Legacy dealii 9.4.1 and PETSc/3.16.6 for StdEnv/2023 (otrs 0277905)

easybuild/easyconfigs/d/dealii/dealii-9.4.1-foss-20203a.eb

@@ -0,0 +1,117 @@
+easyblock = 'CMakeMake'
+
+name = 'dealii'
+version = '9.4.1'
+
+homepage = 'http://www.dealii.org/'
+description = """A C++ software library supporting the creation of finite element codes and an open community of users and developers."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+#toolchain = {'name': 'gofb', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'pic': True, 'strict': True}
+
+source_urls = ['https://github.com/dealii/%(namelower)s/releases/download/v%(version)s']
+sources = ['%(namelower)s-%(version)s.tar.gz']
+patches = ['dealii-9.4.1-step70-boost.patch']
+checksums = [
+  'bfe5e4bf069159f93feb0f78529498bfee3da35baf5a9c6852aa59d7ea7c7a48',
+  '6fbcdbe0c41709356f76c2142c0fd81ef56dd19b292f7a90d8d0bc39b15a1536',
+]
+
+# Note: this package is often built with software called candi
+# (due to it's specific dependencies/requirements)
+#    https://aspect-documentation.readthedocs.io/en/latest/user/install/local-installation/using-candi.html
+# This isn't feasible with easybuild, but the candi page has a good test afterwards to ensure
+# it's built correctly:
+#    cp -R $EBROOTDEALII/examples/step-32 .
+#    cd step-32
+#    cmake . && make
+#    mpirun -n 2 ./step-32
+
+separate_build_dir = True
+
+builddependencies = [
+   ('CMake', '3.31.0'),
+   ('Boost', '1.82.0'),
+   ('SymEngine', '0.14.0'),
+   ('nanoflann', '1.7.1'),
+]
+
+dependencies = [
+   ('p4est', '2.8.6'),
+   ('GSL', '2.7'),
+   ('SuiteSparse', '5.13.0'),
+   ('tbb', '2021.10.0'),
+   ('SUNDIALS', '6.6.0'),
+   ('gmsh', '4.13.1'),
+   ('ADOL-C', '2.7.2'),
+   ('arpack-ng', '3.9.1'),
+   ('ASSIMP', '5.2.5'),
+   ('HDF5', '1.14.2', '-mpi'),
+   ('METIS', '5.1.0'),
+   ('muParser', '2.3.4'),
+   ('netCDF-C++4', '4.3.1', '-mpi'),
+   ('PETSc', '3.16.6', '-64bits'),
+   ('SLEPc', '3.16.3', '-64bits'),
+   ('occt', '7.7.1'),
+   ('Trilinos', '13.4.1'),
+   ('METIS', '5.1.0'),
+   ('LLVM', '16.0.6'),
+]
+
+preconfigopts = 'export TRILINOS_DIR=$EBROOTTRILINOS && '
+preconfigopts += 'declare -A ARCH_MAP=( [sse3]=SSE2 [avx]=AVX [avx2]=AVX [avx512]=AVX512 ) && '
+
+configopts = '-DDEAL_II_ALLOW_PLATFORM_INTROSPECTION=OFF '
+configopts += '-DDEAL_II_HAVE_${ARCH_MAP[$RSNT_ARCH]}=ON '
+configopts += '-DDEAL_II_WITH_BOOST=ON -DBOOST_DIR=$EBROOTBOOST '
+configopts += '-DDEAL_II_WITH_P4EST=ON '
+configopts += '-DDEAL_II_WITH_MPI=ON '
+configopts += '-DDEAL_II_WITH_TRILINOS=ON '
+configopts += '-DTBB_DIR=$EBROOTTBB '
+configopts += '-DTrilinos_ENABLE_Sacado=ON '
+configopts += '-DTrilinos_ENABLE_Stratimikos=ON '
+configopts += '-DTrilinos_FIND_COMPONENTS="Pike;PikeImplicit;PikeBlackBox;TrilinosCouplings;Panzer;PanzerMiniEM;PanzerAdaptersSTK;PanzerDiscFE;PanzerDofMgr;PanzerCore;Piro;ROL;Stokhos;Tempus;Rythmos;ShyLU;ShyLU_DD;ShyLU_DDCommon;ShyLU_DDFROSch;ShyLU_DDBDDC;Zoltan2;Zoltan2Sphynx;MueLu;Moertel;NOX;Phalanx;Percept;STK;STKExprEval;STKDoc_tests;STKUnit_tests;STKBalance;STKTools;STKTransfer;STKSearchUtil;STKSearch;STKUnit_test_utils;STKNGP_TEST;STKIO;STKMesh;STKTopology;STKSimd;STKUtil;STKMath;Compadre;Intrepid2;Intrepid;Teko;FEI;Stratimikos;Ifpack2;Anasazi;Komplex;SEACAS;SEACASEx2ex1v2;SEACASTxtexo;SEACASNumbers;SEACASNemspread;SEACASNemslice;SEACASMat2exo;SEACASMapvar-kd;SEACASMapvar;SEACASMapvarlib;SEACASExplore;SEACASGrepos;SEACASGenshell;SEACASGen3D;SEACASGjoin;SEACASFastq;SEACASEx1ex2v2;SEACASExo_format;SEACASExotxt;SEACASExomatlab;SEACASExodiff;SEACASExo2mat;SEACASEpu;SEACASEjoin;SEACASConjoin;SEACASBlot;SEACASAprepro;SEACASAlgebra;SEACASPLT;SEACASSVDI;SEACASSuplibCpp;SEACASSuplibC;SEACASSuplib;SEACASSupes;SEACASAprepro_lib;SEACASChaco;SEACASIoss;SEACASNemesis;SEACASExoIIv2for32;SEACASExodus_for;SEACASExodus;Amesos2;ShyLU_Node;ShyLU_NodeTacho;ShyLU_NodeHTS;Belos;ML;Ifpack;Zoltan2Core;Pamgen;Amesos;Galeri;AztecOO;Pliris;Isorropia;Xpetra;Thyra;ThyraTpetraAdapters;ThyraEpetraExtAdapters;ThyraEpetraAdapters;ThyraCore;Domi;TrilinosSS;Tpetra;TpetraCore;TpetraTSQR;TpetraClassic;EpetraExt;Triutils;Shards;Zoltan;Epetra;MiniTensor;Sacado;RTOp;KokkosKernels;Teuchos;TeuchosKokkosComm;TeuchosKokkosCompat;TeuchosRemainder;TeuchosNumerics;TeuchosComm;TeuchosParameterList;TeuchosParser;TeuchosCore;Kokkos;KokkosAlgorithms;KokkosContainers;KokkosCore;Gtest;TrilinosATDMConfigTests;TrilinosFrameworkTests" '
+configopts += '-DCMAKE_BUILD_TYPE=Release '
+configopts += '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON '
+configopts += '-DBUILD_SHARED_LIBS=ON '
+configopts += '-DCMAKE_C_COMPILER=mpicc '
+configopts += '-DCMAKE_CXX_COMPILER=mpiCC '
+configopts += '-DCMAKE_Fortran_COMPILER=mpif90 '
+configopts += '-DLAPACK_FOUND=true '
+configopts += '-DLAPACK_LIBRARIES="$LIBLAPACK" '
+configopts += '-DSCALAPACK_DIR=$SCALAPACK_LIB_DIR '
+configopts += '-DSCALAPACK_LIBRARIES="$LIBSCALAPACK -lm" '
+configopts += '-DP4EST_DIR=${EBROOTP4EST} '
+configopts += '-DTRILINOS_DIR=${EBROOTTRILINOS} '
+configopts += '-DGSL_LIBRARIES=${EBROOTGSL}/lib/libgsl.a '
+configopts += '-DGSL_INCLUDE_DIRS=${EBROOTGSL}/include '
+configopts += '-DDEAL_II_HAVE_USABLE_FLAGS_RELEASE=ON '
+configopts += '-DGMSH_DIR=$EBROOTGMSH '
+configopts += '-DSUNDIALS_DIR=$EBROOTSUNDIALS '
+configopts += '-DUMFPACK_DIR=$EBROOTSUITESPARSE/UMFPACK '
+configopts += '-DZLIB_INCLUDE_DIR=$EBROOTGENTOO/include '
+configopts += '-DZLIB_LIBRARY=$EBROOTGENTOO/lib64/libz.so '
+configopts += '-DADOLC_DIR=$EBROOTADOLMINC '
+configopts += '-DARPACK_DIR=$EBROOTARPACKMINNG '
+configopts += '-DASSIMP_DIR=$EBROOTASSIMP '
+configopts += '-DHDF5_DIR=$EBROOTHDF5 '
+configopts += '-DMETIS_DIR=$EBROOTMETIS '
+configopts += '-DMETIS_INCLUDE_DIR=$EBROOTMETIS/include '
+configopts += '-DMETIS_LIBRARY=$EBROOTMETIS/lib/libmetis.so '
+configopts += '-DMUPARSER_DIR=$EBROOTMUPARSER '
+configopts += '-DNETCDF_DIR=$EBROOTNETCDFMINCPLUSPLUS '
+configopts += '-DPETSC_DIR=$EBROOTPETSC '
+configopts += '-DSLEPC_DIR=$EBROOTSLEPC '
+configopts += '-DDEAL_II_LINKER_FLAGS=-L$EBROOTGENTOO/lib64/fltk '
+
+# Too parallel is too slow, and may cause build/tests to fail:
+
+maxparallel = 10
+
+sanity_check_paths = {
+    'files': [('lib/libdeal_II.so')],
+    'dirs': ['include', 'lib'],
+}
+
+moduleclass = 'numlib'

easybuild/easyconfigs/d/dealii/dealii-9.4.1-step70-boost.patch

@@ -0,0 +1,31 @@
+From 89b89043c3fc45883e9b11bba6276a23cfd9feb3 Mon Sep 17 00:00:00 2001
+From: David Wells <drwells@email.unc.edu>
+Date: Thu, 8 Dec 2022 10:09:03 -0500
+Subject: [PATCH] step-70: remove a dependency on boost.
+
+---
+ examples/step-70/step-70.cc | 10 ++++++----
+ 1 file changed, 6 insertions(+), 4 deletions(-)
+
+diff --git a/examples/step-70/step-70.cc b/examples/step-70/step-70.cc
+index 2ce4d97488..879e5c1641 100644
+--- a/examples/step-70/step-70.cc
++++ b/examples/step-70/step-70.cc
+@@ -837,8 +835,12 @@ namespace Step70
+         const auto &manifold_id   = pair.first;
+         const auto &cad_file_name = pair.second;
+
+-        const auto extension = boost::algorithm::to_lower_copy(
+-          cad_file_name.substr(cad_file_name.find_last_of('.') + 1));
++        std::string extension =
++          cad_file_name.substr(cad_file_name.find_last_of('.') + 1);
++        std::transform(extension.begin(),
++                       extension.end(),
++                       extension.begin(),
++                       [](const char c) -> char { return std::tolower(c); });
+
+         TopoDS_Shape shape;
+         if (extension == "iges" || extension == "igs")
+-- 
+2.50.1
+

easybuild/easyconfigs/p/PETSc/PETSc-3.16.6-foss-2023a-64bits.eb

@@ -0,0 +1,118 @@
+# Built with EasyBuild version 5.1.1 on 2025-09-14_15-13-05
+name = 'PETSc'
+version = "3.16.6"
+versionsuffix = '-64bits'
+
+homepage = 'http://www.mcs.anl.gov/petsc'
+description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the
+ scalable (parallel) solution of scientific applications modeled by partial differential equations."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'pic': True}
+
+source_urls = ['https://web.cels.anl.gov/projects/%(namelower)s/download/release-snapshots/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = [
+    'bfc836b52f57686b583c16ab7fae0c318a7b28141ca01656ad673c8ca23037fa',
+]
+
+dependencies = [
+    ('HDF5', '1.14.2', '-mpi'),
+]
+
+# For the extension
+builddependencies = [
+    ('SciPy-Stack', '2025a'),
+    ('mpi4py', '4.0.3'),
+]
+
+multi_deps = {'Python': ['3.10']}
+multi_deps_extensions_only = True
+
+configopts = " ".join([
+    '--with-hdf5=1',
+    '--with-hdf5-dir=$EBROOTHDF5',
+    '--with-cxx-dialect=C++14',
+    '--with-memalign=64',
+    '--with-python=no',
+    '--with-mpi4py=no',
+    '--with-64-bit-indices=1',
+])
+# Fix usage of MAKEFLAGS (can't add to start as may be missing leading dash and can't add to end as contains --)
+prebuildopts = 'sed -i -e \'s/MAKEFLAGS="\\([^"]*\\) $(MAKEFLAGS)" \\+\\([^ ]*\\)/\\2 \\1/\' lib/petsc/conf/* && '
+
+
+download_deps = [
+    'triangle',
+    'hpddm',
+    'strumpack',
+]
+
+postinstallcmds = [
+    'ln -sf %(installdir)s/lib/%(namelower)s/bin %(installdir)s/bin',
+    'ln -sf %(installdir)s/lib/%(namelower)s/conf %(installdir)s/conf',
+]
+
+keepsymlinks = True
+
+shared_libs = 1
+
+download_deps_static = [
+    'f2cblaslapack',
+    'mumps',
+    'ptscotch',
+    #'superlu',
+    'superlu_dist',
+    'parmetis',
+    'metis',
+    #'ml',
+    'SuiteSparse',
+    'hypre',
+    'prometheus',
+    'spooles',
+    #'chaco',
+    'slepc',
+    #'spai',
+    #'party',
+]
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    # disable "pip check" which would fail with several:
+    # > $PACKAGE requires (numpy|mpi4py|msgpack), which is not installed 
+    'sanity_pip_check': False,
+}
+exts_list = [
+    ('petsc4py', version, {
+        'buildopts': '#',
+        'check_ldshared': False,
+        'modulename': 'petsc4py',
+        'preconfigopts': '#',
+        #'preconfigopts': 'find -name \'*.c\' -print0 | xargs -0 sed -i -e \'/# *include.*longintrepr/d\'',
+        'use_pip': True,
+        'runtest': False,
+        'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'],
+        'checksums' : ['a9b4ed19ca2e62b38da51ac3a70539d9581a1354cc4464c93963d7e95bd8ef66'],
+    }),
+]
+
+exts_filter = ("python -c 'import %(ext_name)s'", '')
+
+sanity_check_paths = {
+    'files': [
+        'lib/libpetsc.so',
+    ],
+    'dirs': [
+        'bin',
+        'conf',
+        'include',
+        'lib',
+        'share',
+        'lib/python%(pyshortver)s/site-packages'
+    ]
+}
+
+moduleclass = 'numlib'
+modluafooter = """
+family("%(namelower)s")
+"""

easybuild/easyconfigs/s/SLEPc/SLEPc-3.16.3-foss-2023a.eb

@@ -0,0 +1,52 @@
+name = 'SLEPc'
+version = '3.16.3'
+versionsuffix = '-64bits'
+
+homepage = 'https://slepc.upv.es/'
+description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution
+ of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for
+ either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a
+ partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems."""
+
+toolchain = {'name': 'foss', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'openmp': True}
+
+source_urls = ['https://slepc.upv.es/download/distrib']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['b92bd170632a3de4d779f3f0697e7cb9b663e2c34606c9e97d899d7c1868014e']
+
+# sources = ['%(namelower)s-%(version)s.tar.gz']
+dependencies = [('PETSc', '3.16.6', '-64bits')]
+# For the extension
+builddependencies = [
+    ('SciPy-Stack', '2025a'),
+    ('mpi4py', '4.0.3'),
+]
+
+multi_deps = {'Python': ['3.10']}
+multi_deps_extensions_only = True
+
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    # disable "pip check" which would fail with several:
+    # > $PACKAGE requires (numpy|mpi4py|msgpack), which is not installed 
+    'sanity_pip_check': False,
+}
+exts_list = [
+    ('slepc4py', '3.16.3', {
+        'modulename': 'slepc4py',
+        'source_urls': [PYPI_SOURCE],
+        'checksums' : ['d97652efe60163d30c24eb1ef1b1ba98bb8239fd7452bdf8207c2505da48d77e'],
+        'preconfigopts': '#',
+	'check_ldshared': False,
+	'buildopts': '#',
+        'runtest': False,
+    }),
+]
+exts_filter = ("python -c 'import %(ext_name)s'", '')
+
+petsc_arch = 'installed-arch-linux2-c-opt'
+
+#modextrapaths = {'EBPYTHONPREFIXES': [''],}
+
+moduleclass = 'numlib'

easybuild/easyconfigs/t/Trilinos/Trilinos-13.4.1-gofb-2023a.eb

@@ -0,0 +1,60 @@
+# Built with EasyBuild version 5.1.1 on 2025-08-23_23-51-35
+name = 'Trilinos'
+version = "13.4.1"
+
+homepage = 'https://trilinos.org'
+description = """The Trilinos Project is an effort to develop algorithms and enabling technologies
+ within an object-oriented software framework for the solution of large-scale, complex multi-physics
+ engineering and scientific problems. A unique design feature of Trilinos is its focus on packages."""
+
+toolchain = {'name': 'gofb', 'version': '2023a'}
+toolchainopts = {'usempi': True, 'pic': True, 'strict': True}
+
+source_urls = [
+    'https://github.com/trilinos/Trilinos/archive'
+]
+sources = ['%%(namelower)s-release-%s.tar.gz' % '-'.join(version.split('.'))]
+patches = ['Trilinos-13.4.1.patch']
+checksums = [
+    '5465cbff3de7ef4ac7d40eeff9d99342c00d9d20eee0a5f64f0a523093f5f1b3',
+    'affdfb65504562d43bcb36d41dfc7641e6b72f11d643cee6bec3fa1e13aa41cb',
+]
+
+multi_deps_load_default = False
+multi_deps = {"Python": ["3.11"]}
+
+builddependencies = [
+    ('Boost', '1.82.0'),
+    ('netCDF', '4.9.2', '-mpi'),
+    ('MATIO', '1.5.26'),
+    ('SWIG', '4.1.1'),
+    ('CMake', '3.27.7'), 
+]
+
+preconfigopts  = "unset EBPYTHONPREFIXES && "
+preconfigopts += "pyver=$(python -c 'import sys; print(\"python%s.%s\"%sys.version_info[:2])') && "
+preconfigopts += "pip install numpy --prefix=%(installdir)s && "
+preconfigopts += "export PYTHONPATH=$PYTHONPATH:%(installdir)s/lib/$pyver/site-packages && "
+preconfigopts += "export CPATH=$CPATH:%(installdir)s/lib/$pyver/site-packages/numpy/core/include && "
+
+configopts  = '-DNetCDF_NEEDS_HDF5=ON -DShyLU_NodeTacho_ENABLE_EXAMPLES=OFF -DShyLU_Node_ENABLE_EXAMPLES=OFF '
+configopts += '-DXpetra_ENABLE_EXAMPLES=OFF -DXpetra_ENABLE_TESTS=OFF -DIfpack2_ENABLE_TESTS=OFF '
+configopts += '-DShyLU_DDFROSch_ENABLE_TESTS=OFF -DShyLU_DD_ENABLE_TESTS=OFF '
+configopts += '-DTrilinosCouplings_ENABLE_EXAMPLES=OFF -DMPI_BASE_DIR=$EBROOTOPENMPI'
+
+openmp = False
+
+build_shared_libs = True
+
+preinstallopts = preconfigopts
+
+postinstallcmds = [
+   "sed -i 's/PyTrilinos;//' %(installdir)s/lib/cmake/Trilinos/TrilinosConfig.cmake",
+]
+
+# too parallel is too slow because of memory requirements (results in swapping), and may cause build/tests to fail
+# building with 20 cores seems to require about 100GB of memory (peak usage)
+
+maxparallel = 10
+
+moduleclass = 'numlib'