From 4b0f3c2db5fbf9a7ea5e839be2a08bf8fcfb5102 Mon Sep 17 00:00:00 2001 From: Max Hausch Date: Thu, 27 Jun 2024 10:44:26 +0200 Subject: [PATCH] petsc: 3.19.4 -> 3.21.0 This also allows building PETSc with hdf5 support. --- .../pe/petsc/filter_mpi_warnings.patch | 60 +++++++++++-------- pkgs/by-name/pe/petsc/package.nix | 50 ++++++++++++---- 2 files changed, 75 insertions(+), 35 deletions(-) diff --git a/pkgs/by-name/pe/petsc/filter_mpi_warnings.patch b/pkgs/by-name/pe/petsc/filter_mpi_warnings.patch index f3a34de9304e..79f44558b351 100644 --- a/pkgs/by-name/pe/petsc/filter_mpi_warnings.patch +++ b/pkgs/by-name/pe/petsc/filter_mpi_warnings.patch @@ -1,12 +1,12 @@ diff --git a/src/snes/tutorials/makefile b/src/snes/tutorials/makefile -index 672a62a..a5fd1c4 100644 +index fa15faad39e..7670e80931e 100644 --- a/src/snes/tutorials/makefile +++ b/src/snes/tutorials/makefile -@@ -13,6 +13,7 @@ include ${PETSC_DIR}/lib/petsc/conf/rules +@@ -13,6 +13,7 @@ ex55: ex55.o ex55k.o # these tests are used by the makefile in PETSC_DIR for basic tests of the install and should not be removed testex5f: ex5f.PETSc -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex5f -snes_rtol 1e-4 > ex5f_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \ if (${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 672a62a..a5fd1c4 100644 ${MAKE} PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} ex5f.rm; testex19: ex19.PETSc -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${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 672a62a..a5fd1c4 100644 ${RM} -f ex19_1.tmp; testex19_mpi: -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${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 \ @@ -30,71 +30,83 @@ index 672a62a..a5fd1c4 100644 #use unpreconditioned norm because HYPRE device installations use different AMG parameters runex19_hypre: -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre"; \ + 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 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type cuda -dm_mat_type aijcusparse -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/cuda"; \ + 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 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type hip -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/hip"; \ + 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 ${MPIEXEC_TAIL} ./ex19 -snes_monitor -dm_mat_type seqaijcusparse -dm_vec_type seqcuda -pc_type gamg -pc_gamg_esteig_ksp_max_it 10 -ksp_monitor -mg_levels_ksp_max_it 3 > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -snes_monitor -dm_mat_type seqaijcusparse -dm_vec_type seqcuda -pc_type gamg -ksp_monitor -mg_levels_ksp_max_it 1 > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${DIFF} output/ex19_cuda_1.out ex19_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with cuda"; \ + 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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type ml > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${DIFF} output/ex19_ml.out ex19_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with ml"; \ + 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 ${MPIEXEC_TAIL} ./ex19 -pc_type fieldsplit -pc_fieldsplit_block_size 4 -pc_fieldsplit_type SCHUR -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type lu -fieldsplit_1_pc_type lu -snes_monitor_short -ksp_monitor_short -fieldsplit_0_pc_factor_mat_solver_type mumps -fieldsplit_1_pc_factor_mat_solver_type mumps > ex19_6.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_6.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_6.tmp; \ if (${DIFF} output/ex19_fieldsplit_5.out ex19_6.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with mumps"; \ + 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 ${MPIEXEC_TAIL} ./ex19 -da_grid_x 20 -da_grid_y 20 -pc_type lu -pc_factor_mat_solver_type superlu_dist > ex19.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19.tmp; \ if (${DIFF} output/ex19_superlu.out ex19.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with superlu_dist"; \ + 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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type lu -pc_factor_mat_solver_type umfpack > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ if (${DIFF} output/ex19_suitesparse.out ex19_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex19 run successfully with suitesparse"; \ + 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 ${MPIEXEC_TAIL} ./ex3k -view_initial -dm_vec_type kokkos -dm_mat_type aijkokkos -use_gpu_aware_mpi 0 -snes_monitor > ex3k_1.tmp 2>&1 ;\ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \ if (${DIFF} output/ex3k_1.out ex3k_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels"; \ + echo "C/C++ example src/snes/tutorials/ex3k run successfully with Kokkos Kernels"; \ else \ +diff --git a/src/vec/vec/tests/makefile b/src/vec/vec/tests/makefile +index d1f047820ec..aab400535dd 100644 +--- a/src/vec/vec/tests/makefile ++++ b/src/vec/vec/tests/makefile +@@ -5,6 +5,7 @@ include ${PETSC_DIR}/lib/petsc/conf/rules + + runex47: ex47.PETSc + -@H5OUT=`mktemp -t petsc.h5.XXXXXX`; ${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex47 -filename $${H5OUT} > ex47_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex47_1.tmp; \ + if (${DIFF} output/ex47_1.out ex47_1.tmp) then \ + echo "C/C++ example src/vec/vec/tests/ex47 run successfully with HDF5"; \ + else \ diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix index 2bf1348cb888..5a547144b491 100644 --- a/pkgs/by-name/pe/petsc/package.nix +++ b/pkgs/by-name/pe/petsc/package.nix @@ -1,7 +1,7 @@ { lib, stdenv, - fetchurl, + fetchzip, darwin, gfortran, python3, @@ -11,6 +11,11 @@ mpi, # generic mpi dependency openssh, # required for openmpi tests petsc-withp4est ? false, + hdf5-support ? false, + hdf5, + metis, + parmetis, + pkg-config, p4est, zlib, # propagated by p4est but required by petsc petsc-optimized ? false, @@ -23,11 +28,11 @@ assert petsc-withp4est -> p4est.mpiSupport; stdenv.mkDerivation rec { pname = "petsc"; - version = "3.19.4"; + version = "3.21.0"; - src = fetchurl { - url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz"; - sha256 = "sha256-fJQbcb5Sw7dkIU5JLfYBCdEvl/fYVMl6RN8MTZWLOQY="; + src = fetchzip { + url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${version}.tar.gz"; + hash = "sha256-2J6jtIKz1ZT9qwN8tuYQNBIeBJdE4Gt9cE3b5rTIeF4="; }; inherit mpiSupport; @@ -37,11 +42,12 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ python3 gfortran + pkg-config ] ++ lib.optional mpiSupport mpi ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh; buildInputs = [ blas lapack - ] ++ lib.optional withp4est p4est; + ] ++ lib.optional hdf5-support hdf5 ++ lib.optional withp4est p4est; prePatch = lib.optionalString stdenv.isDarwin '' substituteInPlace config/install.py \ @@ -69,6 +75,10 @@ stdenv.mkDerivation rec { "--with-cxx=mpicxx" "--with-fc=mpif90" "--with-mpi=1" + "--with-metis=1" + "--with-metis-dir=${metis}" + "--with-parmetis=1" + "--with-parmetis-dir=${parmetis}" '' } ${lib.optionalString withp4est '' @@ -76,27 +86,45 @@ stdenv.mkDerivation rec { "--with-zlib-include=${zlib.dev}/include" "--with-zlib-lib=-L${zlib}/lib -lz" ''} + ${lib.optionalString hdf5-support '' + "--with-hdf5=1" + "--with-hdf5-fortran-bindings=1" + "--with-hdf5-lib=-L${hdf5}/lib -lhdf5" + "--with-hdf5-include=${hdf5.dev}/include" + ''} "--with-blas=1" "--with-lapack=1" "--with-scalar-type=${petsc-scalar-type}" "--with-precision=${petsc-precision}" ${lib.optionalString petsc-optimized '' "--with-debugging=0" - COPTFLAGS='-g -O3' - FOPTFLAGS='-g -O3' - CXXOPTFLAGS='-g -O3' + COPTFLAGS='-O3' + FOPTFLAGS='-O3' + CXXOPTFLAGS='-O3' + CXXFLAGS='-O3' ''} ) ''; + hardeningDisable = lib.optionals (!petsc-optimized) [ + "fortify" + "fortify3" + ]; + configureScript = "python ./configure"; enableParallelBuilding = true; - doCheck = stdenv.hostPlatform == stdenv.buildPlatform; + + # This is needed as the checks need to compile and link the test cases with + # -lpetsc, which is not available in the checkPhase, which is executed before + # the installPhase. The installCheckPhase comes after the installPhase, so + # the library is installed and available. + doInstallCheck = true; + installCheckTarget = "check_install"; meta = with lib; { description = "Portable Extensible Toolkit for Scientific computation"; - homepage = "https://www.mcs.anl.gov/petsc/index.html"; + homepage = "https://petsc.org/release/"; license = licenses.bsd2; maintainers = with maintainers; [ cburstedde ]; };