upgrade ubuntu in docker containers

.github/workflows/regression.yml

@@ -54,12 +54,12 @@ jobs:
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2:260329-0132
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
@@ -70,7 +70,7 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -97,12 +97,12 @@ jobs:
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:260329-0132
         with:
           args: -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
@@ -113,7 +113,7 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2-tsan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -137,12 +137,12 @@ jobs:
           key: ${{ matrix.config_set }}-${{ github.sha }}
           restore-keys: ${{ matrix.config_set }}
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-asan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
       - name: Build
-        run: docker run --rm --cap-add SYS_PTRACE -v $(pwd):${{ github.workspace }} -w ${{ github.workspace }} ghcr.io/su2code/su2/build-su2-asan:250717-1402 -b ${{github.ref}} -f "${{matrix.flags}}"
+        run: docker run --rm --cap-add SYS_PTRACE -v $(pwd):${{ github.workspace }} -w ${{ github.workspace }} ghcr.io/su2code/su2/build-su2-asan:260329-0132 -b ${{github.ref}} -f "${{matrix.flags}}"
       - name: Compress binaries
         run: tar -zcvf install_bin.tgz install/*
       - name: Upload Binaries
@@ -151,7 +151,7 @@ jobs:
           name: ${{ matrix.config_set }}
           path: install_bin.tgz
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/build-su2-asan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2-asan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -182,7 +182,7 @@ jobs:
             tag: OMP
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -208,12 +208,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}}
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -231,7 +231,7 @@ jobs:
             tag: TagNoMPI
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -257,12 +257,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--tapetests"
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -277,7 +277,7 @@ jobs:
         testscript: ['hybrid_regression.py', 'hybrid_regression_AD.py']
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -303,12 +303,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:260329-0132
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--tsan"
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2-tsan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -322,7 +322,7 @@ jobs:
         testscript: ['serial_regression.py', 'serial_regression_AD.py']
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-asan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -348,12 +348,12 @@ jobs:
           chmod a+x $BIN_FOLDER/*
           ls -lahR $BIN_FOLDER
       - name: Run Tests in Container
-        uses: docker://ghcr.io/su2code/su2/test-su2-asan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:260329-0132
         with:
           # -t <Tutorials-branch> -c <Testcases-branch>
           args: -b ${{github.ref}} -t develop -c develop -s ${{matrix.testscript}} -a "--asan"
       - name: Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2-asan:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2-asan:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -374,7 +374,7 @@ jobs:
             tag: MPI
     steps:
       - name: Pre Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}
@@ -435,11 +435,11 @@ jobs:
           echo $PWD
           ls -lahR
       - name: Run Unit Tests
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           entrypoint: install/bin/${{matrix.testdriver}}
       - name: Post Cleanup
-        uses: docker://ghcr.io/su2code/su2/test-su2:250717-1402
+        uses: docker://ghcr.io/su2code/su2/test-su2:260329-0132
         with:
           entrypoint: /bin/rm
           args: -rf install install_bin.tgz src ccache ${{ matrix.config_set }}

.github/workflows/release-management.yml

@@ -35,7 +35,7 @@ jobs:
           key: ${{ matrix.os_bin }}-${{ github.sha }}
           restore-keys: ${{ matrix.os_bin }}
       - name: Build
-        uses: docker://ghcr.io/su2code/su2/build-su2-cross:250717-1402
+        uses: docker://ghcr.io/su2code/su2/build-su2-cross:260329-0132
         with:
           args: -b ${{ github.sha }} -f "${{matrix.flags}}"
       - name: Create Archive

Common/include/code_config.hpp

@@ -28,6 +28,12 @@
 
 #include <type_traits>
 
+#if defined(_MSC_VER)
+#define PRAGMIZE(X) __pragma(X)
+#else
+#define PRAGMIZE(X) _Pragma(#X)
+#endif
+
 #if defined(_MSC_VER)
 #define FORCEINLINE __forceinline
 #elif defined(__GNUC__) || defined(__clang__) || defined(__INTEL_COMPILER)
@@ -151,3 +157,13 @@ using su2mixedfloat = passivedouble;
 #define HAVE_OMPT
 #endif
 #endif
+
+#ifdef __GNUC__
+#define SU2_IGNORE_WARNING(WARNING) \
+  PRAGMIZE(GCC diagnostic push)     \
+  PRAGMIZE(GCC diagnostic ignored WARNING)
+#define SU2_RESTORE_WARNING PRAGMIZE(GCC diagnostic pop)
+#else
+#define SU2_IGNORE_WARNING(WARNING)
+#define SU2_RESTORE_WARNING
+#endif

Common/include/containers/C2DContainer.hpp

@@ -545,7 +545,10 @@ class C2DContainer
    * \brief Set value of all entries to "value".
    */
   void setConstant(const Scalar_t& value) noexcept {
+    // GCC 13 has a false-positive about overflow of memcpy due to size being uint64_t, and its memcpy just int64_t.
+    SU2_IGNORE_WARNING("-Wstringop-overflow")
     for (size_t i = 0; i < size(); ++i) m_data[i] = value;
+    SU2_RESTORE_WARNING
   }
 
   /*!

Common/include/parallelization/omp_structure.hpp

@@ -43,12 +43,6 @@
 
 #include "../code_config.hpp"
 
-#if defined(_MSC_VER)
-#define PRAGMIZE(X) __pragma(X)
-#else
-#define PRAGMIZE(X) _Pragma(#X)
-#endif
-
 #if defined(HAVE_OMP)
 #include <omp.h>
 

Common/src/linear_algebra/CSysSolve.cpp

@@ -25,10 +25,6 @@
  * License along with SU2. If not, see <http://www.gnu.org/licenses/>.
  */
 
-#include "Eigen/Core"
-#include "Eigen/Dense"
-#include "Eigen/Eigenvalues"
-
 #include "../../include/linear_algebra/CSysSolve.hpp"
 #include "../../include/linear_algebra/CSysSolve_b.hpp"
 #include "../../include/parallelization/omp_structure.hpp"
@@ -38,6 +34,12 @@
 #include "../../include/linear_algebra/CMatrixVectorProduct.hpp"
 #include "../../include/linear_algebra/CPreconditioner.hpp"
 
+SU2_IGNORE_WARNING("-Wmaybe-uninitialized")
+#include "Eigen/Core"
+#include "Eigen/Dense"
+#include "Eigen/Eigenvalues"
+SU2_RESTORE_WARNING
+
 #include <complex>
 #include <iostream>
 #include <limits>

SU2_CFD/include/numerics/CNumerics.hpp

@@ -563,7 +563,7 @@ class CNumerics {
   NEVERINLINE static void ComputePerturbedRSM(size_t nDim, size_t uq_eigval_comp, bool uq_permute, su2double uq_delta_b,
                                               su2double uq_urlx, const Mat1& velgrad, Scalar density,
                                               Scalar viscosity, Scalar turb_ke, Mat2& MeanPerturbedRSM) {
-    Scalar MeanReynoldsStress[3][3];
+    Scalar MeanReynoldsStress[3][3] = {{}};
     ComputeStressTensor(nDim, MeanReynoldsStress, velgrad, viscosity, density, turb_ke, true);
     for (size_t iDim = 0; iDim < 3; iDim++)
       for (size_t jDim = 0; jDim < 3; jDim++)

SU2_CFD/src/solvers/CSolver.cpp

@@ -4045,7 +4045,7 @@ void CSolver::ComputeVertexTractions(CGeometry *geometry, const CConfig *config)
         // Calculate tn in the fluid nodes for the viscous term
         if (viscous_flow) {
           const su2double Viscosity = base_nodes->GetLaminarViscosity(iPoint);
-          su2double Tau[3][3];
+          su2double Tau[3][3] = {{}};
           CNumerics::ComputeStressTensor(nDim, Tau, base_nodes->GetVelocityGradient(iPoint), Viscosity);
           for (unsigned short iDim = 0; iDim < nDim; iDim++) {
             auxForce[iDim] += GeometryToolbox::DotProduct(nDim, Tau[iDim], Normal);

TestCases/hybrid_regression.py

@@ -28,6 +28,10 @@
 # make print(*args) function available in PY2.6+, does'nt work on PY < 2.6
 from __future__ import print_function
 
+import os
+os.environ["OMPI_MCA_osc"] = "pt2pt"
+os.environ["OMPI_MCA_btl"] = "self,tcp"
+
 import sys
 from TestCase import TestCase
 from TestCase import parse_args

TestCases/parallel_regression.py

@@ -28,14 +28,34 @@
 # make print(*args) function available in PY2.6+, does'nt work on PY < 2.6
 from __future__ import print_function
 
+import os
+os.environ["OMPI_MCA_osc"] = "pt2pt"
+os.environ["OMPI_MCA_btl"] = "self,vader,tcp"
+
 import sys
 from TestCase import TestCase
 
+import subprocess
+
 def main():
     '''This program runs SU2 and ensures that the output matches specified values.
        This will be used to do checks when code is pushed to github
        to make sure nothing is broken. '''
 
+    result = subprocess.run(
+        ['df', '-h', '/dev/shm'],
+        capture_output=True,
+        text=True
+    )
+
+    print("STDOUT:")
+    print(result.stdout)
+
+    print("STDERR:")
+    print(result.stderr)
+
+    print("Return code:", result.returncode)
+
     test_list = []
 
     #######################

externals/cgns/hdf5/meson.build

@@ -16,7 +16,9 @@ if target_machine.system() != 'windows' and cc.get_id() != 'intel'
                       '-Wno-pedantic',
                       '-Wno-error=stringop-truncation',
                       '-Wno-error=cast-function-type',
-                      '-Wno-stringop-truncation']
+                      '-Wno-stringop-truncation',
+                      '-Wno-dangling-pointer',
+                      '-Wno-format-truncation']
   foreach flag : desired_warnings
     if cc.has_argument(flag)
       hdf5_default_warnings += flag

externals/cgns/meson.build

@@ -11,7 +11,13 @@ if build_machine.system() != 'windows' and meson.get_compiler('c').get_id() != '
                       '-Wno-error=stringop-truncation',
                       '-Wno-stringop-truncation',
                       '-Wno-error=absolute-value',
-                      '-Wno-error=class-memaccess']
+                      '-Wno-error=class-memaccess',
+                      '-Wno-dangling-pointer',
+                      '-Wno-format-truncation',
+                      '-Wno-maybe-uninitialized',
+                      '-Wno-array-bounds',
+                      '-Wno-array-parameter',
+                      '-Wno-stringop-overflow']
   foreach flag : desired_warnings
     if meson.get_compiler('c').has_argument(flag)
       cgns_default_warnings += flag

externals/tecio/meson.build

@@ -1,11 +1,11 @@
-check_dir = run_command(python, 
+check_dir = run_command(python,
                         script_path / 'check_dir.py',
                         'boost')
 if check_dir.returncode() != 0
   message('Extracting boost ...')
-  extract_boost = run_command(python, 
+  extract_boost = run_command(python,
                               script_path / 'extract_file.py',
-                              'boost.tar.gz', 
+                              'boost.tar.gz',
                               meson.current_source_dir(), check: true)
 else
   message('Boost sources found.')