diff options
-rw-r--r-- | pkgs/development/libraries/science/math/petsc/default.nix | 10 | ||||
-rw-r--r-- | pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch | 100 |
2 files changed, 108 insertions, 2 deletions
diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix index c2fabae1c20b7..06494a1dddcb9 100644 --- a/pkgs/development/libraries/science/math/petsc/default.nix +++ b/pkgs/development/libraries/science/math/petsc/default.nix @@ -18,11 +18,11 @@ assert petsc-withp4est -> p4est.mpiSupport; stdenv.mkDerivation rec { pname = "petsc"; - version = "3.17.4"; + version = "3.19.1"; src = fetchurl { url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz"; - sha256 = "sha256-mcEnSGcio//ZWiaLTOsJdsvyF5JsaBqWMb1yRuq4yyo="; + sha256 = "sha256-dNtgxTyAtI1cOeB7w5qIPsztiLnySl3hfPb0hakD4SA="; }; mpiSupport = !withp4est || p4est.mpiSupport; @@ -42,6 +42,12 @@ stdenv.mkDerivation rec { --replace /usr/bin/install_name_tool ${darwin.cctools}/bin/install_name_tool ''; + # Both OpenMPI and MPICH get confused by the sandbox environment and spew errors like this (both to stdout and stderr): + # [hwloc/linux] failed to find sysfs cpu topology directory, aborting linux discovery. + # [1684747490.391106] [localhost:14258:0] tcp_iface.c:837 UCX ERROR opendir(/sys/class/net) failed: No such file or directory + # These messages contaminate test output, which makes the quicktest suite to fail. The patch adds filtering for these messages. + patches = [ ./filter_mpi_warnings.patch ]; + preConfigure = '' export FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran" patchShebangs ./lib/petsc/bin diff --git a/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch b/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch new file mode 100644 index 0000000000000..590528446f611 --- /dev/null +++ b/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch @@ -0,0 +1,100 @@ +diff --git a/src/snes/tutorials/makefile b/src/snes/tutorials/makefile +index 168febb34b6..71068469066 100644 +--- a/src/snes/tutorials/makefile ++++ b/src/snes/tutorials/makefile +@@ -13,6 +13,7 @@ include ${PETSC_DIR}/lib/petsc/conf/rules + # these tests are used by the makefile in PETSC_DIR for basic tests of the install and should not be removed + testex5f: ex5f.PETSc + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex5f -snes_rtol 1e-4 > ex5f_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \ + if (${DIFF} output/ex5f_1.testout ex5f_1.tmp > /dev/null 2>&1) then \ + echo "Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process"; \ + else \ +@@ -25,6 +26,7 @@ testex5f: ex5f.PETSc + ${MAKE} PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} ex5f.rm; + testex19: ex19.PETSc + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_1.testout ex19_1.tmp > /dev/null 2>&1) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process"; \ + else \ +@@ -36,6 +38,7 @@ testex19: ex19.PETSc + ${RM} -f ex19_1.tmp; + testex19_mpi: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_1.testout ex19_1.tmp > /dev/null 2>&1) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes"; \ + else \ +@@ -48,6 +51,7 @@ testex19_mpi: + #use unpreconditioned norm because HYPRE device installations use different AMG parameters + runex19_hypre: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre"; \ + else \ +@@ -57,6 +61,7 @@ runex19_hypre: + ${RM} -f ex19_1.tmp + runex19_hypre_cuda: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type cuda -dm_mat_type aijcusparse -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/cuda"; \ + else \ +@@ -66,6 +71,7 @@ runex19_hypre_cuda: + ${RM} -f ex19_1.tmp + runex19_hypre_hip: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type hip -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/hip"; \ + else \ +@@ -75,6 +81,7 @@ runex19_hypre_hip: + ${RM} -f ex19_1.tmp + runex19_cuda: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -snes_monitor -dm_mat_type seqaijcusparse -dm_vec_type seqcuda -pc_type gamg -pc_gamg_esteig_ksp_max_it 10 -ksp_monitor -mg_levels_ksp_max_it 3 > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_cuda_1.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with cuda"; \ + else \ +@@ -84,6 +91,7 @@ runex19_cuda: + ${RM} -f ex19_1.tmp + runex19_ml: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type ml > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_ml.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with ml"; \ + else \ +@@ -93,6 +101,7 @@ runex19_ml: + ${RM} -f ex19_1.tmp + runex19_fieldsplit_mumps: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -pc_type fieldsplit -pc_fieldsplit_block_size 4 -pc_fieldsplit_type SCHUR -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type lu -fieldsplit_1_pc_type lu -snes_monitor_short -ksp_monitor_short -fieldsplit_0_pc_factor_mat_solver_type mumps -fieldsplit_1_pc_factor_mat_solver_type mumps > ex19_6.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_6.tmp; \ + if (${DIFF} output/ex19_fieldsplit_5.out ex19_6.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with mumps"; \ + else \ +@@ -102,6 +111,7 @@ runex19_fieldsplit_mumps: + ${RM} -f ex19_6.tmp + runex19_superlu_dist: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_grid_x 20 -da_grid_y 20 -pc_type lu -pc_factor_mat_solver_type superlu_dist > ex19.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19.tmp; \ + if (${DIFF} output/ex19_superlu.out ex19.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with superlu_dist"; \ + else \ +@@ -111,6 +121,7 @@ runex19_superlu_dist: + ${RM} -f ex19.tmp + runex19_suitesparse: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type lu -pc_factor_mat_solver_type umfpack > ex19_1.tmp 2>&1; \ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_suitesparse.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with suitesparse"; \ + else \ +@@ -120,6 +131,7 @@ runex19_suitesparse: + ${RM} -f ex19_1.tmp + runex3k_kokkos: ex3k.PETSc + -@OMP_PROC_BIND=false ${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex3k -view_initial -dm_vec_type kokkos -dm_mat_type aijkokkos -use_gpu_aware_mpi 0 -snes_monitor > ex3k_1.tmp 2>&1 ;\ ++ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \ + if (${DIFF} output/ex3k_1.out ex3k_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels"; \ + else \ |