diff options
Diffstat (limited to 'pkgs/development/libraries/science/math/petsc')
| -rw-r--r-- | pkgs/development/libraries/science/math/petsc/default.nix | 96 | ||||
| -rw-r--r-- | pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch | 100 |
2 files changed, 0 insertions, 196 deletions
diff --git a/pkgs/development/libraries/science/math/petsc/default.nix b/pkgs/development/libraries/science/math/petsc/default.nix deleted file mode 100644 index c07250c660a33..0000000000000 --- a/pkgs/development/libraries/science/math/petsc/default.nix +++ /dev/null @@ -1,96 +0,0 @@ -{ lib -, stdenv -, fetchurl -, darwin -, gfortran -, python3 -, blas -, lapack -, mpiSupport ? true -, mpi # generic mpi dependency -, openssh # required for openmpi tests -, 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 -assert petsc-withp4est -> p4est.mpiSupport; - -stdenv.mkDerivation rec { - pname = "petsc"; - version = "3.19.4"; - - src = fetchurl { - url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz"; - sha256 = "sha256-fJQbcb5Sw7dkIU5JLfYBCdEvl/fYVMl6RN8MTZWLOQY="; - }; - - inherit mpiSupport; - withp4est = petsc-withp4est; - - strictDeps = true; - nativeBuildInputs = [ python3 gfortran ] - ++ lib.optional mpiSupport mpi - ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh - ; - buildInputs = [ blas lapack ] - ++ lib.optional withp4est p4est - ; - - prePatch = lib.optionalString stdenv.isDarwin '' - substituteInPlace config/install.py \ - --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 = '' - patchShebangs ./lib/petsc/bin - configureFlagsArray=( - $configureFlagsArray - ${if !mpiSupport then '' - "--with-mpi=0" - '' else '' - "--CC=mpicc" - "--with-cxx=mpicxx" - "--with-fc=mpif90" - "--with-mpi=1" - ''} - ${lib.optionalString withp4est '' - "--with-p4est=1" - "--with-zlib-include=${zlib.dev}/include" - "--with-zlib-lib=-L${zlib}/lib -lz" - ''} - "--with-blas=1" - "--with-lapack=1" - "--with-scalar-type=${petsc-scalar-type}" - "--with-precision=${petsc-precision}" - ${lib.optionalString petsc-optimized '' - "--with-debugging=0" - COPTFLAGS='-g -O3' - FOPTFLAGS='-g -O3' - CXXOPTFLAGS='-g -O3' - ''} - ) - ''; - - configureScript = "python ./configure"; - - enableParallelBuilding = true; - doCheck = stdenv.hostPlatform == stdenv.buildPlatform; - - meta = with lib; { - description = "Portable Extensible Toolkit for Scientific computation"; - homepage = "https://www.mcs.anl.gov/petsc/index.html"; - license = licenses.bsd2; - maintainers = with maintainers; [ cburstedde ]; - }; -} diff --git a/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch b/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch deleted file mode 100644 index f3a34de9304e3..0000000000000 --- a/pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch +++ /dev/null @@ -1,100 +0,0 @@ -diff --git a/src/snes/tutorials/makefile b/src/snes/tutorials/makefile -index 672a62a..a5fd1c4 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 ${MPIEXEC_TAIL} ./ex5f -snes_rtol 1e-4 > ex5f_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type cuda -dm_mat_type aijcusparse -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type hip -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -snes_monitor -dm_mat_type seqaijcusparse -dm_vec_type seqcuda -pc_type gamg -pc_gamg_esteig_ksp_max_it 10 -ksp_monitor -mg_levels_ksp_max_it 3 > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type ml > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -pc_type fieldsplit -pc_fieldsplit_block_size 4 -pc_fieldsplit_type SCHUR -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type lu -fieldsplit_1_pc_type lu -snes_monitor_short -ksp_monitor_short -fieldsplit_0_pc_factor_mat_solver_type mumps -fieldsplit_1_pc_factor_mat_solver_type mumps > ex19_6.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_6.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_grid_x 20 -da_grid_y 20 -pc_type lu -pc_factor_mat_solver_type superlu_dist > ex19.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type lu -pc_factor_mat_solver_type umfpack > ex19_1.tmp 2>&1; \ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ - if (${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 ${MPIEXEC_TAIL} ./ex3k -view_initial -dm_vec_type kokkos -dm_mat_type aijkokkos -use_gpu_aware_mpi 0 -snes_monitor > ex3k_1.tmp 2>&1 ;\ -+ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \ - if (${DIFF} output/ex3k_1.out ex3k_1.tmp) then \ - echo "C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels"; \ - else \ |