* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
@ 2019-08-05 6:52 Matthias Maier
0 siblings, 0 replies; 5+ messages in thread
From: Matthias Maier @ 2019-08-05 6:52 UTC (permalink / raw
To: gentoo-commits
commit: 44c266fd90ff2510b3d5ee74ed1dcff364eebcb1
Author: Matthias Maier <tamiko <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 5 04:48:15 2019 +0000
Commit: Matthias Maier <tamiko <AT> gentoo <DOT> org>
CommitDate: Mon Aug 5 06:51:11 2019 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=44c266fd
sci-mathematics/petsc: package migration from ::science overlay
After years in ::science it is stable enough to be hosted in ::gentoo.
Package-Manager: Portage-2.3.70, Repoman-2.3.16
Signed-off-by: Matthias Maier <tamiko <AT> gentoo.org>
sci-mathematics/petsc/Manifest | 1 +
.../petsc/files/petsc-3.7.0-disable-rpath.patch | 18 ++
.../files/petsc-3.9.0-fix_sandbox_violation.patch | 17 ++
sci-mathematics/petsc/metadata.xml | 23 +++
sci-mathematics/petsc/petsc-3.11.3.ebuild | 193 +++++++++++++++++++++
5 files changed, 252 insertions(+)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
new file mode 100644
index 00000000000..3be30d7421f
--- /dev/null
+++ b/sci-mathematics/petsc/Manifest
@@ -0,0 +1 @@
+DIST petsc-3.11.3.tar.gz 33279017 BLAKE2B 870b8245e5e06d8538ea3ee1d01fa2cebade4a0bd79dfcf17d74e6201f41d21ca021e206744ece28847b434ece142a2789851b5514a8a1e3f82a8551288b695b SHA512 e545f69e87bc72950939ff3cec3e0ba225a5b3e7f1cb93b0fb6123194eb7240ac1d97ba397235d8ab872c653caab1427673124e5e1e706b796c0ae46ec1bcffa
diff --git a/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
new file mode 100644
index 00000000000..8d0d993309b
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.7.0-disable-rpath.patch
@@ -0,0 +1,18 @@
+diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py
+index 219a35b..ad2ed8c 100644
+--- a/config/BuildSystem/config/setCompilers.py
++++ b/config/BuildSystem/config/setCompilers.py
+@@ -1385,12 +1385,7 @@ class Configure(config.base.Configure):
+ for language in languages:
+ flag = '-L'
+ self.pushLanguage(language)
+- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options.
+- if not Configure.isDarwin(self.log):
+- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,']
+- else:
+- testFlags = ['-Wl,-rpath,']
+- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not.
++ testFlags = []
+ if self.isSun(self.framework.getCompiler(), self.log):
+ testFlags.insert(0,'-R')
+ for testFlag in testFlags:
diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
new file mode 100644
index 00000000000..97f8dfed4d7
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
@@ -0,0 +1,17 @@
+diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
+index 92f190d..047c85b 100644
+--- a/config/PETSc/options/installDir.py
++++ b/config/PETSc/options/installDir.py
+@@ -41,12 +41,6 @@ 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:
+- 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/metadata.xml b/sci-mathematics/petsc/metadata.xml
new file mode 100644
index 00000000000..8c9c01d8326
--- /dev/null
+++ b/sci-mathematics/petsc/metadata.xml
@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>tamiko@gentoo.org</email>
+ <name>Matthias Maier</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-mathematics@gentoo.org</email>
+ <name>Gentoo Mathematics Project</name>
+ </maintainer>
+ <use>
+ <flag name="afterimage">Use Afterstep image library (media-libs/libafterimage)</flag>
+ <flag name="boost">Use boost (dev-libs/boost)</flag>
+ <flag name="hypre">Use HYPRE (sci-mathematics/hypre) and for preconditioning</flag>
+ <flag name="complex-scalars">Make scalars complex</flag>
+ <flag name="metis">Add support for metis (<pkg>sci-libs/parmetis</pkg>)</flag>
+ <flag name="sparse">Use suitesparse (sci-libs/suitesparse) including cholmod (sci-libs/cholmod) for sparse factorization</flag>
+ <flag name="superlu">Use superlu (sci-libs/superlu) for preconditioning</flag>
+ <flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag>
+ <flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag>
+ </use>
+</pkgmetadata>
diff --git a/sci-mathematics/petsc/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.11.3.ebuild
new file mode 100644
index 00000000000..88fb1f58da1
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.11.3.ebuild
@@ -0,0 +1,193 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 )
+
+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/${P}.tar.gz"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="afterimage boost complex-scalars cxx debug doc fftw
+ fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
+
+# hypre and superlu curretly exclude each other due to missing linking to hypre
+# if both are enabled
+REQUIRED_USE="
+ afterimage? ( X )
+ complex-scalars? ( !hypre !superlu )
+ hdf5? ( mpi )
+ hypre? ( cxx mpi !superlu )
+ mumps? ( mpi scotch )
+ scotch? ( mpi )
+ superlu? ( !hypre )
+"
+
+RDEPEND="
+ virtual/blas
+ virtual/lapack
+ afterimage? ( media-libs/libafterimage )
+ boost? ( dev-libs/boost )
+ fftw? ( sci-libs/fftw:3.0[mpi?] )
+ hdf5? ( sci-libs/hdf5[mpi?] )
+ hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
+ metis? ( >=sci-libs/parmetis-4 )
+ mpi? ( virtual/mpi[cxx?,fortran?] )
+ mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
+ scotch? ( sci-libs/scotch[mpi?] )
+ sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
+ superlu? ( >=sci-libs/superlu-5 )
+ X? ( x11-libs/libX11 )
+"
+
+DEPEND="${RDEPEND}
+ ${PYTHON_DEPS}
+ virtual/pkgconfig
+ dev-util/cmake
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
+ "${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
+)
+
+src_prepare() {
+ default
+
+ sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
+}
+
+# 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) \
+ $(petsc_with hdf5) \
+ $(petsc_with hypre hypre \
+ /usr/include/hypre -lHYPRE) \
+ $(petsc_with sparse suitesparse) \
+ $(petsc_with superlu superlu \
+ /usr/include/superlu -lsuperlu) \
+ $(petsc_with X x) \
+ $(petsc_with X x11) \
+ $(petsc_with scotch ptscotch \
+ /usr/include/scotch \
+ [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
+ $(petsc_with mumps scalapack \
+ /usr/include/scalapack -lscalapack) \
+ $(petsc_with mumps mumps \
+ /usr/include \
+ [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
+ --with-imagemagick=0 \
+ --with-python=0 \
+ $(petsc_with boost) \
+ $(petsc_with fftw)
+}
+
+src_install() {
+ emake DESTDIR="${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
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
@ 2020-04-29 21:35 Matthias Maier
0 siblings, 0 replies; 5+ messages in thread
From: Matthias Maier @ 2020-04-29 21:35 UTC (permalink / raw
To: gentoo-commits
commit: 53490294521a32eb37e6131b1f9931930368e70c
Author: Matthias Maier <tamiko <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 29 21:07:13 2020 +0000
Commit: Matthias Maier <tamiko <AT> gentoo <DOT> org>
CommitDate: Wed Apr 29 21:35:37 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=53490294
sci-mathematics/petsc: drop old
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Matthias Maier <tamiko <AT> gentoo.org>
sci-mathematics/petsc/Manifest | 2 -
.../files/petsc-3.12.1-do_not_run_mpiexec.patch | 32 ----
.../files/petsc-3.12.1-make_hypre_configure.patch | 90 ----------
.../files/petsc-3.9.0-fix_sandbox_violation.patch | 17 --
sci-mathematics/petsc/petsc-3.11.3.ebuild | 193 --------------------
sci-mathematics/petsc/petsc-3.12.1.ebuild | 195 ---------------------
6 files changed, 529 deletions(-)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index f7372ecf5e1..c224c776882 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,3 +1 @@
-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-3.12.1-do_not_run_mpiexec.patch b/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
deleted file mode 100644
index 9c3d5047b0a..00000000000
--- a/sci-mathematics/petsc/files/petsc-3.12.1-do_not_run_mpiexec.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-diff --git a/config/BuildSystem/config/packages/MPI.py b/config/BuildSystem/config/packages/MPI.py
-index c85bb504..7720eba9 100644
---- a/config/BuildSystem/config/packages/MPI.py
-+++ b/config/BuildSystem/config/packages/MPI.py
-@@ -209,26 +209,11 @@ 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 = 10, log = self.log)
-- 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 = 10, log = self.log)
-- if ret: raise RuntimeError('Unable to run '+self.mpiexec+' with option "-n 1"\n'+err)
-- 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-3.12.1-make_hypre_configure.patch b/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch
deleted file mode 100644
index 9460d57e461..00000000000
--- a/sci-mathematics/petsc/files/petsc-3.12.1-make_hypre_configure.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-diff --git a/config/BuildSystem/config/packages/hypre.py b/config/BuildSystem/config/packages/hypre.py
-index 869a1661..76067c8d 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 = '2.18.1'
-- self.minversion = '2.14'
-- self.versionname = 'HYPRE_RELEASE_VERSION'
-- self.versioninclude = 'HYPRE_config.h'
-- self.requiresversion = 1
- self.gitcommit = 'v'+self.version
- self.download = ['git://https://github.com/hypre-space/hypre','https://github.com/hypre-space/hypre/archive/'+self.gitcommit+'.tar.gz']
- self.functions = ['HYPRE_IJMatrixCreate']
-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 <HYPRE_config.h>
- #include <HYPRE_utilities.h>
-
--/* 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<double>
-diff --git a/src/mat/impls/hypre/mhypre.c b/src/mat/impls/hypre/mhypre.c
-index 8e8fe678..3533b99a 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
--
- PETSC_INTERN PetscErrorCode MatPtAP_IS_XAIJ(Mat,Mat,MatReuse,PetscReal,Mat*);
-
- static PetscErrorCode MatHYPRE_CreateFromMat(Mat,Mat_HYPRE*);
-@@ -65,7 +61,6 @@ 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);
-@@ -75,9 +70,6 @@ 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);
- }
-@@ -235,11 +227,7 @@ 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; i<pdiag->nz; i++) hjj[i] = pjj[i];
--#else
-- for (i=0; i<pdiag->nz; 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);
-@@ -249,12 +237,8 @@ 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; i<poffd->nz; i++) jj[i] = garray[pjj[i]];
-
diff --git a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
deleted file mode 100644
index 97f8dfed4d7..00000000000
--- a/sci-mathematics/petsc/files/petsc-3.9.0-fix_sandbox_violation.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/config/PETSc/options/installDir.py b/config/PETSc/options/installDir.py
-index 92f190d..047c85b 100644
---- a/config/PETSc/options/installDir.py
-+++ b/config/PETSc/options/installDir.py
-@@ -41,12 +41,6 @@ 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:
-- 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/petsc-3.11.3.ebuild b/sci-mathematics/petsc/petsc-3.11.3.ebuild
deleted file mode 100644
index 50ce3b7f663..00000000000
--- a/sci-mathematics/petsc/petsc-3.11.3.ebuild
+++ /dev/null
@@ -1,193 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-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/${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="afterimage boost complex-scalars cxx debug doc fftw
- fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
- afterimage? ( X )
- complex-scalars? ( !hypre !superlu )
- hdf5? ( mpi )
- hypre? ( cxx mpi !superlu )
- mumps? ( mpi scotch )
- scotch? ( mpi )
- superlu? ( !hypre )
-"
-
-RDEPEND="
- virtual/blas
- virtual/lapack
- afterimage? ( media-libs/libafterimage )
- boost? ( dev-libs/boost )
- fftw? ( sci-libs/fftw:3.0[mpi?] )
- hdf5? ( sci-libs/hdf5[mpi?] )
- hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] )
- metis? ( >=sci-libs/parmetis-4 )
- mpi? ( virtual/mpi[cxx?,fortran?] )
- mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
- scotch? ( sci-libs/scotch[mpi?] )
- sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
- superlu? ( >=sci-libs/superlu-5 )
- X? ( x11-libs/libX11 )
-"
-
-DEPEND="${RDEPEND}
- ${PYTHON_DEPS}
- virtual/pkgconfig
- dev-util/cmake
-"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch \
- "${FILESDIR}"/${PN}-3.9.0-fix_sandbox_violation.patch
-)
-
-src_prepare() {
- default
-
- sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-# 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) \
- $(petsc_with sparse suitesparse) \
- $(petsc_with superlu superlu \
- /usr/include/superlu -lsuperlu) \
- $(petsc_with X x) \
- $(petsc_with X x11) \
- $(petsc_with scotch ptscotch \
- /usr/include/scotch \
- [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
- $(petsc_with mumps scalapack \
- /usr/include/scalapack -lscalapack) \
- $(petsc_with mumps mumps \
- /usr/include \
- [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
- --with-imagemagick=0 \
- --with-python=0 \
- $(petsc_with boost) \
- $(petsc_with fftw)
-}
-
-src_install() {
- emake DESTDIR="${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
-}
diff --git a/sci-mathematics/petsc/petsc-3.12.1.ebuild b/sci-mathematics/petsc/petsc-3.12.1.ebuild
deleted file mode 100644
index 845d7ff75d6..00000000000
--- a/sci-mathematics/petsc/petsc-3.12.1.ebuild
+++ /dev/null
@@ -1,195 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-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}"/${PN}-3.9.0-fix_sandbox_violation.patch
- "${FILESDIR}"/${PN}-3.12.1-make_hypre_configure.patch
- "${FILESDIR}"/${PN}-3.12.1-do_not_run_mpiexec.patch
-)
-
-src_prepare() {
- default
-
- sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die
-}
-
-# 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
-}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
@ 2020-04-29 21:35 Matthias Maier
0 siblings, 0 replies; 5+ messages in thread
From: Matthias Maier @ 2020-04-29 21:35 UTC (permalink / raw
To: gentoo-commits
commit: e50be8a41d664ed38d2903406bac8f3f28ffb695
Author: Matthias Maier <tamiko <AT> gentoo <DOT> org>
AuthorDate: Wed Apr 29 20:45:17 2020 +0000
Commit: Matthias Maier <tamiko <AT> gentoo <DOT> org>
CommitDate: Wed Apr 29 21:35:33 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e50be8a4
sci-mathematics/petsc: version bump to 13.0
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Matthias Maier <tamiko <AT> gentoo.org>
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(+)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index 35342d214c5..f7372ecf5e1 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 00000000000..4c46658dec7
--- /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 00000000000..c0dfd53a011
--- /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 00000000000..1453fd519e8
--- /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 <HYPRE_config.h>
+ #include <HYPRE_utilities.h>
+
+-/* 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<double>
+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; i<pdiag->nz; i++) hjj[i] = pjj[i];
+-#else
+- for (i=0; i<pdiag->nz; 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; i<poffd->nz; 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 00000000000..961ff927f72
--- /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
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
@ 2021-12-01 21:25 Sam James
0 siblings, 0 replies; 5+ messages in thread
From: Sam James @ 2021-12-01 21:25 UTC (permalink / raw
To: gentoo-commits
commit: 2c0aea17b396af99413234f7a84607817f31dbd3
Author: Fabio Rossi <rossi.f <AT> inwind <DOT> it>
AuthorDate: Wed Dec 1 18:04:37 2021 +0000
Commit: Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Wed Dec 1 21:25:12 2021 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2c0aea17
sci-mathematics/petsc: version bump to 3.16.0 and bugfix
The latest release is needed to backport the patch from upstream
to solve the issue of Gentoo bug #827185 (build issue with
USE="fftw -mpi").
Upstream fix is at https://gitlab.com/petsc/petsc/-/merge_requests/4604
Closes: https://bugs.gentoo.org/827185
Signed-off-by: Fabio Rossi <rossi.f <AT> inwind.it>
Closes: https://github.com/gentoo/gentoo/pull/23136
Signed-off-by: Sam James <sam <AT> gentoo.org>
sci-mathematics/petsc/Manifest | 2 +
.../files/petsc-3.16.0-fix_sandbox_violation.patch | 15 ++
sci-mathematics/petsc/petsc-3.16.0.ebuild | 192 +++++++++++++++++++++
3 files changed, 209 insertions(+)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index b8a099ec30dc..66543b456f86 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,3 +1,5 @@
DIST petsc-3.13.1.tar.gz 35097687 BLAKE2B fccf64fd3694deffdd0dc561069ffa7e9342fe279b5c9123edeb011df931874083839d27b7b9a0c63faea6487b104b54fd4ce68a88a074c82de91e8baaf270b0 SHA512 41c3138a6ae6c1f2d9077b464c6aeda96287e5a76849582b8f432e2ee93d2594a78ba2181eac0054a77b6165692be5f1a057049313f2be9743d4246383dfdc77
DIST petsc-3.14.6.tar.gz 39719179 BLAKE2B d3047baf87c67eb64ef02c0c54d6313ea06f091b377b3cdf6dcf6d96c7d68cec5958a007ddd84b52a3ab39bfc0adf146307fa1785a10f39386393371186a3fba SHA512 9766e164446ac5a69b8bf761a0e8a235b1a2b85ed9c96a7fd59e668ae4cceb9d9559a38b175b4aa9747e78d7b44d0018a3c02748dcd3d783d28f861f8382d44c
DIST petsc-3.15.0.tar.gz 15976488 BLAKE2B babfbeb05321c9cb2f7d70ef8ffca974a016eae73ca1a3359d9a8d38aa5aa90ff34571169a5711627d738b93f89fdee3d0a0ff1bd0e51cb7300bbb9b0a8675cb SHA512 d1565823d8a5ce5e1c2c576bbe1b4ebf467cef20bbd8e0cf6c303c6c2af2bf902b66c79468f4e125496f9242be4bd6ac162535ee30252cfb902c0d906a6f27c0
+DIST petsc-3.16.0-fftw-without-mpi.patch.bz2 5824 BLAKE2B 59615b1bbaf8ca1da92d7d193a45a2dd434f762cd741d711d4f408183a201a276ac3c968a3e7d740d19212120271701bce52bb7b0f4e311268f40915c81f9dcb SHA512 8e07dfe56a9150ce9a3a5ab8012657875ef84e6e7daa60560bbdd9062078c876a826057f3f3eaf1697ce046a82756ee6eb6a8b819eb51245367c9d5c8a72ee8e
+DIST petsc-3.16.0.tar.gz 16748960 BLAKE2B 87f9fdb79a9c44e5f476fa4746ad0cbe72f3eda9f6039f2e4743105626701d7c8d6c010fdb9d89becf8619288d0b7a60c8bc4e2fc0793eac5b39030b02c04fd9 SHA512 5280032fb4ec4d058733788bb0ae674e7400565e204133bd10ed88a2965230ec7adeaca2d498267ce661377ca7e6f9d948992206b1d679587606cb422c004655
diff --git a/sci-mathematics/petsc/files/petsc-3.16.0-fix_sandbox_violation.patch b/sci-mathematics/petsc/files/petsc-3.16.0-fix_sandbox_violation.patch
new file mode 100644
index 000000000000..d1ed880bddfd
--- /dev/null
+++ b/sci-mathematics/petsc/files/petsc-3.16.0-fix_sandbox_violation.patch
@@ -0,0 +1,15 @@
+--- a/config/PETSc/options/installDir.py
++++ b/config/PETSc/options/installDir.py
+@@ -40,13 +40,7 @@ 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.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/petsc-3.16.0.ebuild b/sci-mathematics/petsc/petsc-3.16.0.ebuild
new file mode 100644
index 000000000000..f39f87d8c281
--- /dev/null
+++ b/sci-mathematics/petsc/petsc-3.16.0.ebuild
@@ -0,0 +1,192 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
+
+DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
+HOMEPAGE="https://www.mcs.anl.gov/petsc/"
+SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${P}.tar.gz"
+SRC_URI+=" https://dev.gentoo.org/~sam/distfiles/${CATEGORY}/${PN}/${P}-fftw-without-mpi.patch.bz2"
+
+LICENSE="BSD-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="afterimage boost complex-scalars cxx debug 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}
+ ${PYTHON_DEPS}
+ virtual/pkgconfig
+ dev-util/cmake
+ sys-apps/which
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
+ "${FILESDIR}"/${P}-fix_sandbox_violation.patch
+ "${WORKDIR}"/${P}-fftw-without-mpi.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=$4"
+}
+
+src_configure() {
+ # bug 548498
+ # PETSc runs mpi processes during configure that result in a sandbox
+ # violation by trying to open /proc/mtrr rw. This is not easy to
+ # mitigate because it happens in libpciaccess.so called by libhwloc.so,
+ # which is used by libmpi.so.
+ addpredict /proc/mtrr
+ # if mpi is built with knem support it needs /dev/knem too
+ addpredict /dev/knem
+
+ # configureMPITypes with openmpi-2* insists on accessing the scaling
+ # governor rw.
+ addpredict /sys/devices/system/cpu/
+
+ # bug 771711
+ # configureMPIEXEC and configureMPITypes access /dev/nvidiactl
+ addpredict /dev/nvidiactl
+
+ # bug 810841
+ addpredict /dev/kfd
+
+ local mylang
+ local myopt
+
+ use cxx && mylang="cxx" || mylang="c"
+ use debug && myopt="debug" || myopt="opt"
+
+ # environmental variables expected by petsc during build
+
+ export PETSC_DIR="${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
+}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/
@ 2022-05-26 1:27 Matthias Maier
0 siblings, 0 replies; 5+ messages in thread
From: Matthias Maier @ 2022-05-26 1:27 UTC (permalink / raw
To: gentoo-commits
commit: e0a89fd9e8bf7f3939ffc6eefaf7ce059a3ab13a
Author: Matthias Maier <tamiko <AT> gentoo <DOT> org>
AuthorDate: Thu May 26 00:05:35 2022 +0000
Commit: Matthias Maier <tamiko <AT> gentoo <DOT> org>
CommitDate: Thu May 26 01:26:54 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e0a89fd9
sci-mathematics/petsc: drop 3.13.1, 3.14.6, 3.15.0, 3.15.0-r1
Signed-off-by: Matthias Maier <tamiko <AT> gentoo.org>
sci-mathematics/petsc/Manifest | 3 -
.../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-3.13.1.ebuild | 196 ---------------------
sci-mathematics/petsc/petsc-3.14.6.ebuild | 194 --------------------
sci-mathematics/petsc/petsc-3.15.0-r1.ebuild | 194 --------------------
sci-mathematics/petsc/petsc-3.15.0.ebuild | 190 --------------------
8 files changed, 919 deletions(-)
diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest
index a53a6158e9b6..8a1dcafa8362 100644
--- a/sci-mathematics/petsc/Manifest
+++ b/sci-mathematics/petsc/Manifest
@@ -1,6 +1,3 @@
-DIST petsc-3.13.1.tar.gz 35097687 BLAKE2B fccf64fd3694deffdd0dc561069ffa7e9342fe279b5c9123edeb011df931874083839d27b7b9a0c63faea6487b104b54fd4ce68a88a074c82de91e8baaf270b0 SHA512 41c3138a6ae6c1f2d9077b464c6aeda96287e5a76849582b8f432e2ee93d2594a78ba2181eac0054a77b6165692be5f1a057049313f2be9743d4246383dfdc77
-DIST petsc-3.14.6.tar.gz 39719179 BLAKE2B d3047baf87c67eb64ef02c0c54d6313ea06f091b377b3cdf6dcf6d96c7d68cec5958a007ddd84b52a3ab39bfc0adf146307fa1785a10f39386393371186a3fba SHA512 9766e164446ac5a69b8bf761a0e8a235b1a2b85ed9c96a7fd59e668ae4cceb9d9559a38b175b4aa9747e78d7b44d0018a3c02748dcd3d783d28f861f8382d44c
-DIST petsc-3.15.0.tar.gz 15976488 BLAKE2B babfbeb05321c9cb2f7d70ef8ffca974a016eae73ca1a3359d9a8d38aa5aa90ff34571169a5711627d738b93f89fdee3d0a0ff1bd0e51cb7300bbb9b0a8675cb SHA512 d1565823d8a5ce5e1c2c576bbe1b4ebf467cef20bbd8e0cf6c303c6c2af2bf902b66c79468f4e125496f9242be4bd6ac162535ee30252cfb902c0d906a6f27c0
DIST petsc-3.16.0-fftw-without-mpi.patch.bz2 5824 BLAKE2B 59615b1bbaf8ca1da92d7d193a45a2dd434f762cd741d711d4f408183a201a276ac3c968a3e7d740d19212120271701bce52bb7b0f4e311268f40915c81f9dcb SHA512 8e07dfe56a9150ce9a3a5ab8012657875ef84e6e7daa60560bbdd9062078c876a826057f3f3eaf1697ce046a82756ee6eb6a8b819eb51245367c9d5c8a72ee8e
DIST petsc-3.16.0.tar.gz 16748960 BLAKE2B 87f9fdb79a9c44e5f476fa4746ad0cbe72f3eda9f6039f2e4743105626701d7c8d6c010fdb9d89becf8619288d0b7a60c8bc4e2fc0793eac5b39030b02c04fd9 SHA512 5280032fb4ec4d058733788bb0ae674e7400565e204133bd10ed88a2965230ec7adeaca2d498267ce661377ca7e6f9d948992206b1d679587606cb422c004655
DIST petsc-3.17.1.tar.gz 17082265 BLAKE2B de1bfe45f93e18e32181499e59912df9225c8e24d75f52e641e552fd43e4d5be48d549d284365b173aa93e51603f5b7740eaac0557ff8c7c96b370f4683257f6 SHA512 8c81cc148b1a899a55e54a013d61519ec7b44f98f7ae30c3f8d0e83ba285b23f4b4d9e2cd483c531d337bc41887e4079b727ba73676b1b653910140291e93575
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
deleted file mode 100644
index 4c46658dec71..000000000000
--- a/sci-mathematics/petsc/files/petsc-3.13.0-do_not_run_mpiexec.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-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
deleted file mode 100644
index c0dfd53a0112..000000000000
--- a/sci-mathematics/petsc/files/petsc-3.13.0-fix_sandbox_violation.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-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
deleted file mode 100644
index 1453fd519e81..000000000000
--- a/sci-mathematics/petsc/files/petsc-3.13.0-make_hypre_configure.patch
+++ /dev/null
@@ -1,90 +0,0 @@
-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 <HYPRE_config.h>
- #include <HYPRE_utilities.h>
-
--/* 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<double>
-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; i<pdiag->nz; i++) hjj[i] = pjj[i];
--#else
-- for (i=0; i<pdiag->nz; 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; i<poffd->nz; i++) jj[i] = garray[pjj[i]];
-
diff --git a/sci-mathematics/petsc/petsc-3.13.1.ebuild b/sci-mathematics/petsc/petsc-3.13.1.ebuild
deleted file mode 100644
index 23e1117a52c6..000000000000
--- a/sci-mathematics/petsc/petsc-3.13.1.ebuild
+++ /dev/null
@@ -1,196 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="https://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=$4"
-}
-
-src_configure() {
- # bug 548498
- # PETSc runs mpi processes during configure that result in a sandbox
- # violation by trying to open /proc/mtrr rw. This is not easy to
- # mitigate because it happens in libpciaccess.so called by libhwloc.so,
- # which is used by libmpi.so.
- addpredict /proc/mtrr
- # if mpi is built with knem support it needs /dev/knem too
- addpredict /dev/knem
-
- # configureMPITypes with openmpi-2* insists on accessing the scaling
- # governor rw.
- addpredict /sys/devices/system/cpu/
-
- # bug 771711
- # configureMPIEXEC and configureMPITypes access /dev/nvidiactl
- addpredict /dev/nvidiactl
-
- # bug 810841
- addpredict /dev/kfd
-
- local mylang
- local myopt
-
- use cxx && mylang="cxx" || mylang="c"
- use debug && myopt="debug" || myopt="opt"
-
- # environmental variables expected by petsc during build
-
- export PETSC_DIR="${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
-}
diff --git a/sci-mathematics/petsc/petsc-3.14.6.ebuild b/sci-mathematics/petsc/petsc-3.14.6.ebuild
deleted file mode 100644
index 5bd50a9d32fe..000000000000
--- a/sci-mathematics/petsc/petsc-3.14.6.ebuild
+++ /dev/null
@@ -1,194 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8} )
-
-inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="https://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
-)
-
-# 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=$4"
-}
-
-src_configure() {
- # bug 548498
- # PETSc runs mpi processes during configure that result in a sandbox
- # violation by trying to open /proc/mtrr rw. This is not easy to
- # mitigate because it happens in libpciaccess.so called by libhwloc.so,
- # which is used by libmpi.so.
- addpredict /proc/mtrr
- # if mpi is built with knem support it needs /dev/knem too
- addpredict /dev/knem
-
- # configureMPITypes with openmpi-2* insists on accessing the scaling
- # governor rw.
- addpredict /sys/devices/system/cpu/
-
- # bug 771711
- # configureMPIEXEC and configureMPITypes access /dev/nvidiactl
- addpredict /dev/nvidiactl
-
- # bug 810841
- addpredict /dev/kfd
-
- local mylang
- local myopt
-
- use cxx && mylang="cxx" || mylang="c"
- use debug && myopt="debug" || myopt="opt"
-
- # environmental variables expected by petsc during build
-
- export PETSC_DIR="${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
-}
diff --git a/sci-mathematics/petsc/petsc-3.15.0-r1.ebuild b/sci-mathematics/petsc/petsc-3.15.0-r1.ebuild
deleted file mode 100644
index 5da94f15ff16..000000000000
--- a/sci-mathematics/petsc/petsc-3.15.0-r1.ebuild
+++ /dev/null
@@ -1,194 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} pypy3 )
-
-inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="https://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 fftw
-fortran hdf5 hypre int64 mpi metis mumps scotch superlu threads X"
-
-# readd sparse when suitesparse-5.6.0 is in tree
-# sparse? ( >=sci-libs/suitesparse-5.6.0 >=sci-libs/cholmod-1.7.0 )
-# $(use_with sparse suitesparse) \
-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[int64?,mpi?] )
- metis? ( >=sci-libs/parmetis-4 )
- mpi? ( virtual/mpi[cxx?,fortran?] )
- mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
- scotch? ( sci-libs/scotch[int64?,mpi?] )
- superlu? ( >=sci-libs/superlu-5 )
- X? ( x11-libs/libX11 )
-"
-DEPEND="
- ${RDEPEND}
- ${PYTHON_DEPS}
-"
-BDEPEND="
- dev-util/cmake
- sys-apps/which
- virtual/pkgconfig
-"
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
- afterimage? ( X )
- complex-scalars? ( !hypre !superlu )
- hdf5? ( mpi )
- hypre? ( cxx mpi !superlu )
- mumps? ( mpi scotch )
- scotch? ( mpi )
- superlu? ( !hypre )
-"
-PATCHES=(
- "${FILESDIR}/${PN}-3.7.0-disable-rpath.patch"
- "${FILESDIR}/${PN}-3.13.0-fix_sandbox_violation.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=$4"
-}
-
-src_configure() {
- # bug 548498
- # PETSc runs mpi processes during configure that result in a sandbox
- # violation by trying to open /proc/mtrr rw. This is not easy to
- # mitigate because it happens in libpciaccess.so called by libhwloc.so,
- # which is used by libmpi.so.
- addpredict /proc/mtrr
- # if mpi is built with knem support it needs /dev/knem too
- addpredict /dev/knem
-
- # configureMPITypes with openmpi-2* insists on accessing the scaling
- # governor rw.
- addpredict /sys/devices/system/cpu/
-
- # bug 771711
- # configureMPIEXEC and configureMPITypes access /dev/nvidiactl
- addpredict /dev/nvidiactl
-
- # bug 810841
- addpredict /dev/kfd
-
- local mylang
- local myopt
-
- use cxx && mylang="cxx" || mylang="c"
- use debug && myopt="debug" || myopt="opt"
-
- # environmental variables expected by petsc during build
-
- export PETSC_DIR="${S}"
- export PETSC_ARCH="linux-gnu-${mylang}-${myopt}"
-
- if use debug; then
- strip-flags
- filter-flags -O*
- fi
-
- tc-export AR RANLIB
-
- # 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 \
- AR="${AR}" \
- CFLAGS="${CFLAGS} -fPIC" \
- CPPFLAGS="${CPPFLAGS}" \
- CXXFLAGS="${CXXFLAGS} -fPIC" \
- CXXOPTFLAGS="${CXXFLAGS} -fPIC" \
- FCFLAGS="${FCFLAGS} -fPIC" \
- FFLAGS="${FFLAGS} -fPIC" \
- LDFLAGS="${LDFLAGS}" \
- MAKEFLAGS="${MAKEFLAGS}" \
- RANLIB="${RANLIB}" \
- --prefix="${EPREFIX}/usr/$(get_libdir)/petsc" \
- --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs blas lapack)" \
- --with-clanguage="${mylang}" \
- --with-cmake:BOOL=1 \
- --with-gnu-compilers \
- --with-imagemagick=0 \
- --with-matlab=0 \
- --with-petsc-arch="${PETSC_ARCH}" \
- --with-precision=double \
- --with-python=0 \
- --with-shared-libraries \
- --with-single-library \
- --with-windows-graphics=0 \
- $(petsc_enable debug debugging) \
- $(petsc_enable fortran) \
- $(petsc_enable mpi) \
- $(petsc_enable mpi mpi-compilers) \
- $(petsc_enable threads pthread) \
- $(petsc_select complex-scalars scalar-type complex real) \
- $(petsc_select mpi cc mpicc $(tc-getCC)) \
- $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \
- $(petsc_with afterimage afterimage /usr/include/libAfterImage -lAfterImage) \
- $(petsc_with hypre hypre /usr/include/hypre -lHYPRE) \
- $(petsc_with superlu superlu /usr/include/superlu -lsuperlu) \
- $(petsc_with scotch ptscotch /usr/include/scotch [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \
- $(petsc_with mumps scalapack /usr/include/scalapack -lscalapack) \
- $(use cxx && ! use complex-scalars && echo "--with-c-support=1") \
- $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \
- $(use int64 && echo "--with-index-size=64") \
- $(use_with boost) \
- $(use_with fftw) \
- $(use_with hdf5) \
- $(use_with mumps mumps /usr/include [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \
- $(use_with X x) \
- $(use_with X x11)
-}
-
-src_install() {
- emake DESTDIR="${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
-}
diff --git a/sci-mathematics/petsc/petsc-3.15.0.ebuild b/sci-mathematics/petsc/petsc-3.15.0.ebuild
deleted file mode 100644
index 8286baab9803..000000000000
--- a/sci-mathematics/petsc/petsc-3.15.0.ebuild
+++ /dev/null
@@ -1,190 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-inherit flag-o-matic fortran-2 python-any-r1 toolchain-funcs
-
-DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation"
-HOMEPAGE="https://www.mcs.anl.gov/petsc/"
-SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${P}.tar.gz"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="afterimage boost complex-scalars cxx debug fftw
- fortran hdf5 hypre mpi metis mumps scotch sparse superlu threads X"
-
-# hypre and superlu curretly exclude each other due to missing linking to hypre
-# if both are enabled
-REQUIRED_USE="
- afterimage? ( X )
- complex-scalars? ( !hypre !superlu )
- hdf5? ( mpi )
- hypre? ( cxx mpi !superlu )
- mumps? ( mpi scotch )
- scotch? ( mpi )
- superlu? ( !hypre )
-"
-
-RDEPEND="
- virtual/blas
- virtual/lapack
- afterimage? ( media-libs/libafterimage )
- boost? ( dev-libs/boost )
- fftw? ( sci-libs/fftw:3.0[mpi?] )
- hdf5? ( sci-libs/hdf5[mpi?] )
- hypre? ( >=sci-libs/hypre-2.18.0[mpi?] )
- metis? ( >=sci-libs/parmetis-4 )
- mpi? ( virtual/mpi[cxx?,fortran?] )
- mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack )
- scotch? ( sci-libs/scotch[mpi?] )
- sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 )
- superlu? ( >=sci-libs/superlu-5 )
- X? ( x11-libs/libX11 )
-"
-
-DEPEND="${RDEPEND}
- ${PYTHON_DEPS}
- virtual/pkgconfig
- dev-util/cmake
- sys-apps/which
-"
-
-PATCHES=(
- "${FILESDIR}"/${PN}-3.7.0-disable-rpath.patch
- "${FILESDIR}"/${PN}-3.13.0-fix_sandbox_violation.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=$4"
-}
-
-src_configure() {
- # bug 548498
- # PETSc runs mpi processes during configure that result in a sandbox
- # violation by trying to open /proc/mtrr rw. This is not easy to
- # mitigate because it happens in libpciaccess.so called by libhwloc.so,
- # which is used by libmpi.so.
- addpredict /proc/mtrr
- # if mpi is built with knem support it needs /dev/knem too
- addpredict /dev/knem
-
- # configureMPITypes with openmpi-2* insists on accessing the scaling
- # governor rw.
- addpredict /sys/devices/system/cpu/
-
- # bug 771711
- # configureMPIEXEC and configureMPITypes access /dev/nvidiactl
- addpredict /dev/nvidiactl
-
- # bug 810841
- addpredict /dev/kfd
-
- local mylang
- local myopt
-
- use cxx && mylang="cxx" || mylang="c"
- use debug && myopt="debug" || myopt="opt"
-
- # environmental variables expected by petsc during build
-
- export PETSC_DIR="${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
-}
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2020-04-29 21:35 [gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/ Matthias Maier
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