gs.washington.edu, 35473, None)

Debugging ViewDescriptions ... 

Debugging ViewDescriptions ... 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=17

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=17
ViewDescription=tpId=0 setupId=17
ViewSetup=BasicViewSetup{name='17', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}

Debugging ViewDescriptions ... 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=16

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=3

Debugging ViewDescriptions ... 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=17
ViewDescription=tpId=0 setupId=17
ViewSetup=BasicViewSetup{name='17', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=11
ViewDescription=tpId=0 setupId=11
ViewSetup=BasicViewSetup{name='11', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=16
ViewDescription=tpId=0 setupId=16
ViewSetup=BasicViewSetup{name='16', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=10
ViewDescription=tpId=0 setupId=10
ViewSetup=BasicViewSetup{name='10', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=16
ViewDescription=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=16
ViewId=tpId=0 setupId=17
ViewDescription=tpId=0 setupId=17
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup=BasicViewSetup{name='17', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewDescription=tpId=0 setupId=17
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=7
ViewDescription=tpId=0 setupId=7
ViewSetup=BasicViewSetup{name='7', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=13
ViewDescription=tpId=0 setupId=13
ViewSetup=BasicViewSetup{name='13', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=6
ViewDescription=tpId=0 setupId=6
ViewSetup=BasicViewSetup{name='6', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=12
ViewDescription=tpId=0 setupId=12
ViewSetup=BasicViewSetup{name='12', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewId=tpId=0 setupId=17
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewSetup=BasicViewSetup{name='17', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=11
ViewDescription=tpId=0 setupId=11
ViewSetup=BasicViewSetup{name='11', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=9
ViewDescription=tpId=0 setupId=9
ViewSetup=BasicViewSetup{name='9', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=15
ViewDescription=tpId=0 setupId=15
ViewSetup=BasicViewSetup{name='15', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=9
ViewDescription=tpId=0 setupId=9
ViewSetup=BasicViewSetup{name='9', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=15
ViewDescription=tpId=0 setupId=15
ViewSetup=BasicViewSetup{name='15', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=6
ViewDescription=tpId=0 setupId=6
ViewSetup=BasicViewSetup{name='6', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=12
ViewDescription=tpId=0 setupId=12
ViewSetup=BasicViewSetup{name='12', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewSetup=BasicViewSetup{name='16', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=10
ViewDescription=tpId=0 setupId=10
ViewSetup=BasicViewSetup{name='10', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=6
ViewDescription=tpId=0 setupId=6
ViewSetup=BasicViewSetup{name='6', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=12
ViewDescription=tpId=0 setupId=12
ViewSetup=BasicViewSetup{name='12', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:44 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-0, 0-6, 0-12: No shift found.
ViewDescription=tpId=0 setupId=16
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='16', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=10
ViewDescription=tpId=0 setupId=10
ViewSetup=BasicViewSetup{name='10', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=9
ViewDescription=tpId=0 setupId=9
ViewSetup=BasicViewSetup{name='9', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=15
ViewDescription=tpId=0 setupId=15
ViewSetup=BasicViewSetup{name='15', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=17
ViewSetup=BasicViewSetup{name='17', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=11
ViewDescription=tpId=0 setupId=11
ViewSetup=BasicViewSetup{name='11', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=11
ViewDescription=tpId=0 setupId=11
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewSetup=BasicViewSetup{name='11', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewId=tpId=0 setupId=11
ViewDescription=tpId=0 setupId=11
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='11', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewDescription=tpId=0 setupId=1
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=6
ViewDescription=tpId=0 setupId=6
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup=BasicViewSetup{name='6', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=7
ViewDescription=tpId=0 setupId=7
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=12
ViewDescription=tpId=0 setupId=12
ViewSetup=BasicViewSetup{name='7', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=13
ViewSetup=BasicViewSetup{name='12', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewDescription=tpId=0 setupId=13
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewSetup=BasicViewSetup{name='13', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:44 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-0, 0-6, 0-12: No shift found.
Mon Mar 17 11:30:44 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-1, 0-7, 0-13: No shift found.
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=8
ViewDescription=tpId=0 setupId=8
ViewSetup=BasicViewSetup{name='8', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=14
ViewDescription=tpId=0 setupId=14
ViewSetup=BasicViewSetup{name='14', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=9
ViewDescription=tpId=0 setupId=9
ViewSetup=BasicViewSetup{name='9', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=15
ViewDescription=tpId=0 setupId=15
ViewSetup=BasicViewSetup{name='15', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=8
ViewDescription=tpId=0 setupId=8
ViewSetup=BasicViewSetup{name='8', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=14
ViewDescription=tpId=0 setupId=14
ViewSetup=BasicViewSetup{name='14', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:46 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-3, 0-9, 0-15: r=0.9589934808169884

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=16
ViewDescription=tpId=0 setupId=16
ViewSetup=BasicViewSetup{name='16', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=10
ViewDescription=tpId=0 setupId=10
ViewSetup=BasicViewSetup{name='10', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=7
ViewDescription=tpId=0 setupId=7
ViewSetup=BasicViewSetup{name='7', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=13
ViewDescription=tpId=0 setupId=13
ViewSetup=BasicViewSetup{name='13', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:46 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-1, 0-7, 0-13: No shift found.

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=9
ViewDescription=tpId=0 setupId=9
ViewSetup=BasicViewSetup{name='9', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=15
ViewDescription=tpId=0 setupId=15
ViewSetup=BasicViewSetup{name='15', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=7
ViewDescription=tpId=0 setupId=7
ViewSetup=BasicViewSetup{name='7', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=13
ViewDescription=tpId=0 setupId=13
ViewSetup=BasicViewSetup{name='13', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:46 PDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-0, 0-6, 0-12: r=0.9290416526134466
Mon Mar 17 11:30:46 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-2, 0-8, 0-14: r=0.955800435940482
Mon Mar 17 11:30:47 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-3, 0-9, 0-15: r=0.9730414262207491

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=16
ViewDescription=tpId=0 setupId=16
ViewSetup=BasicViewSetup{name='16', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=10
ViewDescription=tpId=0 setupId=10
ViewSetup=BasicViewSetup{name='10', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=8
ViewDescription=tpId=0 setupId=8
ViewSetup=BasicViewSetup{name='8', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=14
ViewDescription=tpId=0 setupId=14
ViewSetup=BasicViewSetup{name='14', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:47 PDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-2, 0-8, 0-14: r=0.9623363667060237

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=8
ViewDescription=tpId=0 setupId=8
ViewSetup=BasicViewSetup{name='8', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=14
ViewDescription=tpId=0 setupId=14
ViewSetup=BasicViewSetup{name='14', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=7
ViewDescription=tpId=0 setupId=7
ViewSetup=BasicViewSetup{name='7', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=13
ViewDescription=tpId=0 setupId=13
ViewSetup=BasicViewSetup{name='13', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:48 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-4, 0-10, 0-16: r=0.9723565991315614
Mon Mar 17 11:30:48 PDT 2025: Compute pairwise: 0-1, 0-7, 0-13 <> 0-0, 0-6, 0-12: r=0.9801891737880244
Mon Mar 17 11:30:48 PDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-1, 0-7, 0-13: r=0.9363659295585218
Mon Mar 17 11:30:48 PDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-1, 0-7, 0-13: r=0.9679939385326735
Mon Mar 17 11:30:49 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-2, 0-8, 0-14: r=0.9777585663957139

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=8
ViewDescription=tpId=0 setupId=8
ViewSetup=BasicViewSetup{name='8', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=14
ViewDescription=tpId=0 setupId=14
ViewSetup=BasicViewSetup{name='14', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=6
ViewDescription=tpId=0 setupId=6
ViewSetup=BasicViewSetup{name='6', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@1, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=12
ViewDescription=tpId=0 setupId=12
ViewSetup=BasicViewSetup{name='12', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@2, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-0, 0-6, 0-12: r=0.9793178941211977

Collecting results

Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-1, 0-7, 0-13 <> 0-0, 0-6, 0-12: r=0.9801891737880244
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-2, 0-8, 0-14: r=0.955800435940482
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-0, 0-6, 0-12: No shift found, skipping pair.
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-3, 0-9, 0-15: r=0.9730414262207491
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-2, 0-8, 0-14: r=0.9777585663957139
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-0, 0-6, 0-12: r=0.9793178941211977
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-4, 0-10, 0-16: r=0.9723565991315614
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-0, 0-6, 0-12: r=0.9290416526134466
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-3, 0-9, 0-15: r=0.9589934808169884
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-1, 0-7, 0-13: No shift found, skipping pair.
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-1, 0-7, 0-13: r=0.9679939385326735
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-4, 0-10, 0-16 <> 0-0, 0-6, 0-12: No shift found, skipping pair.
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-5, 0-11, 0-17 <> 0-1, 0-7, 0-13: No shift found, skipping pair.
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-3, 0-9, 0-15 <> 0-2, 0-8, 0-14: r=0.9623363667060237
Mon Mar 17 11:30:51 PDT 2025: Compute pairwise: 0-2, 0-8, 0-14 <> 0-1, 0-7, 0-13: r=0.9363659295585218
Mon Mar 17 11:30:51 PDT 2025: Remaining pairs: 11
Mon Mar 17 11:30:51 PDT 2025: Applying filter minR=0.3
Mon Mar 17 11:30:51 PDT 2025: Applying filter maxR=1.0
Mon Mar 17 11:30:51 PDT 2025: Remaining pairs after applying filters: 11
Saving resulting XML ... 
Saving interest points multi-threaded ... 
Saving PSFs multi-threaded ... 
(Mon Mar 17 11:30:51 PDT 2025): Saved xml 'file:/net/beliveau/vol1/project/VB_ImageProcessing/Spark-Snakemake-dev/test_data_n5/dataset.xml~3'.

[StephanPreibisch]

@vbrow29 when you deploy it, it doesn't even produce the System.out.println's in the respective jobs, that is very very weird. The big difference seems to be the Spark version. Locally you use 3.3.2 (as it is compiled with), on the cluster 3.5.1 ... it could be related to that. Any chance that you can use 3.3.2 on the cluster?

[nvladimus]

Hi, @StephanPreibisch ,
I uploaded your JAR file to the google cloud and specified Spark version == 3.3.2, with the following command:

(bigstitcheruzh)$ gcloud dataproc batches submit spark --region=europe-west6 --jars=gs://bigstitcher-test-example1/BigStitcher-Spark-0.1.0-SNAPSHOT.jar --class=net.preibisch.bigstitcher.spark.SparkPairwiseStitching --version=2.1 -- -x gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml --channelId 0 

According to Dataproc 2.1 release notes this should set the Spark to 3.3.2. However, I still get the same error unfortunately:

Batch [0e09ec8a2a844e60b6232b7ef2177737] submitted.
Using the default container image
Waiting for container log creation
PYSPARK_PYTHON=/opt/dataproc/conda/bin/python
JAVA_HOME=/usr/lib/jvm/temurin-17-jdk-amd64
SPARK_EXTRA_CLASSPATH=
:: loading settings :: file = /etc/spark/conf/ivysettings.xml
[-x, gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml, --channelId, 0]
xml: gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml
Compression 'org.janelia.saalfeldlab.n5.blosc.BloscCompression' could not be registered
Parsing selected angle ids ... all
Parsing selected channel ids ... [0]
Parsing selected illumination ids ... all
Parsing selected tile ids ... all
Parsing selected timepoint ids ... all
The following ViewIds will be processed: 
[0,0] [0,1] [0,2] [0,3] [0,4] [0,5] 

Debugging ViewDescriptions ... 
ViewId=tpId=0 setupId=0
ViewDescription=tpId=0 setupId=0
ViewSetup=BasicViewSetup{name='0', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@3, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=1
ViewDescription=tpId=0 setupId=1
ViewSetup=BasicViewSetup{name='1', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@4, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=2
ViewDescription=tpId=0 setupId=2
ViewSetup=BasicViewSetup{name='2', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@5, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=3
ViewDescription=tpId=0 setupId=3
ViewSetup=BasicViewSetup{name='3', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@6, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=4
ViewDescription=tpId=0 setupId=4
ViewSetup=BasicViewSetup{name='4', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@7, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
ViewId=tpId=0 setupId=5
ViewDescription=tpId=0 setupId=5
ViewSetup=BasicViewSetup{name='5', size=512x512x86, voxelSize=FinalVoxelDimensions{unit='pixels', dimensions=[1.0, 1.0, 3.0]}, attributes={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}}
ViewSetup.getAttributes()={illumination=mpicbg.spim.data.sequence.Illumination@0, channel=mpicbg.spim.data.sequence.Channel@0, tile=mpicbg.spim.data.sequence.Tile@8, angle=mpicbg.spim.data.sequence.Angle@0}
ViewSetup.getAttributes().size()=4
(Tue Mar 18 10:25:43 UTC 2025): Downsampling used for stitching: (2, 2, 1)
(Tue Mar 18 10:25:43 UTC 2025): Finding pairs to compute overlap ... 
Tue Mar 18 10:25:43 UTC 2025: Removed 4 non-overlapping view-pairs for computing.
(Tue Mar 18 10:25:43 UTC 2025): For the following pairs pairwise stitching will be computed:
        0-5 <=> 0-4
        0-5 <=> 0-3
        0-5 <=> 0-2
        0-5 <=> 0-1
        0-5 <=> 0-0
        0-4 <=> 0-3
        0-4 <=> 0-2
        0-4 <=> 0-1
        0-4 <=> 0-0
        0-3 <=> 0-2
        0-3 <=> 0-1
        0-3 <=> 0-0
        0-2 <=> 0-1
        0-2 <=> 0-0
        0-1 <=> 0-0
(Tue Mar 18 10:25:43 UTC 2025): In total: 15 pair(s).
25/03/18 10:26:03 WARN TaskSetManager: Lost task 6.0 in stage 1.0 (TID 5) (10.172.0.34 executor 1): java.lang.NullPointerException: Cannot invoke "Object.getClass()" because "e" is null
        at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineOrSplitBy(Group.java:234)
        at net.preibisch.mvrecon.process.interestpointregistration.pairwise.constellation.grouping.Group.combineBy(Group.java:172)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.pickBrightest(GroupedViewAggregator.java:119)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator$Action.aggregate(GroupedViewAggregator.java:102)
        at net.preibisch.stitcher.algorithm.GroupedViewAggregator.aggregate(GroupedViewAggregator.java:396)
        at net.preibisch.stitcher.algorithm.globalopt.TransformationTools.computeStitching(TransformationTools.java:277)
        at net.preibisch.bigstitcher.spark.SparkPairwiseStitching.lambda$call$c9354d04$1(SparkPairwiseStitching.java:247)
        at org.apache.spark.api.java.JavaPairRDD$.$anonfun$toScalaFunction$1(JavaPairRDD.scala:1070)
        at scala.collection.Iterator$$anon$9.next(Iterator.scala:577)
        at org.apache.spark.storage.memory.MemoryStore.putIterator(MemoryStore.scala:224)
        at org.apache.spark.storage.memory.MemoryStore.putIteratorAsValues(MemoryStore.scala:302)
        at org.apache.spark.storage.BlockManager.$anonfun$doPutIterator$1(BlockManager.scala:1531)
        at org.apache.spark.storage.BlockManager.org$apache$spark$storage$BlockManager$$doPut(BlockManager.scala:1458)
        at org.apache.spark.storage.BlockManager.doPutIterator(BlockManager.scala:1522)
        at org.apache.spark.storage.BlockManager.getOrElseUpdate(BlockManager.scala:1349)
        at org.apache.spark.rdd.RDD.getOrCompute(RDD.scala:375)
        at org.apache.spark.rdd.RDD.iterator(RDD.scala:326)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:92)
        at org.apache.spark.TaskContext.runTaskWithListeners(TaskContext.scala:161)
        at org.apache.spark.scheduler.Task.run(Task.scala:139)
        at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:554)
        at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1529)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:557)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
        at java.base/java.lang.Thread.run(Thread.java:840)


Collecting results

Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-4 <> 0-2: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-4 <> 0-1: No shift found, skipping pair.
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-4 <> 0-0: No shift found, skipping pair.
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-3 <> 0-2: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-3 <> 0-1: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-3 <> 0-0: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-5 <> 0-4: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-2 <> 0-1: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-5 <> 0-3: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-2 <> 0-0: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-5 <> 0-2: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-1 <> 0-0: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-5 <> 0-1: No shift found, skipping pair.
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-5 <> 0-0: No shift found, skipping pair.
Tue Mar 18 10:26:11 UTC 2025: Compute pairwise: 0-4 <> 0-3: r=0.0
Tue Mar 18 10:26:11 UTC 2025: Remaining pairs: 11
Tue Mar 18 10:26:11 UTC 2025: Applying filter minR=0.3
Tue Mar 18 10:26:11 UTC 2025: Applying filter maxR=1.0
Tue Mar 18 10:26:11 UTC 2025: Remaining pairs after applying filters: 0
Saving resulting XML ... 
gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml
Saving interest points multi-threaded ... 
Saving PSFs multi-threaded ... 
(Tue Mar 18 10:26:13 UTC 2025): Saved xml 'gs://bigstitcher-test-example1/Stitching_N5_XML/dataset.xml'.
Batch [0e09ec8a2a844e60b6232b7ef2177737] finished.
metadata:
  '@type': type.googleapis.com/google.cloud.dataproc.v1.BatchOperationMetadata
  batch: projects/bigstitcheruzh/locations/europe-west6/batches/0e09ec8a2a844e60b6232b7ef2177737
  batchUuid: c6c91529-9338-44a8-acd2-c203eb71a5ff
  createTime: '2025-03-18T10:24:22.759547Z'
  description: Batch
  labels:
    goog-dataproc-batch-id: 0e09ec8a2a844e60b6232b7ef2177737
    goog-dataproc-batch-uuid: c6c91529-9338-44a8-acd2-c203eb71a5ff
    goog-dataproc-drz-resource-uuid: batch-c6c91529-9338-44a8-acd2-c203eb71a5ff
    goog-dataproc-location: europe-west6
  operationType: BATCH
name: projects/bigstitcheruzh/regions/europe-west6/operations/5037589e-fc97-35f3-a581-d4b1fde68810
mesospim_cloud@cloudshell:~ (bigstitcheruzh)$ 

[agustleoa]

• for local: which java version are you using locally? Please use Zulu JDK 8 + FX … it looks like you use Java21, which has issues with the Spark version we are using.

Just wanted to report that using Zulu JDK 8 + FX fixed a similar error I experienced when trying resave the test dataset on a local machine. Thanks!

For reference, here is the error I got while using java-8-openjdk-amd64, as opposed to zulu-fx-8-amd64:

Exception in thread "main" java.lang.IllegalAccessError: class org.apache.spark.storage.StorageUtils$ (in unnamed module @0x6b57696f) cannot access class sun.nio.ch.DirectBuffer (in module java.base) because module java.base does not export sun.nio.ch to unnamed module @0x6b57696f
	at org.apache.spark.storage.StorageUtils$.<init>(StorageUtils.scala:213)
	at org.apache.spark.storage.StorageUtils$.<clinit>(StorageUtils.scala)
	at org.apache.spark.storage.BlockManagerMasterEndpoint.<init>(BlockManagerMasterEndpoint.scala:114)
	at org.apache.spark.SparkEnv$.$anonfun$create$9(SparkEnv.scala:353)
	at org.apache.spark.SparkEnv$.registerOrLookupEndpoint$1(SparkEnv.scala:290)
	at org.apache.spark.SparkEnv$.create(SparkEnv.scala:339)
	at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:194)
	at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:279)
	at org.apache.spark.SparkContext.<init>(SparkContext.scala:464)
	at org.apache.spark.api.java.JavaSparkContext.<init>(JavaSparkContext.scala:58)
	at net.preibisch.bigstitcher.spark.SparkResaveN5.call(SparkResaveN5.java:241)
	at net.preibisch.bigstitcher.spark.SparkResaveN5.call(SparkResaveN5.java:63)
	at picocli.CommandLine.executeUserObject(CommandLine.java:2045)
	at picocli.CommandLine.access$1500(CommandLine.java:148)
	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2465)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2457)
	at picocli.CommandLine$RunLast.handle(CommandLine.java:2419)
	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2277)
	at picocli.CommandLine$RunLast.execute(CommandLine.java:2421)
	at picocli.CommandLine.execute(CommandLine.java:2174)
	at net.preibisch.bigstitcher.spark.SparkResaveN5.main(SparkResaveN5.java:366)

[StephanPreibisch]

@agustleoa that error is (most likely) related to the java version and suggests you are actually using Java21. Please try mvn -version and java -version to double-check the Java version that is being used.