petsc: 3.17.4 -> 3.19.1, fixed build
PETSc versions earlier than 3.18.6 are broken because of incorrect make option generation.
This commit is contained in:
Alexander Kiselyov
parent
f491fc656a
commit
f7e665ccce
@ -18,11 +18,11 @@ assert petsc-withp4est -> p4est.mpiSupport;
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stdenv.mkDerivation rec {
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pname = "petsc";
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version = "3.17.4";
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version = "3.19.1";
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src = fetchurl {
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url = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-${version}.tar.gz";
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sha256 = "sha256-mcEnSGcio//ZWiaLTOsJdsvyF5JsaBqWMb1yRuq4yyo=";
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sha256 = "sha256-dNtgxTyAtI1cOeB7w5qIPsztiLnySl3hfPb0hakD4SA=";
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};
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mpiSupport = !withp4est || p4est.mpiSupport;
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@ -42,6 +42,12 @@ stdenv.mkDerivation rec {
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--replace /usr/bin/install_name_tool ${darwin.cctools}/bin/install_name_tool
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'';
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# Both OpenMPI and MPICH get confused by the sandbox environment and spew errors like this (both to stdout and stderr):
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# [hwloc/linux] failed to find sysfs cpu topology directory, aborting linux discovery.
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# [1684747490.391106] [localhost:14258:0] tcp_iface.c:837 UCX ERROR opendir(/sys/class/net) failed: No such file or directory
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# These messages contaminate test output, which makes the quicktest suite to fail. The patch adds filtering for these messages.
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patches = [ ./filter_mpi_warnings.patch ];
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preConfigure = ''
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export FC="${gfortran}/bin/gfortran" F77="${gfortran}/bin/gfortran"
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patchShebangs ./lib/petsc/bin
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@ -0,0 +1,100 @@
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diff --git a/src/snes/tutorials/makefile b/src/snes/tutorials/makefile
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index 168febb34b6..71068469066 100644
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--- a/src/snes/tutorials/makefile
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+++ b/src/snes/tutorials/makefile
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@@ -13,6 +13,7 @@ include ${PETSC_DIR}/lib/petsc/conf/rules
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# these tests are used by the makefile in PETSC_DIR for basic tests of the install and should not be removed
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testex5f: ex5f.PETSc
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-@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex5f -snes_rtol 1e-4 > ex5f_1.tmp 2>&1; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \
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if (${DIFF} output/ex5f_1.testout ex5f_1.tmp > /dev/null 2>&1) then \
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echo "Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process"; \
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else \
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@@ -25,6 +26,7 @@ testex5f: ex5f.PETSc
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${MAKE} PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} ex5f.rm;
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testex19: ex19.PETSc
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-@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_1.testout ex19_1.tmp > /dev/null 2>&1) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process"; \
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else \
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@@ -36,6 +38,7 @@ testex19: ex19.PETSc
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${RM} -f ex19_1.tmp;
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testex19_mpi:
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-@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_1.testout ex19_1.tmp > /dev/null 2>&1) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with 2 MPI processes"; \
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else \
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@@ -48,6 +51,7 @@ testex19_mpi:
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#use unpreconditioned norm because HYPRE device installations use different AMG parameters
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runex19_hypre:
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-@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre"; \
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else \
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@@ -57,6 +61,7 @@ runex19_hypre:
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${RM} -f ex19_1.tmp
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runex19_hypre_cuda:
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-@${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; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/cuda"; \
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else \
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@@ -66,6 +71,7 @@ runex19_hypre_cuda:
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${RM} -f ex19_1.tmp
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runex19_hypre_hip:
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-@${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; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with hypre/hip"; \
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else \
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@@ -75,6 +81,7 @@ runex19_hypre_hip:
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${RM} -f ex19_1.tmp
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runex19_cuda:
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-@${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; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_cuda_1.out ex19_1.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with cuda"; \
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else \
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@@ -84,6 +91,7 @@ runex19_cuda:
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${RM} -f ex19_1.tmp
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runex19_ml:
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-@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type ml > ex19_1.tmp 2>&1; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_ml.out ex19_1.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with ml"; \
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else \
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@@ -93,6 +101,7 @@ runex19_ml:
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${RM} -f ex19_1.tmp
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runex19_fieldsplit_mumps:
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-@${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; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_6.tmp; \
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if (${DIFF} output/ex19_fieldsplit_5.out ex19_6.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with mumps"; \
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else \
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@@ -102,6 +111,7 @@ runex19_fieldsplit_mumps:
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${RM} -f ex19_6.tmp
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runex19_superlu_dist:
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-@${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; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19.tmp; \
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if (${DIFF} output/ex19_superlu.out ex19.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with superlu_dist"; \
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else \
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@@ -111,6 +121,7 @@ runex19_superlu_dist:
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${RM} -f ex19.tmp
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runex19_suitesparse:
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-@${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; \
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \
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if (${DIFF} output/ex19_suitesparse.out ex19_1.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex19 run successfully with suitesparse"; \
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else \
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@@ -120,6 +131,7 @@ runex19_suitesparse:
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${RM} -f ex19_1.tmp
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runex3k_kokkos: ex3k.PETSc
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-@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 ;\
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+ sed -i '/\[hwloc\/linux\]/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \
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if (${DIFF} output/ex3k_1.out ex3k_1.tmp) then \
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echo "C/C++ example src/snes/tutorials/ex3k run successfully with kokkos-kernels"; \
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else \
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