Unverified Commit 3c49f77e authored by Silvan Mosberger's avatar Silvan Mosberger Committed by GitHub
Browse files

Merge pull request #269243 from twesterhout/petsc-update 

petsc: 3.19.2 -> 3.19.4, fix tests, add more options
parents 811278c9 b48ec762

pkgs/development/libraries/science/math/petsc/default.nix

+16 −5
Original line number Diff line number Diff line
@@ -6,11 +6,15 @@ 
, python3

, blas

, lapack

, mpiSupport ? true

, mpi                   # generic mpi dependency

, openssh               # required for openmpi tests

, petsc-withp4est ? true

, petsc-withp4est ? false

, p4est

, zlib                  # propagated by p4est but required by petsc

, petsc-optimized ? false

, petsc-scalar-type ? "real"

, petsc-precision ? "double"

}:



# This version of PETSc does not support a non-MPI p4est build
@@ -18,14 +22,14 @@ assert petsc-withp4est -> p4est.mpiSupport; 


stdenv.mkDerivation rec {

  pname = "petsc";

  version = "3.19.2";

  version = "3.19.4";



  src = fetchurl {

    url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz";

    sha256 = "sha256-EU82P3ebsWg5slwOcPiwrg2UfVDnL3xs3csRsAEHmxY=";

    sha256 = "sha256-fJQbcb5Sw7dkIU5JLfYBCdEvl/fYVMl6RN8MTZWLOQY=";

  };



  mpiSupport = !withp4est || p4est.mpiSupport;

  inherit mpiSupport;

  withp4est = petsc-withp4est;



  strictDeps = true;
@@ -49,7 +53,6 @@ stdenv.mkDerivation rec { 
  patches = [ ./filter_mpi_warnings.patch ];



  preConfigure = ''

    export FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"

    patchShebangs ./lib/petsc/bin

    configureFlagsArray=(

      $configureFlagsArray
@@ -68,6 +71,14 @@ stdenv.mkDerivation rec { 
      ''}

      "--with-blas=1"

      "--with-lapack=1"

      "--with-scalar-type=${petsc-scalar-type}"

      "--with-precision=${petsc-precision}"

      ${lib.optionalString petsc-optimized ''

        "--with-debugging=0"

        COPTFLAGS='-g -O3'

        FOPTFLAGS='-g -O3'

        CXXOPTFLAGS='-g -O3'

      ''}

    )

  '';

pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch

+12 −12
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ index 168febb34b6..71068469066 100644 
 #  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; \

+        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 \
@@ -14,7 +14,7 @@ index 168febb34b6..71068469066 100644 
         ${MAKE} PETSC_ARCH=${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; \

+        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 \
@@ -22,7 +22,7 @@ index 168febb34b6..71068469066 100644 
         ${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; \

+        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 \
@@ -30,7 +30,7 @@ index 168febb34b6..71068469066 100644 
 #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; \

+        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  \
@@ -38,7 +38,7 @@ index 168febb34b6..71068469066 100644 
           ${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; \

+        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  \
@@ -46,7 +46,7 @@ index 168febb34b6..71068469066 100644 
 	   ${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; \

+        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 \
@@ -54,7 +54,7 @@ index 168febb34b6..71068469066 100644 
 	   ${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; \

+        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  \
@@ -62,7 +62,7 @@ index 168febb34b6..71068469066 100644 
 	   ${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; \

+        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 \
@@ -70,7 +70,7 @@ index 168febb34b6..71068469066 100644 
            ${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; \

+        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  \
@@ -78,7 +78,7 @@ index 168febb34b6..71068469066 100644 
            ${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; \

+        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  \
@@ -86,7 +86,7 @@ index 168febb34b6..71068469066 100644 
 	   ${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; \

+        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 \
@@ -94,7 +94,7 @@ index 168febb34b6..71068469066 100644 
 	   ${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; \

+        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 \