adding easyconfigs: muParser-2.3.4-GCCcore-13.2.0.eb, R-INLA-24.10.07…

…-2-foss-2023b.eb, Rmath-4.4.1-foss-2023b.eb, SuiteSparse-7.7.0-foss-2023b.eb and patches: R-INLA-24.10.07_remove-hardcoding.patch, R-INLA-24.10.07-2_fix-hardcoded-deps.patch
sassy-crick · Oct 14, 2024 · a136c4e · a136c4e
1 parent 4872376
commit a136c4e
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diff --git a/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/muParser/muParser-2.3.4-GCCcore-13.2.0.eb
@@ -0,0 +1,32 @@
+easyblock = 'CMakeMake'
+
+name = 'muParser'
+version = '2.3.4'
+
+homepage = 'https://beltoforion.de/article.php?a=muparser'
+description = """
+ muParser is an extensible high performance math expression parser library
+ written in C++. It works by transforming a mathematical expression into
+ bytecode and precalculating constant parts of the expression.
+"""
+
+toolchain = {'name': 'GCCcore', 'version': '13.2.0'}
+toolchainopts = {'pic': True}
+
+source_urls = ['https://github.com/beltoforion/muparser/archive/']
+sources = ['v%(version)s.tar.gz']
+checksums = ['0c3fa54a3ebf36dda0ed3e7cd5451c964afbb15102bdbcba08aafb359a290121']
+
+builddependencies = [
+    ('binutils', '2.40'),
+    ('CMake', '3.27.6'),
+]
+
+configopts = "-DENABLE_SAMPLES=OFF -DBUILD_SHARED_LIBS=ON"
+
+sanity_check_paths = {
+    'files': ['include/%(name)s.h', 'lib/libmuparser.%s' % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-24.10.07-2-foss-2023b.eb b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.10.07-2-foss-2023b.eb
@@ -0,0 +1,108 @@
+# Updated to 24.10.07-2
+# Author: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'Bundle'
+
+name = 'R-INLA'
+version = '24.10.07-2'
+
+homepage = 'https://www.r-inla.org'
+description = "R-INLA is a package in R that do approximate Bayesian inference for Latent Gaussian Models."
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'openmp': True}
+
+dependencies = [
+    ('R', '4.4.1'),
+    ('R-bundle-CRAN', '2024.06'),
+    ('GSL', '2.7'),
+    ('zlib', '1.2.13'),
+    ('SuiteSparse', '7.7.0'),
+    ('METIS', '5.1.0'),
+    ('muParser', '2.3.4'),
+    ('Rmath', '%(rver)s'),
+    ('X11', '20231019'),
+    ('libtool', '2.4.7'),  # provides libltdl
+]
+
+default_easyblock = 'ConfigureMake'
+# all components are installed from the same source tarball
+default_component_specs = {
+    'source_urls': ['https://github.com/hrue/r-inla/archive/refs/tags/'],
+    'sources': [{'download_filename': 'Version_%s.tar.gz' % version, 'filename': 'R-INLA-%s.tar.gz' % version}],
+    'skipsteps': ['configure'],
+    'checksums': ['6e3bf7fd403290928ce5f9bd89092a750f8b9faf40bb99a3b3265116143260db']
+}
+
+local_gmrflib_prebuildopts = ' cd r-inla-Version_%(version)s && ln -s gmrflib GMRFLib && cd - && '
+local_gmrflib_buildopts = ' -C r-inla-*/gmrflib PREFIX=%(installdir)s CC="$CC" FC="$FC" '
+local_gmrflib_buildopts += ' FLAGS="$CXXFLAGS -DINLA_LINK_WITH_OPENBLAS " '
+
+local_rinla_prebuildopts = "export CPATH=$EBROOTR/lib64/R/include/:$CPATH && "
+local_rinla_prebuildopts += "cp r-inla-Version_%(version)s/gmrflib/sha.h %(installdir)s/include/GMRFLib/ && "
+
+local_inla_buildopts = '-C r-inla-*/inlaprog PREFIX=%(installdir)s '
+local_inla_buildopts += ' CC="$CC" CXX="$CXX" FC="$FC" LD="$CXX -lltdl" '
+local_inla_buildopts += ' FLAGS="$CXXFLAGS -DINLA_LINK_WITH_OPENBLAS"'
+
+components = [
+    ('taucs', version, {
+        'easyblock': 'MakeCp',
+        'prebuildopts': "cd r-inla-*/extlibs && tar xvfz taucs-2.2--my-fix.tgz && cd taucs-2.2--my-fix && ",
+        'buildopts': 'CC="$CC" CFLAGS="$CFLAGS" FC="$FC" FFLAGS="$FFLAGS" LIBBLAS="$LIBBLAS" LIBLAPACK="$LIBLAPACK"',
+        'files_to_copy': [(['r-inla-*/extlibs/taucs-2.2--my-fix/lib/linux/libtaucs.a'], 'lib')],
+    }),
+    ('fmesher-R-INLA', version, {
+        'patches': ['R-INLA-24.10.07-2_fix-hardcoded-deps.patch'],
+        'checksums': default_component_specs['checksums'] + [
+            '2e81c16c06eb1a9355e50dfac5f92477c093d94137ee49ae35e78e75d67a853d',
+        ],
+        'buildopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s CC="$CC" CXX="$CXX" LD="$CXX" FLAGS="$CXXFLAGS"',
+        'installopts': '-C r-inla-*/fmesher PREFIX=%(installdir)s',
+    }),
+    ('GMRFLib', version, {
+        'prebuildopts': local_gmrflib_prebuildopts,
+        'buildopts': local_gmrflib_buildopts,
+        'installopts': '-C r-inla-*/gmrflib PREFIX=%(installdir)s',
+    }),
+    ('fmesher', '0.1.7', {
+        'easyblock': 'RPackage',
+        'source_urls': [
+            'https://cran.r-project.org/src/contrib/Archive/fmesher',  # package archive
+            'https://cran.r-project.org/src/contrib/',  # current version of packages
+        ],
+        'sources': ['fmesher_%(version)s.tar.gz'],
+        'checksums': ['b59af73ac4e30e5d4287fb6ddfc0b6e21b007243bd94a652f3725ea431019ecf'],
+        'start_dir': 'fmesher',
+    }),
+    ('rinla', version, {
+        'patches': ['R-INLA-24.10.07_remove-hardcoding.patch'],
+        'checksums': default_component_specs['checksums'] + [
+            '8a1fd63611e1ad64ed8702b5ba07b5f3969afcaf0454605074c1d717590ca603',
+        ],
+        'easyblock': 'RPackage',
+        'start_dir': 'r-inla-Version_%(version)s/rinla',
+        'preinstallopts': "export R_LIBS_SITE=%(installdir)s:$R_LIBS_SITE && ",
+    }),
+    (name, version, {
+        'prebuildopts': local_rinla_prebuildopts,
+        'buildopts': local_inla_buildopts,
+        'installopts': '-C r-inla-*/inlaprog PREFIX=%(installdir)s',
+    }),
+]
+
+local_bins = ['inla', 'fmesher']
+
+postinstallcmds = ['ln -s %%(installdir)s/bin/%s %%(installdir)s/INLA/bin/linux/64bit/%s' % (x, x) for x in local_bins]
+
+sanity_check_paths = {
+    'files': ['%s/%s' % (p, x) for p in ['bin', 'INLA/bin/linux/64bit'] for x in local_bins] +
+             ['lib/libGMRFLib.a', 'lib/libtaucs.a'],
+    'dirs': ['doc', 'include/GMRFLib'],
+}
+
+sanity_check_commands = ["Rscript -e 'library(INLA)'"] + ["%s -h" % x for x in local_bins]
+
+modextrapaths = {'R_LIBS_SITE': ''}
+
+moduleclass = 'math'
diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-24.10.07-2_fix-hardcoded-deps.patch b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.10.07-2_fix-hardcoded-deps.patch
@@ -0,0 +1,77 @@
+use dependencies provided by EasyBuild
+authors: Denis Kristak (INUITS), Kenneth Hoste (HPC-UGent)
+updated to 24.10.07-2: J. Sassmannshausen (Imperial College London/UK)
+diff --git a/r-inla-Version_24.10.07-2.orig/gmrflib/old-stuff/smtp-taucs.c b/r-inla-Version_24.10.07-2/gmrflib/old-stuff/smtp-taucs.c
+index 07d3b13..d2964c6 100644
+--- a/r-inla-Version_24.10.07-2.orig/gmrflib/old-stuff/smtp-taucs.c
++++ b/r-inla-Version_24.10.07-2/gmrflib/old-stuff/smtp-taucs.c
+@@ -43,7 +43,7 @@
+
+ #include "GMRFLib/GMRFLib.h"
+ #include "GMRFLib/GMRFLibP.h"
+-#include "amd.h"
++#include "suitesparse/amd.h"
+ #include "metis.h"
+
+ GMRFLib_taucs_cache_tp *GMRFLib_taucs_cache_duplicate(GMRFLib_taucs_cache_tp *cache)
+diff --git a/r-inla-Version_24.10.07-2.orig/gmrflib/smtp-taucs.c b/r-inla-Version_24.10.07-2/gmrflib/smtp-taucs.c
+index ba7331f..dc09aba 100644
+--- a/r-inla-Version_24.10.07-2.orig/gmrflib/smtp-taucs.c
++++ b/r-inla-Version_24.10.07-2/gmrflib/smtp-taucs.c
+@@ -43,7 +43,7 @@
+
+ #include "GMRFLib/GMRFLib.h"
+ #include "GMRFLib/GMRFLibP.h"
+-#include "amd.h"
++#include "suitesparse/amd.h"
+ #include "metis.h"
+
+ #define TIME_FUNCTIONS 0
+diff --git a/r-inla-Version_24.10.07-2.orig/inlaprog/Makefile b/r-inla-Version_24.10.07-2/inlaprog/Makefile
+index c2a5bc3..64e9ede 100644
+--- a/r-inla-Version_24.10.07-2.orig/inlaprog/Makefile
++++ b/r-inla-Version_24.10.07-2/inlaprog/Makefile
+@@ -2,8 +2,8 @@
+
+ PREFIX = /usr/local
+
+-RLIB_INC = -DINLA_WITH_LIBR -I/usr/include/R -I/usr/share/R/include
+-RLIB_LIB = -L/usr/lib -lRmath -L/usr/lib/R/lib -lR
++RLIB_INC = -DINLA_WITH_LIBR 
++RLIB_LIB = -lRmath -lR
+
+ # select compilers and optimized compiler-options, add -fopenmp or similar to use OpenMP
+ CC = gcc
+@@ -19,7 +19,7 @@ LEXTPREFIX = $(PREFIX)
+
+ # The external libraries to link with
+ EXTLIBS1 = -L$(PREFIX)/lib -lGMRFLib -L$(LEXTPREFIX)/lib 
+-EXTLIBS2 = -lgsl -ltaucs -lmetis -llapack -lblas -lgslcblas -lamd -lmuparser -lz -lgfortran -lcrypto
++EXTLIBS2 = -lgsl -ltaucs -lmetis -lscalapack -lflexiblas -lgslcblas -lamd -lmuparser -lz -lgfortran -lcrypto
+ EXTLIBS3 = -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lm
+
+ ################################################################################
+@@ -55,8 +55,8 @@ install: $(INLA)
+ 	 done; \
+ 	 install -m755 $(INLA) $(PREFIX)/bin/$(INLA);\
+ 	 install -m755 $(INLA) $(PREFIX)/bin/$(INLA);\
+-	 rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete doc/* $(PREFIX)/doc/inla; \
+-	 rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete examples/* $(PREFIX)/doc/inla/examples; 
++	 # rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete doc/* $(PREFIX)/doc/inla; \
++	 # rsync -auv --no-p --no-o --no-g --chmod=ugo=rwX --delete examples/* $(PREFIX)/doc/inla/examples; 
+
+ clean:; -$(RM) $(OBJ) $(INLA)
+
+diff --git a/r-inla-Version_24.10.07-2.orig/inlaprog/src/eval.c b/r-inla-Version_24.10.07-2/inlaprog/src/eval.c
+index bc9819b..c352fca 100644
+--- a/r-inla-Version_24.10.07-2.orig/inlaprog/src/eval.c
++++ b/r-inla-Version_24.10.07-2/inlaprog/src/eval.c
+@@ -35,7 +35,7 @@
+ #include <stdio.h>
+
+ #if defined(INLA_WITH_MUPARSER)
+-#include <muParser/muParserDLL.h>
++#include <muParserDLL.h>
+ #endif
+
+ #include "GMRFLib/GMRFLib.h"
diff --git a/easybuild/easyconfigs/r/R-INLA/R-INLA-24.10.07_remove-hardcoding.patch b/easybuild/easyconfigs/r/R-INLA/R-INLA-24.10.07_remove-hardcoding.patch
@@ -0,0 +1,48 @@
+remove hardcoded paths from scripts
+authors: Denis Kristak (INUITS), Kenneth Hoste (HPC-UGent)
+Updated to 24.10.07: J. Sassmannshausen (Imperial College London/UK)
+diff --git a/r-inla-Version_24.10.07.orig/rinla/inst/bin/linux/64bit/fmesher.run b/r-inla-Version_24.10.07/rinla/inst/bin/linux/64bit/fmesher.run
+index 5a273e9..3195d02 100755
+--- a/r-inla-Version_24.10.07.orig/rinla/inst/bin/linux/64bit/fmesher.run
++++ b/r-inla-Version_24.10.07/rinla/inst/bin/linux/64bit/fmesher.run
+@@ -4,18 +4,6 @@ tmp=$(basename "$cmd")
+ prog=${tmp%%.run}
+ DIR=$(dirname "$cmd")
+
+-D=""
+-for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do
+-    if [ -d "$d" ]; then
+-	if [ -z "$D" ]; then
+-	    D="$d"
+-	else
+-	    D="$D:$d"
+-	fi
+-    fi
+-done
+-export LD_LIBRARY_PATH="$DIR/first:$D:$DIR:$LD_LIBRARY_PATH"
+-
+ if [ "${INLA_DEBUG}XX" != "XX" ]; then
+     echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
+     ldd -r "$DIR/$prog"
+diff --git a/r-inla-Version_24.10.07.orig/rinla/inst/bin/linux/64bit/inla.run b/r-inla-Version_24.10.07/rinla/inst/bin/linux/64bit/inla.run
+index 49a6424..555d007 100755
+--- a/r-inla-Version_24.10.07.orig/rinla/inst/bin/linux/64bit/inla.run
++++ b/r-inla-Version_24.10.07/rinla/inst/bin/linux/64bit/inla.run
+@@ -13,17 +13,6 @@ if [ ! -z ${R_HOME+x} ]; then
+     fi
+ fi
+
+-D=""
+-for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do
+-    if [ -d "$d" ]; then
+-	if [ -z "$D" ]; then
+-	    D="$d"
+-	else
+-	    D="$D:$d"
+-	fi
+-    fi
+-done
+-
+ if [ -n "${INLA_NATIVE_LD_LIBRARY_PATH}" ]; then
+     ## so we can revert back to old behaviour
+     export LD_LIBRARY_PATH="$DIR/first:$D:$DIR:$LD_LIBRARY_PATH"
diff --git a/easybuild/easyconfigs/r/Rmath/Rmath-4.4.1-foss-2023b.eb b/easybuild/easyconfigs/r/Rmath/Rmath-4.4.1-foss-2023b.eb
@@ -0,0 +1,47 @@
+# Easyconfig for Rmath
+# Author: Caspar van Leeuwen
+# SURFsara, Amsterdam, The Netherlands
+# Updated to 4.4.1: J. Sassmannshausen (Imperial College London/UK)
+
+easyblock = 'ConfigureMake'
+
+name = 'Rmath'
+version = '4.4.1'
+
+homepage = "https://www.r-project.org/"
+description = """Rmath is the standalone version of the R math library.
+ Rmath can be used in your own C/C++ routines."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+
+source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s/']
+sources = ['R-%(version)s.tar.gz']
+checksums = ['b4cb675deaaeb7299d3b265d218cde43f192951ce5b89b7bb1a5148a36b2d94d']
+
+dependencies = [
+    ('bzip2', '1.0.8'),
+    ('cURL', '8.3.0'),
+    ('libreadline', '8.2'),
+    ('PCRE2', '10.42'),
+    ('XZ', '5.4.4'),
+    ('zlib', '1.2.13')
+]
+
+# Copied from R-3.3.1-intel-2016b.eb.
+# Again, unsure if these affect R-math: R documentation doesn't specify.
+configopts = "--with-pic --enable-threads --with-x=no --with-pcre2"
+
+# Since we're only installing Rmath anyway, we don't care about R packages.
+configopts += " --with-recommended-packages=no"
+
+# To build Rmath, docs say you need to execute 'make' in src/nmath/standalone
+# https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Configuration-options
+prebuildopts = 'cd src/nmath/standalone;'
+preinstallopts = prebuildopts
+
+sanity_check_paths = {
+    'files': ['lib/libRmath.a', 'lib/libRmath.%s' % SHLIB_EXT, 'include/Rmath.h'],
+    'dirs': []
+}
+
+moduleclass = 'numlib'
diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-7.7.0-foss-2023b.eb
@@ -0,0 +1,26 @@
+name = 'SuiteSparse'
+version = '7.7.0'
+
+homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html'
+description = """SuiteSparse is a collection of libraries to manipulate sparse matrices."""
+
+toolchain = {'name': 'foss', 'version': '2023b'}
+toolchainopts = {'unroll': True, 'pic': True}
+
+source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive']
+sources = ['v%(version)s.tar.gz']
+checksums = ['529b067f5d80981f45ddf6766627b8fc5af619822f068f342aab776e683df4f3']
+
+builddependencies = [
+    ('CMake', '3.27.6'),
+    ('pkgconf', '2.0.3'),
+]
+
+dependencies = [
+    ('MPFR', '4.2.1'),
+]
+
+# uncomment the next row if need customization
+# cmake_options = ''
+
+moduleclass = 'numlib'