[gentoo-commits] repo/gentoo:master commit in: sci-mathematics/petsc/, sci-mathematics/petsc/files/

[Matthias Maier]

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
-}