From e50be8a41d664ed38d2903406bac8f3f28ffb695 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Wed, 29 Apr 2020 15:45:17 -0500 Subject: sci-mathematics/petsc: version bump to 13.0 Package-Manager: Portage-2.3.99, Repoman-2.3.22 Signed-off-by: Matthias Maier --- sci-mathematics/petsc/Manifest | 1 + .../files/petsc-3.13.0-do_not_run_mpiexec.patch | 34 ++++ .../files/petsc-3.13.0-fix_sandbox_violation.patch | 18 ++ .../files/petsc-3.13.0-make_hypre_configure.patch | 90 ++++++++++ sci-mathematics/petsc/petsc-3.13.0.ebuild | 189 +++++++++++++++++++++ 5 files changed, 332 insertions(+) create mode 100644 sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch create mode 100644 sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch create mode 100644 sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch create mode 100644 sci-mathematics/petsc/petsc-3.13.0.ebuild (limited to 'sci-mathematics/petsc') diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest index 35342d214c52..f7372ecf5e15 100644 --- a/sci-mathematics/petsc/Manifest +++ b/sci-mathematics/petsc/Manifest @@ -1,2 +1,3 @@ DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa DIST petsc-3.12.1.tar.gz 34592587 BLAKE2B b48056a1fe1d507338f7d145f5fceeab2b2f576470d8af90c9d7828de9b775daadf11198fecc46b5e48fcf1eb38addb366e3a908dab5c4ffaf7f9b71ff17b3d8 SHA512 df33170922c0b34136d2fd5bdc3c68a80d3a5873d66bfb03b2cea4a6456393c7181a8da673911b89ea0fcb51d5fd89b5b4c8b76ddb1df573180a92d029fbc1fb +DIST petsc-3.13.0.tar.gz 35080264 BLAKE2B 0ac58e53751dbc6e053e3591cdf2363194e0cf7a493f252d879031e0135da16fa24e66974dd7bf07ce18558a75f8dd794e87f96590ad9e550d11edfeb462f727 SHA512 0590bb63d9c6dfd6ac03b1b88e5a8c11d42a0fd014084603d4d085060b126aa4341b4ec3a4d2b12146b971da327ccc7ede370e5633282bf44f269465aea32953 diff --git a/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch new file mode 100644 index 000000000000..4c46658dec71 --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch @@ -0,0 +1,34 @@ +diff --git a/config/BuildSystem/config/packages/MPI.py b/config/BuildSystem/config/packages/MPI.py +index 7e424e71..ee502bd2 100644 +--- a/config/BuildSystem/config/packages/MPI.py ++++ b/config/BuildSystem/config/packages/MPI.py +@@ -210,28 +210,11 @@ shared libraries and run with --known-mpi-shared-libraries=1') + raise RuntimeError('Could not locate MPIEXEC - please specify --with-mpiexec option') + # Support for spaces and () in executable names; also needs to handle optional arguments at the end + # TODO: This support for spaces and () should be moved to core BuildSystem +- self.mpiexec = self.mpiexec.replace(' ', '\\ ').replace('(', '\\(').replace(')', '\\)').replace('\ -',' -') +- if (hasattr(self, 'ompi_major_version') and int(self.ompi_major_version) >= 3): +- (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -help all', checkCommand = noCheck, timeout = 60, log = self.log, threads = 1) +- if out.find('--oversubscribe') >=0: +- self.mpiexec = self.mpiexec + ' --oversubscribe' ++ self.mpiexec = self.mpiexec + ' --oversubscribe' + + # using mpiexec environmental variables make sure mpiexec matches the MPI libraries and save the variables for testing in PetscInitialize() + # the variable HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE is not currently used. PetscInitialize() can check the existence of the environmental variable to + # determine if the program has been started with the correct mpiexec (will only be set for parallel runs so not clear how to check appropriately) +- (out, err, ret) = Configure.executeShellCommand(self.mpiexec+' -n 1 printenv', checkCommand = noCheck, timeout = 60, threads = 1, log = self.log) +- if ret: +- self.logWrite('Unable to run '+self.mpiexec+' with option "-n 1 printenv"\nThis could be ok, some MPI implementations such as SGI produce a non-zero status with non-MPI programs\n'+out+err) +- else: +- if out.find('MPIR_CVAR_CH3') > -1: +- if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH"); +- self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPIR_CVAR_CH3') +- elif out.find('MPIR_CVAR_CH3') > -1: +- if hasattr(self,'ompi_major_version'): raise RuntimeError("Your libraries are from OpenMPI but it appears your mpiexec is from MPICH"); +- self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'MPICH') +- elif out.find('OMPI_COMM_WORLD_SIZE') > -1: +- if hasattr(self,'mpich_numversion'): raise RuntimeError("Your libraries are from MPICH but it appears your mpiexec is from OpenMPI"); +- self.addDefine('HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE', 'OMP') + + self.addMakeMacro('MPIEXEC', self.mpiexec) + self.mpiexec = self.mpiexec + ' -n 1' diff --git a/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch new file mode 100644 index 000000000000..c0dfd53a0112 --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch @@ -0,0 +1,18 @@ +diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py +index 860faf0f..87898811 100755 +--- a/config/PETSc/options/installDir.py ++++ b/config/PETSc/options/installDir.py +@@ -40,13 +40,6 @@ class Configure(config.base.Configure): + self.dir = os.path.abspath(os.path.expanduser(self.framework.argDB['prefix'])) + self.petscDir = self.dir + self.petscArch = '' +- try: +- os.makedirs(os.path.join(self.dir,'PETScTestDirectory')) +- os.rmdir(os.path.join(self.dir,'PETScTestDirectory')) +- except Exception as e: +- self.logPrint('Error trying to to test write permissions on directory '+str(e)) +- self.installSudoMessage = 'You do not have write permissions to the --prefix directory '+self.dir+'\nYou will be prompted for the sudo password for any external package installs' +- self.installSudo = 'sudo ' + else: + self.dir = os.path.abspath(os.path.join(self.petscdir.dir, self.arch.arch)) + self.petscDir = self.petscdir.dir diff --git a/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch b/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch new file mode 100644 index 000000000000..1453fd519e81 --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch @@ -0,0 +1,90 @@ +diff --git a/config/BuildSystem/config/packages/hypre.py b/config/BuildSystem/config/packages/hypre.py +index 4d915c31..1b05a1ee 100644 +--- a/config/BuildSystem/config/packages/hypre.py ++++ b/config/BuildSystem/config/packages/hypre.py +@@ -5,10 +5,6 @@ class Configure(config.package.GNUPackage): + def __init__(self, framework): + config.package.GNUPackage.__init__(self, framework) + #self.version = '2.18.2' +- self.minversion = '2.14' +- self.versionname = 'HYPRE_RELEASE_VERSION' +- self.versioninclude = 'HYPRE_config.h' +- self.requiresversion = 1 + #self.gitcommit = 'v'+self.version + self.gitcommit = '93baaa8c9' # v2.18.2+valgrind-fix + self.download = ['git://https://github.com/hypre-space/hypre','https://github.com/hypre-space/hypre/archive/'+self.gitcommit+'.tar.gz'] +diff --git a/include/petsc/private/petschypre.h b/include/petsc/private/petschypre.h +index 81ca7136..b403e70e 100644 +--- a/include/petsc/private/petschypre.h ++++ b/include/petsc/private/petschypre.h +@@ -6,12 +6,6 @@ + #include + #include + +-/* from version 2.16 on, HYPRE_BigInt is 64 bit for 64bit installations +- and 32 bit for 32bit installations -> not the best name for a variable */ +-#if PETSC_PKG_HYPRE_VERSION_LT(2,16,0) +-typedef PetscInt HYPRE_BigInt; +-#endif +- + /* + With scalar type == real, HYPRE_Complex == PetscScalar; + With scalar type == complex, HYPRE_Complex is double __complex__ while PetscScalar may be std::complex +diff --git a/src/mat/impls/hypre/mhypre.c b/src/mat/impls/hypre/mhypre.c +index 0f7470e6..cce3e2b0 100644 +--- a/src/mat/impls/hypre/mhypre.c ++++ b/src/mat/impls/hypre/mhypre.c +@@ -15,10 +15,6 @@ + #include <_hypre_parcsr_ls.h> + #include <_hypre_sstruct_ls.h> + +-#if PETSC_PKG_HYPRE_VERSION_LT(2,18,0) +-#define hypre_ParCSRMatrixClone(A,B) hypre_ParCSRMatrixCompleteClone(A) +-#endif +- + static PetscErrorCode MatHYPRE_CreateFromMat(Mat,Mat_HYPRE*); + static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat,Mat,HYPRE_IJMatrix); + static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat,HYPRE_IJMatrix); +@@ -63,7 +59,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat + nnz_o[i] = 0; + } + } +-#if PETSC_PKG_HYPRE_VERSION_GE(2,16,0) + { /* If we don't do this, the columns of the matrix will be all zeros! */ + hypre_AuxParCSRMatrix *aux_matrix; + aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij); +@@ -73,9 +68,6 @@ static PetscErrorCode MatHYPRE_IJMatrixPreallocate(Mat A_d, Mat A_o, HYPRE_IJMat + aux_matrix = (hypre_AuxParCSRMatrix*)hypre_IJMatrixTranslator(ij); + hypre_AuxParCSRMatrixNeedAux(aux_matrix) = 1; + } +-#else +- PetscStackCallStandard(HYPRE_IJMatrixSetDiagOffdSizes,(ij,nnz_d,nnz_o)); +-#endif + ierr = PetscFree(nnz_d);CHKERRQ(ierr); + ierr = PetscFree(nnz_o);CHKERRQ(ierr); + } +@@ -233,11 +225,7 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij) + /* need to shift the diag column indices (hdiag->j) back to global numbering since hypre is expecting this */ + hjj = hdiag->j; + pjj = pdiag->j; +-#if PETSC_PKG_HYPRE_VERSION_GE(2,16,0) + for (i=0; inz; i++) hjj[i] = pjj[i]; +-#else +- for (i=0; inz; i++) hjj[i] = cstart + pjj[i]; +-#endif + ierr = PetscArraycpy(hdiag->data,pdiag->a,pdiag->nz);CHKERRQ(ierr); + if (sameint) { + ierr = PetscArraycpy(hoffd->i,poffd->i,pA->A->rmap->n + 1);CHKERRQ(ierr); +@@ -247,12 +235,8 @@ static PetscErrorCode MatHYPRE_IJMatrixFastCopy_MPIAIJ(Mat A, HYPRE_IJMatrix ij) + + /* need to move the offd column indices (hoffd->j) back to global numbering since hypre is expecting this + If we hacked a hypre a bit more we might be able to avoid this step */ +-#if PETSC_PKG_HYPRE_VERSION_GE(2,16,0) + PetscStackCallStandard(hypre_CSRMatrixBigInitialize,(hoffd)); + jj = (PetscInt*) hoffd->big_j; +-#else +- jj = (PetscInt*) hoffd->j; +-#endif + pjj = poffd->j; + for (i=0; inz; i++) jj[i] = garray[pjj[i]]; + diff --git a/sci-mathematics/petsc/petsc-3.13.0.ebuild b/sci-mathematics/petsc/petsc-3.13.0.ebuild new file mode 100644 index 000000000000..961ff927f725 --- /dev/null +++ b/sci-mathematics/petsc/petsc-3.13.0.ebuild @@ -0,0 +1,189 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6,7,8} ) + +inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs + +DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" +HOMEPAGE="http://www.mcs.anl.gov/petsc/" +SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${P}.tar.gz" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="afterimage boost complex-scalars cxx debug doc fftw + fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X" + +# hypre and superlu curretly exclude each other due to missing linking to hypre +# if both are enabled +REQUIRED_USE=" + afterimage? ( X ) + complex-scalars? ( !hypre !superlu ) + hdf5? ( mpi ) + hypre? ( cxx mpi !superlu ) + mumps? ( mpi scotch ) + scotch? ( mpi ) + superlu? ( !hypre ) +" + +RDEPEND=" + virtual/blas + virtual/lapack + afterimage? ( media-libs/libafterimage ) + boost? ( dev-libs/boost ) + fftw? ( sci-libs/fftw:3.0[mpi?] ) + hdf5? ( sci-libs/hdf5[mpi?] ) + hypre? ( >=sci-libs/hypre-2.18.0[mpi?] ) + metis? ( >=sci-libs/parmetis-4 ) + mpi? ( virtual/mpi[cxx?,fortran?] ) + mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) + scotch? ( sci-libs/scotch[mpi?] ) + sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) + superlu? ( >=sci-libs/superlu-5 ) + X? ( x11-libs/libX11 ) +" + +DEPEND="${RDEPEND} + ${PYTHON_DEPS} + virtual/pkgconfig + dev-util/cmake +" + +PATCHES=( + "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch + "${FILESDIR}"/${PN}-3.13.0-fix_sandbox_violation.patch + "${FILESDIR}"/${PN}-3.13.0-make_hypre_configure.patch + "${FILESDIR}"/${PN}-3.13.0-do_not_run_mpiexec.patch +) + +# petsc uses --with-blah=1 and --with-blah=0 to en/disable options +petsc_enable() { + use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" +} +# add external library: +# petsc_with use_flag libname libdir +# petsc_with use_flag libname include linking_libs +petsc_with() { + local myuse p=${2:-${1}} + if use ${1}; then + myuse="--with-${p}=1" + if [[ $# -ge 4 ]]; then + myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" + shift 3 + myuse="${myuse} --with-${p}-lib=$@" + else + myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" + fi + else + myuse="--with-${p}=0" + fi + echo ${myuse} +} + +# select between configure options depending on use flag +petsc_select() { + use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" +} + +src_configure() { + # bug 548498 + # PETSc runs mpi processes during configure that result in a sandbox + # violation by trying to open /proc/mtrr rw. This is not easy to + # mitigate because it happens in libpciaccess.so called by libhwloc.so, + # which is used by libmpi.so. + addpredict /proc/mtrr + # if mpi is built with knem support it needs /dev/knem too + addpredict /dev/knem + + # configureMPITypes with openmpi-2* insists on accessing the scaling + # governor rw. + addpredict /sys/devices/system/cpu/ + + local mylang + local myopt + + use cxx && mylang="cxx" || mylang="c" + use debug && myopt="debug" || myopt="opt" + + # environmental variables expected by petsc during build + + export PETSC_DIR="${S}" + export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" + + if use debug; then + strip-flags + filter-flags -O* + fi + + # C Support on CXX builds is enabled if possible i.e. when not using + # complex scalars (no complex type for both available at the same time) + + econf \ + scrollOutput=1 \ + FFLAGS="${FFLAGS} -fPIC" \ + CFLAGS="${CFLAGS} -fPIC" \ + CXXFLAGS="${CXXFLAGS} -fPIC" \ + LDFLAGS="${LDFLAGS}" \ + --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \ + --with-shared-libraries \ + --with-single-library \ + --with-clanguage=${mylang} \ + $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ + --with-petsc-arch=${PETSC_ARCH} \ + --with-precision=double \ + --with-gnu-compilers \ + --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs blas lapack)" \ + $(petsc_enable debug debugging) \ + $(petsc_enable mpi) \ + $(petsc_select mpi cc mpicc $(tc-getCC)) \ + $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ + $(petsc_enable fortran) \ + $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ + $(petsc_enable mpi mpi-compilers) \ + $(petsc_select complex-scalars scalar-type complex real) \ + --with-windows-graphics=0 \ + --with-matlab=0 \ + --with-cmake:BOOL=1 \ + $(petsc_enable threads pthread) \ + $(petsc_with afterimage afterimage \ + /usr/include/libAfterImage -lAfterImage) \ + $(use_with hdf5) \ + $(petsc_with hypre hypre \ + /usr/include/hypre -lHYPRE) \ + $(use_with sparse suitesparse) \ + $(petsc_with superlu superlu \ + /usr/include/superlu -lsuperlu) \ + $(use_with X x) \ + $(use_with X x11) \ + $(petsc_with scotch ptscotch \ + /usr/include/scotch \ + [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ + $(petsc_with mumps scalapack \ + /usr/include/scalapack -lscalapack) \ + $(use_with mumps mumps \ + /usr/include \ + [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ + --with-imagemagick=0 \ + --with-python=0 \ + $(use_with boost) \ + $(use_with fftw) +} + +src_install() { + emake DESTDIR="${ED}" install + + # add PETSC_DIR to environmental variables + cat >> 99petsc <<- EOF + PETSC_DIR=${EPREFIX}/usr/$(get_libdir)/petsc + LDPATH=${EPREFIX}/usr/$(get_libdir)/petsc/lib + EOF + doenvd 99petsc + + if use doc ; then + docinto html + dodoc -r docs/*.html docs/changes docs/manualpages + fi +} -- cgit v1.2.3-65-gdbad