tFix dependencies, download external - petsc-git-PKGBUILD - build template for non-complex PETSC with petsc4py
(HTM) git clone git://src.adamsgaard.dk/petsc-git-PKGBUILD
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(DIR) commit 4df4a1efe749f56b84f6e08107c7ac8dd43c827c
(DIR) parent acf8ee6afcc1b738e1337c2901eeb948346c64d6
(HTM) Author: Lucas Heitzmann Gabrielli <heitzmann@gmail.com>
Date: Thu, 21 May 2020 09:12:04 -0300
Fix dependencies, download external
Diffstat:
M .SRCINFO | 34 +++++++++----------------------
M PKGBUILD | 118 ++++++++++++++++++-------------
D test_optdepends.sh | 139 ------------------------------
3 files changed, 80 insertions(+), 211 deletions(-)
---
(DIR) diff --git a/.SRCINFO b/.SRCINFO
t@@ -1,6 +1,6 @@
pkgbase = petsc-git
- pkgdesc = Portable, extensible toolkit for scientific computation with MUMPS, Hypre, FFTW, HDF5, Scalapack, Suitesparse, Metis, Scotch, Superlu, OpenBLAS, Eigen, OpenMP, HWloc, CGNS, PNG, MED and trilinos
- pkgver = 20200512
+ pkgdesc = Portable, extensible toolkit for scientific computation (external downloads enabled)
+ pkgver = 20200520
pkgrel = 1
url = https://www.mcs.anl.gov/petsc/
install = petsc.install
t@@ -11,37 +11,23 @@ pkgbase = petsc-git
makedepends = gcc-fortran
makedepends = cmake
makedepends = sowing
- depends = python2
+ makedepends = python2
depends = openmpi
- depends = boost
depends = lapack
depends = fftw
depends = hdf5
- optdepends = hdf5: large files
- optdepends = fftw: Fast-Fourier Transform
- optdepends = openblas: Linear algebra libraries
- optdepends = scalapack: Parallel memory linear algebra
- optdepends = mumps: Sparse solver library
- optdepends = hypre: Large and sparse linear with massive parallel computing
- optdepends = suitesparse: Sparse matrix library
- optdepends = metis: Partitioning library (for meshes)
- optdepends = scotch: Partitioning with sparse matrices
- optdepends = superlu: Subroutines for sparsse linear systems
- optdepends = eigen: Lightweight C++ template library for vector and matrix math
- optdepends = openmp: Parallel distributed tasks
- optdepends = hwloc: Portable Hardware Locality (abstraction of hierarchical architectures)
- optdepends = cgns: Recording and recovering computer data
- optdepends = png
- optdepends = med>=4.0: Data Modelization and Exchanges (meshes)
- optdepends = boost: Free peer-reviewed portable C++ source libraries
- optdepends = yaml: configuration files
+ depends = suitesparse
optdepends = opencl: GPU computing
+ optdepends = hwloc: hardware locality
+ optdepends = cgns: CFD data support
+ optdepends = libpng: PNG support
+ optdepends = libyaml: YAML configuration support
+ optdepends = libx11: GUI tools
+ optdepends = python: Tools, examples, tutorials
provides = petsc
conflicts = petsc
source = petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint
- source = test_optdepends.sh
sha256sums = SKIP
- sha256sums = 2c21313b21b7a76ed4d39d040ef60462f8760ae3d4b76ff6aa717ebc43a2275b
pkgname = petsc-git
(DIR) diff --git a/PKGBUILD b/PKGBUILD
t@@ -1,44 +1,27 @@
-# Based on AUR petsc and petsc-git package. Adapted to my
-# MOOSE requirements
-
# Maintainer: Lucas H. Gabrielli <heitzmann@gmail.com>
pkgname=petsc-git
-pkgver=20200512
+pkgver=20200520
pkgrel=1
_config=linux-c-opt
-pkgdesc="Portable, extensible toolkit for scientific computation with MUMPS, Hypre, FFTW, HDF5, Scalapack, Suitesparse, Metis, Scotch, Superlu, OpenBLAS, Eigen, OpenMP, HWloc, CGNS, PNG, MED and trilinos"
+pkgdesc="Portable, extensible toolkit for scientific computation (external downloads enabled)"
provides=(petsc)
conflicts=(petsc)
arch=('i686' 'x86_64')
url="https://www.mcs.anl.gov/petsc/"
license=('BSD')
-depends=('python2' 'openmpi' 'boost' 'lapack' 'fftw' 'hdf5')
-makedepends=('gcc' 'gcc-fortran' 'cmake' 'sowing')
-optdepends=("hdf5: large files"
- "fftw: Fast-Fourier Transform"
- "openblas: Linear algebra libraries"
- "scalapack: Parallel memory linear algebra"
- "mumps: Sparse solver library"
- "hypre: Large and sparse linear with massive parallel computing"
- "suitesparse: Sparse matrix library"
- "metis: Partitioning library (for meshes)"
- "scotch: Partitioning with sparse matrices"
- "superlu: Subroutines for sparsse linear systems"
- "eigen: Lightweight C++ template library for vector and matrix math"
- "openmp: Parallel distributed tasks"
- "hwloc: Portable Hardware Locality (abstraction of hierarchical architectures)"
- "cgns: Recording and recovering computer data"
- "png"
- "med>=4.0: Data Modelization and Exchanges (meshes)"
- "boost: Free peer-reviewed portable C++ source libraries"
- "yaml: configuration files"
- "opencl: GPU computing")
+depends=('openmpi' 'lapack' 'fftw' 'hdf5' 'suitesparse')
+makedepends=('gcc' 'gcc-fortran' 'cmake' 'sowing' 'python2')
+optdepends=("opencl: GPU computing"
+ "hwloc: hardware locality"
+ "cgns: CFD data support"
+ "libpng: PNG support"
+ "libyaml: YAML configuration support"
+ "libx11: GUI tools"
+ "python: Tools, examples, tutorials")
install=petsc.install
-source=(petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint
- test_optdepends.sh)
-sha256sums=('SKIP'
- '2c21313b21b7a76ed4d39d040ef60462f8760ae3d4b76ff6aa717ebc43a2275b')
+source=(petsc::git+https://gitlab.com/petsc/petsc.git#branch=maint)
+sha256sums=('SKIP')
_petsc_arch="arch-${_config}"
t@@ -60,16 +43,16 @@ _petsc_arch="arch-${_config}"
generic_flags="-fPIC -fopenmp -O3 -march=x86-64 -mtune=generic"
# generic_flags="-fPIC -fopenmp -O3 -march=amdfam10 -mtune=generic"
-export COPTFLAGS=-O3
+export COPTFLAGS=-O3
export CXXOPTFLAGS=-O3
-export FOPTFLAGS=-O3
-export CPPFLAGS="$generic_flags -O2 -D-FORTIFY-SOURCE=2"
-export CFLAGS="$generic_flags"
-export CXXFLAGS="$generic_flags"
-export FFLAGS="$generic_flags"
-export FCFLAGS="$generic_flags"
-export F90FLAGS="$generic_flags"
-export F77FLAGS="$generic_flags"
+export FOPTFLAGS=-O3
+export CPPFLAGS="$generic_flags -O2 -D-FORTIFY-SOURCE=2"
+export CFLAGS="$generic_flags"
+export CXXFLAGS="$generic_flags"
+export FFLAGS="$generic_flags"
+export FCFLAGS="$generic_flags"
+export F90FLAGS="$generic_flags"
+export F77FLAGS="$generic_flags"
pkgver() {
t@@ -86,9 +69,7 @@ prepare() {
done < <( find ${srcdir} -name "*" -type f -exec grep -le "$MATCH" \{\} + )
cd "${srcdir}/petsc"
- # patch -p1 < ../patch.diff
sed -i 's-\(self.publicInstall[^=]*=[[:space:]]\)[^#]*-\10 -g' config/BuildSystem/config/package.py
-
sed -i "s/\(raise RuntimeError('--download-openblas libraries cannot be used')\)/#\1/" config/BuildSystem/config/packages/BlasLapack.py
}
t@@ -96,11 +77,11 @@ prepare() {
build() {
cd petsc
- declare -a CONFOPTS
# Run python2 ./configure --help for the meaning of this
+ declare -a CONFOPTS
CONFOPTS=(
--COPTFLAGS="$COPTFLAGS"
- --CXXOPTFLAGS="CXXOPTFLAGS"
+ --CXXOPTFLAGS="$CXXOPTFLAGS"
--CPPFLAGS="$CPPFLAGS"
--CFLAGS="$CFLAGS"
--CXXFLAGS="$CXXFLAGS"
t@@ -115,18 +96,59 @@ build() {
--with-shared-libraries=1
--with-zlib=1
+ --with-fftw=1
+ --with-hdf5=1
+ --with-suitesparse=1
+
--with-scalar-type=complex
- # Add this to test_optdepends.sh
- --with-opencl=1
- --with-yaml=1
+
+ --download-amd=1
+ --download-eigen=1
+ --download-hypre=1
+ --download-metis=1
+ --download-mumps=1
+ --download-parmetis=1
+ #--download-party=1 # not working
+ --download-ptscotch=1
+ --download-scalapack=1
+ #--download-suitesparse=1 # not working
+ #--download-sundials=1 # incompatible with complex
+ --download-superlu=1
+ --download-superlu_dist=1
)
+ CONFOPTS=( "${CONFOPTS[@]}" )
+
+ # Add OpenCL support
+ OPENCL_DIR="/usr/include/CL/"
+ if [ -f "${OPENCL_DIR}/cl.h" ]; then
+ CONFOPTS="${CONFOPTS} --with-opencl=1"
+ fi
+
+ # Add hwloc support
+ if [ -f "/usr/lib/libhwloc.so" ]; then
+ CONFOPTS="${CONFOPTS} --with-hwloc=1 --with-hwloc-pkg-config=/usr/lib/pkgconfig/"
+ fi
+
+ # Add CGNS support
+ if [ -f "/usr/lib/libcgns.so" ]; then
+ CONFOPTS="${CONFOPTS} --with-cgns=1"
+ fi
+
+ # Add PNG support
+ if [ -f "/usr/lib/libpng.so" ]; then
+ CONFOPTS="${CONFOPTS} --with-png=1 --with-png-pkg-config=/usr/lib/pkgconfig/"
+ fi
+
+ # Add YAML support
+ if [ -f "/usr/lib/libyaml.so" ]; then
+ CONFOPTS="${CONFOPTS} --with-yaml=1 --with-yaml-pkg-config=/usr/lib/pkgconfig/"
+ fi
+
# if --with-debugging=1 is set then PETSC_ARCH is automatically set to
# "linux-c-debug" for some things, so _config should be changed to "linux-c-debug"
#CONFOPTS="${CONFOPTS} --with-debugging=1"
- CONFOPTS=( "${CONFOPTS[@]}" $(sh "${srcdir}"/test_optdepends.sh) )
-
dirpkg=${srcdir}/petsc/${_petsc_arch}/externalpackages/
export PETSC_DIR="${srcdir}/petsc"
(DIR) diff --git a/test_optdepends.sh b/test_optdepends.sh
t@@ -1,139 +0,0 @@
-#!/bin/bash
-
-# Test if external packages for PETSC are installed
-
-# CONFOPTS=""
-
-# # External downloads
-# for external_pkg in hypre fblaslapack metis parmetis superlu_dist mumps scalapack; do
-# CONFOPTS="${CONFOPTS} --download-${external_pkg}=1"
-# done
-
-# Add hypre support
-if [ -f "/usr/lib/libHYPRE.so" ]; then
- CONFOPTS="${CONFOPTS} --with-hypre=1"
-fi
-
-# Add mumps support
-if [ -f "/usr/lib/libmumps_common.so" ]; then
- CONFOPTS="${CONFOPTS} --with-mumps=1"
-fi
-
-# Add fftw support
-if [ -f "/usr/lib/libfftw3_mpi.so" ]; then
- CONFOPTS="${CONFOPTS} --with-fftw=1"
-fi
-
-# Add hdf5 support
-if [[ "$(h5stat -V)" ]]; then
- CONFOPTS="${CONFOPTS} --with-hdf5=1"
-fi
-
-# Add scalapack support
-if [ -f "/usr/lib/pkgconfig/scalapack.pc" ]; then
- CONFOPTS="${CONFOPTS} --with-scalapack=1"
-fi
-
-# Add suitesparse support
-if [ -f "/usr/include/SuiteSparse_config.h" ]; then
- CONFOPTS="${CONFOPTS} --with-suitesparse=1"
-fi
-
-# Add metis support
-if [ -f "/usr/include/metis.h" ]; then
- CONFOPTS="${CONFOPTS} --with-metis=1"
- # Add parmetis support
- if [ -f "/usr/include/parmetis.h" ]; then
- CONFOPTS="${CONFOPTS} --with-parmetis=1"
- fi
-fi
-
-# Add scotch support
-SCOTCH_DIR="/usr/include/scotch"
-if [ -d "${SCOTCH_DIR}" ]; then
- SCOTCH_LIBS="libesmumps.so,libptscotch.so,libptscotcherr.so,libscotch.so,libscotcherr.so"
- # Include bzip2 if scotch was build with bzip2 support
- if [ -f /usr/include/bzlib.h ];then
- SCOTCH_LIBS="${SCOTCH_LIBS},libbz2.so"
- fi
- SCOTCH_LIBS="[${SCOTCH_LIBS}]"
- CONFOPTS="${CONFOPTS} --with-ptscotch=1 --with-ptscotch-lib=${SCOTCH_LIBS} --with-ptscotch-include=${SCOTCH_DIR}"
-fi
-
-# Add superlu support
-SUPERLU_DIR="/usr/include/superlu"
-if [ -d "${SUPERLU_DIR}" ]; then
- CONFOPTS="${CONFOPTS} --with-superlu=1 --with-superlu-lib=-lsuperlu --with-superlu-include=${SUPERLU_DIR}"
-fi
-
-# Incompatible with complex
-# # Add sundials support
-# SUNDIALS_DIR="/usr/include/sundials/"
-# if [ -d "${SUNDIALS_DIR}" ]; then
-# CONFOPTS="${CONFOPTS} --with-sundials=1 --with-sundials-include=${SUNDIALS_DIR}"
-# fi
-
-# Add openblas support
-if [ -f "/usr/lib/libblas.so" ]; then
- CONFOPTS="${CONFOPTS} --with-openblas=1"
-fi
-
-# Add OpenCL support
-OPENCL_DIR="/usr/include/CL/"
-if [ -f "${OPENCL_DIR}/cl.h" ]; then
- CONFOPTS="${CONFOPTS} --with-opencl=1"
-else
- CONFOPTS="${CONFOPTS} --with-opencl=0"
-fi
-
-# Add eigen support
-EIGEN_DIR="/usr/include/eigen3"
-if [ -d "${EIGEN_DIR}" ]; then
- CONFOPTS="${CONFOPTS} --with-eigen=1 --with-eigen-include=${EIGEN_DIR}"
-fi
-
-# Add OpenMP support
-if [ -f "/usr/lib/libomp.so" ]; then
- CONFOPTS="${CONFOPTS} --with-openmp=1"
-fi
-
-# Add hwloc support
-if [ -f "/usr/lib/libhwloc.so" ]; then
- CONFOPTS="${CONFOPTS} --with-hwloc=1 --with-hwloc-pkg-config=/usr/lib/pkgconfig/"
-fi
-
-# Add CGNS support
-if [ -f "/usr/lib/libcgns.so" ]; then
- CONFOPTS="${CONFOPTS} --with-cgns=1"
-fi
-
-# Add PNG support
-if [ -f "/usr/lib/libpng.so" ]; then
- CONFOPTS="${CONFOPTS} --with-png=1 --with-png-pkg-config=/usr/lib/pkgconfig/"
-fi
-
-# Add MED support
-if [ -f "/usr/lib/libmed.so" ]; then
- CONFOPTS="${CONFOPTS} --with-med=1"
-fi
-
-# # Add pastix support
-# PASTIX_CONF=$(which pastix-conf)
-# if [ -f "${PASTIX_CONF}" ]; then
-# PASTIX_DIR="$($PASTIX_CONF --incs | sed 's/-I//')"
-# if [ ! -d ${PASTIX_DIR} ]; then
-# PASTIX_DIR="[]"
-# fi
-# #PASTIX_LIBS="$($PASTIX_CONF --libs)"
-# PASTIX_LIBS="[libpastix.a,librt.so,libhwloc.so,libpthread.a]"
-# CONFOPTS="${CONFOPTS} --with-pastix=1 --with-pastix-lib=${PASTIX_LIBS} --with-pastix-include=${PASTIX_DIR}"
-# fi
-
-# Add trilinos support
-if [ "${TRILINOS_DIR}" ]; then
- CONFOPTS="${CONFOPTS} --with-ml-dir=${TRILINOS_DIR}"
- # Add boost support (may be useful for trilinos)
- CONFOPTS="${CONFOPTS} --with-boost=1"
-fi
-
-echo "${CONFOPTS}"