diff options
Diffstat (limited to 'pkgs/by-name/pe')
| -rw-r--r-- | pkgs/by-name/pe/pegtl/package.nix | 39 | ||||
| -rw-r--r-- | pkgs/by-name/pe/pest/package.nix | 2 | ||||
| -rw-r--r-- | pkgs/by-name/pe/petsc/filter_mpi_warnings.patch | 112 | ||||
| -rw-r--r-- | pkgs/by-name/pe/petsc/package.nix | 131 |
4 files changed, 283 insertions, 1 deletions
diff --git a/pkgs/by-name/pe/pegtl/package.nix b/pkgs/by-name/pe/pegtl/package.nix new file mode 100644 index 0000000000000..d7a57caa58fe0 --- /dev/null +++ b/pkgs/by-name/pe/pegtl/package.nix @@ -0,0 +1,39 @@ +{ + cmake, + fetchFromGitHub, + gitUpdater, + lib, + ninja, + stdenv, +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "pegtl"; + version = "3.2.7"; + + src = fetchFromGitHub { + owner = "taocpp"; + repo = "PEGTL"; + rev = finalAttrs.version; + hash = "sha256-IV5YNGE4EWVrmg2Sia/rcU8jCuiBynQGJM6n3DCWTQU="; + }; + + nativeBuildInputs = [ + cmake + ninja + ]; + + passthru.updateScript = gitUpdater { }; + + meta = { + homepage = "https://github.com/taocpp/pegtl"; + description = "Parsing Expression Grammar Template Library"; + longDescription = '' + Zero-dependency C++ header-only parser combinator library + for creating parsers according to a Parsing Expression Grammar (PEG). + ''; + license = lib.licenses.boost; + maintainers = with lib.maintainers; [ ]; + platforms = lib.platforms.all; + }; +}) diff --git a/pkgs/by-name/pe/pest/package.nix b/pkgs/by-name/pe/pest/package.nix index 6b7231ec8f8e9..6157da0d8a810 100644 --- a/pkgs/by-name/pe/pest/package.nix +++ b/pkgs/by-name/pe/pest/package.nix @@ -21,6 +21,6 @@ php.buildComposerProject (finalAttrs: { homepage = "https://pestphp.com"; license = lib.licenses.mit; mainProgram = "pest"; - maintainers = with lib.maintainers; [ patka ]; + maintainers = with lib.maintainers; [ ]; }; }) diff --git a/pkgs/by-name/pe/petsc/filter_mpi_warnings.patch b/pkgs/by-name/pe/petsc/filter_mpi_warnings.patch new file mode 100644 index 0000000000000..79f44558b3518 --- /dev/null +++ b/pkgs/by-name/pe/petsc/filter_mpi_warnings.patch @@ -0,0 +1,112 @@ +diff --git a/src/snes/tutorials/makefile b/src/snes/tutorials/makefile +index fa15faad39e..7670e80931e 100644 +--- a/src/snes/tutorials/makefile ++++ b/src/snes/tutorials/makefile +@@ -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 ${MPIEXEC_TAIL} ./ex5f -snes_rtol 1e-4 > ex5f_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex5f_1.tmp; \ + if (${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 \ +@@ -25,6 +26,7 @@ testex5f: ex5f.PETSc + ${MAKE} PETSC_ARCH=${PETSC_ARCH} PETSC_DIR=${PETSC_DIR} ex5f.rm; + testex19: ex19.PETSc + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${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 \ +@@ -36,6 +38,7 @@ testex19: ex19.PETSc + ${RM} -f ex19_1.tmp; + testex19_mpi: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${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 \ +@@ -48,6 +51,7 @@ testex19_mpi: + #use unpreconditioned norm because HYPRE device installations use different AMG parameters + runex19_hypre: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE"; \ + else \ +@@ -57,6 +61,7 @@ runex19_hypre: + ${RM} -f ex19_1.tmp + runex19_hypre_cuda: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type cuda -dm_mat_type aijcusparse -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE/CUDA"; \ + else \ +@@ -66,6 +71,7 @@ runex19_hypre_cuda: + ${RM} -f ex19_1.tmp + runex19_hypre_hip: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -dm_vec_type hip -da_refine 3 -snes_monitor_short -ksp_norm_type unpreconditioned -pc_type hypre > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_hypre.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with HYPRE/HIP"; \ + else \ +@@ -75,6 +81,7 @@ runex19_hypre_hip: + ${RM} -f ex19_1.tmp + runex19_cuda: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -snes_monitor -dm_mat_type seqaijcusparse -dm_vec_type seqcuda -pc_type gamg -ksp_monitor -mg_levels_ksp_max_it 1 > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_cuda_1.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with CUDA"; \ + else \ +@@ -84,6 +91,7 @@ runex19_cuda: + ${RM} -f ex19_1.tmp + runex19_ml: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type ml > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_ml.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with ML"; \ + else \ +@@ -93,6 +101,7 @@ runex19_ml: + ${RM} -f ex19_1.tmp + runex19_fieldsplit_mumps: + -@${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex19 -pc_type fieldsplit -pc_fieldsplit_block_size 4 -pc_fieldsplit_type SCHUR -pc_fieldsplit_0_fields 0,1,2 -pc_fieldsplit_1_fields 3 -fieldsplit_0_pc_type lu -fieldsplit_1_pc_type lu -snes_monitor_short -ksp_monitor_short -fieldsplit_0_pc_factor_mat_solver_type mumps -fieldsplit_1_pc_factor_mat_solver_type mumps > ex19_6.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_6.tmp; \ + if (${DIFF} output/ex19_fieldsplit_5.out ex19_6.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with MUMPS"; \ + else \ +@@ -102,6 +111,7 @@ runex19_fieldsplit_mumps: + ${RM} -f ex19_6.tmp + runex19_superlu_dist: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_grid_x 20 -da_grid_y 20 -pc_type lu -pc_factor_mat_solver_type superlu_dist > ex19.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19.tmp; \ + if (${DIFF} output/ex19_superlu.out ex19.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with SuperLU_DIST"; \ + else \ +@@ -111,6 +121,7 @@ runex19_superlu_dist: + ${RM} -f ex19.tmp + runex19_suitesparse: + -@${MPIEXEC} -n 1 ${MPIEXEC_TAIL} ./ex19 -da_refine 3 -snes_monitor_short -pc_type lu -pc_factor_mat_solver_type umfpack > ex19_1.tmp 2>&1; \ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex19_1.tmp; \ + if (${DIFF} output/ex19_suitesparse.out ex19_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex19 run successfully with SuiteSparse"; \ + else \ +@@ -120,6 +131,7 @@ runex19_suitesparse: + ${RM} -f ex19_1.tmp + runex3k_kokkos: ex3k.PETSc + -@OMP_PROC_BIND=false ${MPIEXEC} -n 2 ${MPIEXEC_TAIL} ./ex3k -view_initial -dm_vec_type kokkos -dm_mat_type aijkokkos -use_gpu_aware_mpi 0 -snes_monitor > ex3k_1.tmp 2>&1 ;\ ++ sed -i '/hwloc\/linux/d ; /ERROR scandir(\/sys\/class\/net) failed/d ; /ERROR opendir(\/sys\/class\/net) failed/d' ex3k_1.tmp; \ + if (${DIFF} output/ex3k_1.out ex3k_1.tmp) then \ + echo "C/C++ example src/snes/tutorials/ex3k run successfully with Kokkos Kernels"; \ + else \ +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 (${DIFF} output/ex47_1.out ex47_1.tmp) then \ + echo "C/C++ example src/vec/vec/tests/ex47 run successfully with HDF5"; \ + else \ diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix new file mode 100644 index 0000000000000..5a547144b491e --- /dev/null +++ b/pkgs/by-name/pe/petsc/package.nix @@ -0,0 +1,131 @@ +{ + lib, + stdenv, + fetchzip, + darwin, + gfortran, + python3, + blas, + lapack, + mpiSupport ? true, + mpi, # generic mpi dependency + openssh, # required for openmpi tests + petsc-withp4est ? false, + hdf5-support ? false, + hdf5, + metis, + parmetis, + pkg-config, + p4est, + zlib, # propagated by p4est but required by petsc + petsc-optimized ? false, + petsc-scalar-type ? "real", + petsc-precision ? "double", +}: + +# This version of PETSc does not support a non-MPI p4est build +assert petsc-withp4est -> p4est.mpiSupport; + +stdenv.mkDerivation rec { + pname = "petsc"; + version = "3.21.0"; + + src = fetchzip { + url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${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 ]; + }; +} |