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Merge pull request #323457 from helsinki-systems/bump/petsc-3.21.0

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petsc: 3.19.4 -> 3.21.0
This commit is contained in:
0x4A6F
2024-07-01 14:56:28 +02:00
committed by GitHub
parent dcffdd1040 4b0f3c2db5
commit 521b6f8ebf
4 changed files with 167 additions and 122 deletions
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60
pkgs/development/libraries/science/math/petsc/filter_mpi_warnings.patch → pkgs/by-name/pe/petsc/filter_mpi_warnings.patch
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@@ -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 \

131
pkgs/by-name/pe/petsc/package.nix Normal file
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@@ -0,0 +1,131 @@
{
lib,
stdenv,
fetchzip,
darwin,
gfortran,
python3,
blas,
lapack,
mpiSupport ? true,
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,
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 = "3.21.0";
src = fetchzip {
url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${version}.tar.gz";
hash = "sha256-2J6jtIKz1ZT9qwN8tuYQNBIeBJdE4Gt9cE3b5rTIeF4=";
};
inherit mpiSupport;
withp4est = petsc-withp4est;
strictDeps = true;
nativeBuildInputs = [
python3
gfortran
pkg-config
] ++ lib.optional mpiSupport mpi ++ lib.optional (mpiSupport && mpi.pname == "openmpi") openssh;
buildInputs = [
blas
lapack
] ++ lib.optional hdf5-support hdf5 ++ 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
${
if !mpiSupport then
''
"--with-mpi=0"
''
else
''
"--CC=mpicc"
"--with-cxx=mpicxx"
"--with-fc=mpif90"
"--with-mpi=1"
"--with-metis=1"
"--with-metis-dir=${metis}"
"--with-parmetis=1"
"--with-parmetis-dir=${parmetis}"
''
}
${lib.optionalString withp4est ''
"--with-p4est=1"
"--with-zlib-include=${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='-O3'
FOPTFLAGS='-O3'
CXXOPTFLAGS='-O3'
CXXFLAGS='-O3'
''}
)
'';
hardeningDisable = lib.optionals (!petsc-optimized) [
"fortify"
"fortify3"
];
configureScript = "python ./configure";
enableParallelBuilding = true;
# 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://petsc.org/release/";
license = licenses.bsd2;
maintainers = with maintainers; [ cburstedde ];
};
}

96
pkgs/development/libraries/science/math/petsc/default.nix
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@@ -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 ];
};
}

2
pkgs/top-level/all-packages.nix
View File

@@ -38020,8 +38020,6 @@ with pkgs;
p4est-sc = p4est-sc-dbg;
};
petsc = callPackage ../development/libraries/science/math/petsc { };
parmetis = callPackage ../development/libraries/science/math/parmetis { };
QuadProgpp = callPackage ../development/libraries/science/math/QuadProgpp { };