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{numlib}[foss/2021a] PETSc v3.17.0 w/ Python 3.9.5 #15519

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{numlib}[foss/2021a] PETSc v3.17.0 w/ Python 3.9.5 #15519

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2a00ed0
adding easyconfigs: PETSc-3.17.0-foss-2021a.eb and patches: webclient…
May 18, 2022
0129118
Tidied up configopts, move Eigen to builddeps
May 18, 2022
1bb8ab8
True replaced with SYSTEM
Oct 13, 2022
cbb3569
HDF5 downgraded to 1.10.7
Oct 13, 2022
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84 changes: 84 additions & 0 deletions easybuild/easyconfigs/p/PETSc/PETSc-3.17.0-foss-2021a.eb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,84 @@
# Updated to version 3.17.0 with significantly more modules added
# J. Sassmannshausen ICL/UK

easyblock = 'ConfigureMake'

name = 'PETSc'
version = '3.17.0'

homepage = 'https://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.

This installation is build with significant amounts of modules in it compared to previous versions."""

toolchain = {'name': 'foss', 'version': '2021a'}
toolchainopts = {'openmp': True, 'usempi': True, 'pic': True}

source_urls = [
'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/',
]
sources = [SOURCELOWER_TAR_GZ]
patches = [
'webclient-3.17.0.patch',
]
checksums = [
'96d5aca684e1ce1425891a620d278773c25611cb144165a93b17531238eaaf8a', # petsc-3.17.0.tar.gz
'2ba253df42853385e2683dbc87dfcb66d4ce4bcd84e054efa8f466274f49bc81', # webclient-3.17.0.patch
]

builddependencies = [('CMake', '3.20.1')]

dependencies = [
('Python', '3.9.5'),
('SciPy-bundle', '2021.05'),
('Boost', '1.76.0'),
('METIS', '5.1.0'),
('SCOTCH', '6.1.0'),
('MUMPS', '5.4.0', '-metis'),
('SuiteSparse', '5.10.1', '-METIS-5.1.0'),
('Hypre', '2.21.0'),
('zlib', '1.2.11'),
('BLIS', '0.8.1'),
('Szip', '2.1.1'),
('HDF5', '1.12.1'),
('Eigen', '3.3.9'),

@jfgrimm jfgrimm May 18, 2022

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Eigen should only need to be a build dependency (since it's header-only). I imagine googletest isn't a runtime requirement either

@sassy-crick sassy-crick May 18, 2022

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True. I forgot about Eigen being only header. I was quite happy that it all worked after 2 days of playing with it to be honest. :-)

('GMP', '6.2.1'),
('GSL', '2.7'),
('libjpeg-turbo', '2.0.6'),
('libpng', '1.6.37'),
('giflib', '5.2.1'),
('OpenSSL', '1.1', '', True),
('libyaml', '0.2.5'),
('zstd', '1.4.9'),
('Mmg', '5.6.0'),
('MPFR', '4.1.0'),
('googletest', '1.11.0'),
('muParser', '2.3.3'),
('ParMETIS', '4.0.3'),
]

# enabling --with-mpi4py seems to be totally broken, leads to make errors like:
# No rule to make target 'mpi4py-build'
configopts = '--configModules=PETSc.Configure --optionsModule=config.compilerOptions '
configopts += '--LIBS="-lm -lpthread -lrt" --with-mpi4py=0 '
configopts += '--CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -fPIC" '
configopts += '--CXXFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -fPIC '
configopts += '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --with-mpi=1 --with-build-step-np=4 '
configopts += '--FFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -fPIC" '
configopts += '--with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 '
configopts += '--with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-scalapack=1 '
configopts += '--with-blaslapack-lib="[/home/sassy/apps/software/FlexiBLAS/3.0.4-GCC-10.3.0/lib/'
configopts += 'libflexiblas.a,libgfortran.a]" '

@jfgrimm jfgrimm May 18, 2022

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this could do with cleaning up, probably something along the lines of:

Suggested change
configopts += '--LIBS="-lm -lpthread -lrt" --with-mpi4py=0 '
configopts += '--CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -fPIC" '
configopts += '--CXXFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -fPIC '
configopts += '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --with-mpi=1 --with-build-step-np=4 '
configopts += '--FFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno -fopenmp -fPIC" '
configopts += '--with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 '
configopts += '--with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-scalapack=1 '
configopts += '--with-blaslapack-lib="[/home/sassy/apps/software/FlexiBLAS/3.0.4-GCC-10.3.0/lib/'
configopts += 'libflexiblas.a,libgfortran.a]" '
configopts += '--LIBS="$LIBS -lrt" --with-mpi4py=0 '
configopts += '--CFLAGS="$CFLAGS" '
configopts += '--CXXFLAGS="$CXXFLAGS '
configopts += '-DOMPI_SKIP_MPICXX -DMPICH_SKIP_MPICXX" --with-mpi=1 --with-build-step-np=4 '
configopts += '--FFLAGS="$FFLAGS" '
configopts += '--with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0 '
configopts += '--with-windows-graphics=0 --with-numpy=1 --with-fftw=1 --with-scalapack=1 '
configopts += '--with-blaslapack-lib="$BLAS_LAPACK_LIB_DIR"
'

@sassy-crick sassy-crick May 18, 2022

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Thanks for the suggestion. much appreciated. The "$BLAS_LAPACK_LIB_DIR" is actually not needed, what is needed are the two libs libflexiblas.a,libgfortran.a which I replaced with -lflexiblas -lgfortran to stick to dynamic libs.
Please have a look at the log file to make sure I am not accidentally build it with the wrong flags. From what I can see, it is all working as intended but that does not mean it is correct.

configopts += '--with-python=1 --with-boost=1 --with-metis=1 -with-ptscotch=1 --with-mumps=1 '
configopts += '--with-hypre=1 --with-suitesparse=1 --with-hwloc=1 --with-openmp=1 --with-zlib=1 --with-blis=1 '
configopts += '--with-hdf5=1 --with-eigen=1 --with-parmetis=1 --with-gmp=1 --with-gsl=1 --with-libjpeg=1 '
configopts += '--with-libpng=1 --with-yaml=1 --with-zstd=1 --with-ssl=1 --with-triangle=0 --with-giflib=1 '

sanity_check_paths = {
'files': ['lib/libpetsc.%s' % SHLIB_EXT],
'dirs': ['include', 'share']
}

moduleclass = 'numlib'
69 changes: 69 additions & 0 deletions easybuild/easyconfigs/p/PETSc/webclient-3.17.0.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,69 @@
Based on https://gitlab.com/petsc/petsc/-/merge_requests/5257
Author: J. Sassmannshausen / ICL (UK)
diff --git a/petsc-3.17.0.orig/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py b/petsc-3.17.0/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py
index ecc3b03..6c6c354 100755
--- a/petsc-3.17.0.orig/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py
+++ b/petsc-3.17.0/config/examples/arch-ci-freebsd-cxx-cmplx-pkgs-dbg.py
@@ -36,6 +36,7 @@ configure_options = [
'--with-mpi-f90module-visibility=0',
'--download-kokkos=1',
'--download-kokkos-kernels=1',
+ '--with-ssl=1',
]

if __name__ == '__main__':
diff --git a/petsc-3.17.0.orig/config/examples/arch-ci-linux-gcc-pkgs-opt.py b/petsc-3.17.0/config/examples/arch-ci-linux-gcc-pkgs-opt.py
index 8828156..132e3d6 100755
--- a/petsc-3.17.0.orig/config/examples/arch-ci-linux-gcc-pkgs-opt.py
+++ b/petsc-3.17.0/config/examples/arch-ci-linux-gcc-pkgs-opt.py
@@ -28,6 +28,7 @@ configure_options = [
'--download-amrex',
'--download-hypre',
'--download-ks',
+ '--with-ssl=1',
]

if __name__ == '__main__':
diff --git a/petsc-3.17.0.orig/src/sys/webclient/box.c b/petsc-3.17.0/src/sys/webclient/box.c
index d306966..eb2fac7 100644
--- a/petsc-3.17.0.orig/src/sys/webclient/box.c
+++ b/petsc-3.17.0/src/sys/webclient/box.c
@@ -304,9 +304,9 @@ PetscErrorCode PetscBoxUpload(MPI_Comm comm,const char access_token[],const char
PetscCall(PetscPushJSONValue(body,"mimeType","text.html",len));
PetscCall(PetscStrcat(body,","));
PetscCall(PetscPushJSONValue(body,"description","a file",len));
- ierr = PetscStrcat(body, "}\r\n\r\n"
- "--foo_bar_baz\r\n"
- "Content-Type: text/html\r\n\r\n");PetscCall(ierr);
+ PetscCall(PetscStrcat(body, "}\r\n\r\n"
+ "--foo_bar_baz\r\n"
+ "Content-Type: text/html\r\n\r\n"));
PetscCall(PetscStrlen(body,&blen));
fd = fopen (filename, "r");
PetscCheck(fd,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to open file: %s",filename);
diff --git a/petsc-3.17.0.orig/src/sys/webclient/client.c b/petsc-3.17.0/src/sys/webclient/client.c
index dfe6b12..350cac9 100644
--- a/petsc-3.17.0.orig/src/sys/webclient/client.c
+++ b/petsc-3.17.0/src/sys/webclient/client.c
@@ -123,7 +123,7 @@ static PetscErrorCode PetscHTTPBuildRequest(const char type[],const char url[],c

if (header) {
PetscCall(PetscStrendswith(header,"\r\n",&flg));
- PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"header must end with \\r\");
+ PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"header must end with \\r\\n");
}

PetscCall(PetscStrlen(type,&typelen));
diff --git a/petsc-3.17.0.orig/src/sys/webclient/google.c b/petsc-3.17.0/src/sys/webclient/google.c
index 8626b7c..c66f8cc 100644
--- a/petsc-3.17.0.orig/src/sys/webclient/google.c
+++ b/petsc-3.17.0/src/sys/webclient/google.c
@@ -158,7 +158,7 @@ PetscErrorCode PetscGoogleDriveUpload(MPI_Comm comm,const char access_token[],co
fd = fopen (filename, "r");
PetscCheck(fd,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to open file: %s",filename);
rd = fread (body+blen, sizeof (unsigned char), sb.st_size, fd);
- PetscCheckFalse(rd != (size_t) sb.st_size,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to read entire file: %s %d %d",filename,(int)rd,sb.st_size);
+ PetscCheckFalse(rd != (size_t) sb.st_size,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Unable to read entire file: %s %d %d",filename,(int)rd,(int)sb.st_size);
fclose(fd);
body[blen + rd] = 0;
ierr = PetscStrcat(body,"\r\n\r\n"