Merge pull request #2 from svalat/fix/idefix-tutorial-dir-env-var

fix: introduce IDEFIX_TUTORIAL_DIR + make directory layout consistent + remove the second venv

Author: glesur

Readme.md

@@ -20,13 +20,16 @@ In the directory of your choice, you then clone the tutorial to the directory `i
 
 ```shell
 git clone --branch asnum2026 https://github.com/idefix-code/tutorial.git ./idefix-tutorial
+export IDEFIX_TUTORIAL_DIR="$PWD/idefix-tutorial"
+cd "$IDEFIX_TUTORIAL_DIR"
 ```
 
 We then create a python environement, install what we need, and launch a jupyter lab session
 ```shell
-python3 -m venv ./idefix-env
-source idefix-env/bin/activate
-pip install -r ./idefix-tutorial/python_requirements.txt
+cd "$IDEFIX_TUTORIAL_DIR"
+python3 -m venv ./idefix.env
+source idefix.env/bin/activate
+pip install -r ./python_requirements.txt
 jupyter lab --sock=~/mysock.sock
 ```
 
@@ -36,7 +39,7 @@ you're now good to go. On your laptop, using your favourite browser, open the li
 http://localhost:8888/lab?token=<your_token>
 ```
 
-Which should open your jupyter lab session running on the distant machine. From there, go to the tutorial directory `idefix-tutorial` created above, and open `start.ipynb`.
+Which should open your jupyter lab session running on the distant machine. From there, open `start.ipynb`.
 
 
 

SimpleSetup/problem1/read_problem.ipynb

@@ -12,7 +12,7 @@
     "import os\n",
     "import sys\n",
     "# Possibly adapt the idefix path depending on where you cloned the sources\n",
-    "sys.path.append(\"../../../idefix.src\")\n",
+    "sys.path.append(\"../../idefix.src\")\n",
     "from pytools.vtk_io import readVTK\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np"

SimpleSetup/solution1/read_problem.ipynb

@@ -12,7 +12,7 @@
     "import os\n",
     "import sys\n",
     "# Possibly adapt the idefix path depending on where you cloned the sources\n",
-    "sys.path.append(\"../../../idefix.src\")\n",
+    "sys.path.append(\"../../idefix.src\")\n",
     "from pytools.vtk_io import readVTK\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np"
@@ -96,7 +96,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,

VisualisationAndPost/nonos/Intro_to_nonos.ipynb

@@ -549,7 +549,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.14"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,

VisualisationAndPost/readVTK/Direct_VTK_visualisation.ipynb

@@ -46,7 +46,7 @@
     "import os\n",
     "import sys\n",
     "# Possibly adapt the idefix path depending on where you cloned the sources\n",
-    "sys.path.append(\"../../../idefix.src/\")\n",
+    "sys.path.append(\"../../idefix.src/\")\n",
     "from pytools.vtk_io import readVTK"
    ]
   },
@@ -320,7 +320,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.13.5"
   }
  },
  "nbformat": 4,

start.ipynb

@@ -26,24 +26,6 @@
     "git clone --recurse-submodules https://github.com/idefix-code/idefix.git idefix.src\n",
     "export IDEFIX_DIR=$PWD/idefix.src\n",
     "```\n",
-    "For conveniance, we set the `IDEFIX_DIR` environment variable to the absolute path of the root directory of idefix (as above). \n",
-    "\n",
-    "If you intend to use the python script provided in this tutorial, best is to deploy a python environement with everything already set up. \n",
-    "We therefore create a python environement in the directory `$IDEFIX_DIR/test` with the right modules\n",
-    "\n",
-    "```shell\n",
-    "cd $IDEFIX_DIR/test\n",
-    "python3 -m venv ./env\n",
-    "source env/bin/activate\n",
-    "pip install -r python_requirements.txt\n",
-    "```"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "6a5f21fb-2d61-4ab6-8539-a666b83ddc05",
-   "metadata": {},
-   "source": [
     "For conveniance, we set the `IDEFIX_DIR` environment variable to the absolute path of the root directory of idefix (as above). "
    ]
   },
@@ -134,10 +116,10 @@
     "\n",
     "Running on a GPU usually requires a specific environement for the architecture you target. For Nvidia gpus, you will need CUDA with a compatible host compiler, on AMD GPUs, this is Rocm with its llvm compiler, while for intel you will need the intel oneapi compiler.\n",
     "\n",
-    "For this tutorial, we have prepared and tested environement for each machine (dgx, h200 and pocamd). You just need to source the right environement from `idefix-tutorial/environement/xxx.sh` in your terminal window. e.g. on dgx:\n",
+    "For this tutorial, we have prepared and tested environement for each machine (dgx, h200 and pocamd). You just need to source the right environement from `idefix-tutorial/environement/xxx.env` in your terminal window. e.g. on dgx:\n",
     "\n",
     "```shell\n",
-    "source <path_to_idefix_tutorial>/environements/dgx.sh\n",
+    "source $IDEFIX_TUTORIAL_DIR/environements/dgx.env\n",
     "```\n",
     "\n",
     "Don't forget to source this environement each time you open a new terminal on the target machine.\n",
@@ -213,7 +195,7 @@
     "For this first simple setup, we move in the SimpleSetup/problem1 directory of the tutorial. i.e\n",
     "\n",
     "```shell\n",
-    "cd <path_to_idefix_tutorial>/SimpleSetup/problem1/\n",
+    "cd $IDEFIX_TUTORIAL_DIR/SimpleSetup/problem1/\n",
     "```\n",
     "\n",
     "## What is an idefix setup?\n",
@@ -278,7 +260,7 @@
     "import os\n",
     "import sys\n",
     "# Possibly adapt the idefix path depending on where you cloned the sources\n",
-    "sys.path.append(\"../idefix.src\")\n",
+    "sys.path.append(\"idefix.src\")\n",
     "from pytools.vtk_io import readVTK\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np"
@@ -402,7 +384,7 @@
     "We first move to the problem directory\n",
     "\n",
     "```shell\n",
-    "cd <path_to_idefix_tutorial>/PythonSetup/problem/\n",
+    "cd $IDEFIX_TUTORIAL_DIR/PythonSetup/problem/\n",
     "```\n",
     "\n",
     "## Your tasks\n",
@@ -465,7 +447,7 @@
     "For now, lets move to the problem directory\n",
     "\n",
     "```shell\n",
-    "cd idefix-tutorial/AdvancedSetup/problem1\n",
+    "cd $IDEFIX_TUTORIAL_DIR/AdvancedSetup/problem1\n",
     "```"
    ]
   },
@@ -657,7 +639,7 @@
     "The first problem is a simple 1D shock tube problem. This can be compiled and run on your laptop or on a cluster.\n",
     "\n",
     "```shell\n",
-    "cd idefix-tutorial/Debugging/problem1\n",
+    "cd $IDEFIX_TUTORIAL_DIR/Debugging/problem1\n",
     "```\n",
     "\n",
     "We then configure, compile and run the code\n",
@@ -740,7 +722,7 @@
     "The second problem is a pure thermal diffusion problem where the gas is kept fixed with 0 velocity. This can be compiled and run *on your laptop*.\n",
     "\n",
     "```shell\n",
-    "cd idefix-tutorial/Debugging/problem2\n",
+    "cd $IDEFIX_TUTORIAL_DIR/Debugging/problem2\n",
     "```\n",
     "\n",
     "We then configure, compile and run the code\n",
@@ -861,7 +843,7 @@
     "Let's move to problem 4, which is again a planet-disk interraction problem. This can be compiled and run *on your laptop* or on the on a cluster, but let's focus for now on the GPU version on the a cluster (you can try to do the exercise on your laptop). First go to the right directory\n",
     "\n",
     "```shell\n",
-    "cd idefix-tutorial/Debugging/problem4\n",
+    "cd $IDEFIX_TUTORIAL_DIR/Debugging/problem4\n",
     "```\n",
     "\n",
     "We then configure\n",
@@ -909,7 +891,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "68fea61b-5fa3-4cfe-85a6-c170b43aeaec",
+   "id": "0e28f9fb-0dc0-4e35-9eca-8ae4254c4529",
    "metadata": {},
    "outputs": [],
    "source": []