easybuild-easyblocks
easybuild-easyblocks copied to clipboard
easybuilders
Latest suitesparse easyblock modified library paths and doesn't install CSparse libs
Latest suitesparse easyblock modified library paths and doesn't install CSparse libs which might cause installations that depend on SuiteSparse to fail, installation of those should be modified to find the libraries. But the issue of the missing CSparse library remains. Why was this lib removed in #3004? @appolloford
Installations that depend on SuiteSparse and might fail if not modified:
AUGUSTUS
CVXOPT
Trilinos
PETSc
igraph
Octave
OpenSees
DOLFIN
FreeFEM
Yade
ARPACK++
pyGIMLi
Installation of PETSc fails. Path to libs can be fixed but it also requires the CSparse lib.
Hi, I found some description from the SuiteSparse README
CSparse a concise sparse matrix package, developed for my
book, "Direct Methods for Sparse Linear Systems",
published by SIAM. Intended primarily for teaching.
Note that the code is (c) Tim Davis, as stated in the book.
For production, use CXSparse instead. In particular, both
CSparse and CXSparse have the same include filename: cs.h.
This package is used for the built-in DMPERM in MATLAB.
author: Tim Davis
CXSparse CSparse Extended. Includes support for complex matrices
and both int or long integers. Use this instead of CSparse
for production use; it creates a libcsparse.so (or *dylib on
the Mac) with the same name as CSparse. It is a superset
of CSparse. Any code that links against CSparse should
also be able to link against CXSparse instead.
author: Tim Davis, David Bateman
CSparse looks like the only one which is not installed by cmake. Although I don't see a libcsparse.so from CXSparse (libcxsparse.so instead), I guess it does this intentionally to avoid some potential conflict with CXSparse. I am wondering whether the softwares in the list can be linked to CXSparse instead? Otherwise, I may copy those CSparse libs manually.
At least for PETSc-3.19.2-foss-2022b.eb. I can successfully install that without CSpase. (require editing petsc easyblock)
Success:
AUGUSTUS/3.5.0-foss-2022b
CVXOPT-1.3.1-foss-2022a.eb (require revising path in easyconfig)
Not to forget that there are extensions on R which depend on suitesparse. We took upstream suitesparse.py because we had an old one pre-suitesparse 6. We have 7.1.0
Not to forget that there are extensions on R which depend on suitesparse. We took upstream suitesparse.py because we had an old one pre-suitesparse 6. We have 7.1.0
Which extensions are that? We don't have SuiteSparse listed as dependency in upstream R easyconfigs...
@SebastianAchilles can you paste the commented-out extensions of our R? I’m on vacations right now and don’t have access to Gitlab
Some easyconfigs need to be updated as well, such as CVXOPT-1.3.1-foss-2022a.eb. I have not checked all of them since there is a long list. I guess some of them will be archived soon. I am not sure whether I should update them at this moment.
from develop branch
./r/R-INLA/R-INLA-21.05.02-foss-2020b-R-4.0.4.eb
./i/igraph/igraph-0.9.4-foss-2021a.eb
./i/igraph/igraph-0.9.5-foss-2021b.eb
./t/Trilinos/Trilinos-13.4.1-foss-2022a.eb
./t/Trilinos/Trilinos-12.12.1-intel-2017b-Python-2.7.14.eb
./t/Trilinos/Trilinos-12.12.1-foss-2019b-Python-3.7.4.eb
./t/Trilinos/Trilinos-12.12.1-foss-2017b-Python-2.7.14.eb
./t/Trilinos/Trilinos-12.12.1-intel-2018a-Python-3.6.4.eb
./t/Trilinos/Trilinos-13.4.1-foss-2022a-zoltan.eb
./t/Trilinos/Trilinos-12.12.1-foss-2018a-Python-3.6.4.eb
./s/S4/S4-1.1.1-20180610-foss-2017b.eb
./a/ARPACK++/ARPACK++-2018.03.26_find-deps.patch
./a/ARPACK++/ARPACK++-2018.03.26-foss-2017b.eb
./a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021b.eb
./a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020b.eb
./a/AUGUSTUS/AUGUSTUS-3.3-foss-2018a.eb
./a/AUGUSTUS/AUGUSTUS-3.3.3-intel-2019b.eb
./a/AUGUSTUS/AUGUSTUS-3.3.3-foss-2019b.eb
./a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2018b-Python-2.7.15.eb
./a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022b.eb
./a/AUGUSTUS/AUGUSTUS-3.2.3-intel-2017a-Python-2.7.13.eb
./a/AUGUSTUS/AUGUSTUS-3.5.0-foss-2022a.eb
./a/AUGUSTUS/AUGUSTUS-3.3.2-foss-2017b-Python-2.7.14.eb
./a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017a-Python-2.7.13.eb
./a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2021a.eb
./a/AUGUSTUS/AUGUSTUS-3.4.0-foss-2020a.eb
./a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2019a.eb
./a/AUGUSTUS/AUGUSTUS-3.3.2-intel-2017b-Python-2.7.14.eb
./f/FreeFem++/FreeFem++-3.58-foss-2017b-downloaded-deps.eb
./f/FreeFem++/FreeFem++-3.61-1-intel-2018a-downloaded-deps.eb
./f/FreeFem++/FreeFem++-3.60-intel-2018a-downloaded-deps.eb
./f/FreeFEM/FreeFEM-4.5-foss-2019b-Python-3.7.4.eb
./o/OpenSees/OpenSees-3.2.0-add_Makefile_def_parallel.patch
./o/OpenSees/OpenSees-3.2.0-add_Makefile_def_sequential.patch
./o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2.eb
./o/OpenSees/OpenSees-3.2.0-intel-2020a-Python-3.8.2-parallel.eb
./o/Octave/Octave-4.0.3-intel-2016b.eb
./o/Octave/Octave-4.2.1-intel-2017a.eb
./o/Octave/Octave-5.1.0-foss-2019a.eb
./o/Octave/Octave-6.2.0-foss-2020b.eb
./o/Octave/Octave-4.2.2-foss-2018a.eb
./o/Octave/Octave-4.2.1-foss-2018a.eb
./o/Octave/Octave-7.1.0-foss-2021b.eb
./o/Octave/Octave-4.0.0-foss-2016a.eb
./o/Octave/Octave-4.4.1-foss-2018b.eb
./o/Octave/Octave-4.2.1-intel-2016b.eb
./o/Octave/Octave-4.2.1-intel-2017a-mt.eb
./o/Octave/Octave-5.1.0-foss-2019b.eb
./c/CVXOPT/CVXOPT-1.1.9-intel-2017a-Python-2.7.13.eb
./c/CVXOPT/CVXOPT-1.2.1-intel-2018a-Python-3.6.4.eb
./c/CVXOPT/CVXOPT-1.2.6-foss-2020b.eb
./c/CVXOPT/CVXOPT-1.1.9-fix-setup-py.patch
./c/CVXOPT/CVXOPT-1.2.3-foss-2019a.eb
./c/CVXOPT/CVXOPT-1.2.4-intel-2019b-Python-3.7.4.eb
./c/CVXOPT/CVXOPT-1.2.3-intel-2018b-Python-3.6.6.eb
./c/CVXOPT/CVXOPT-1.2.6-foss-2021a.eb
./c/CVXOPT/CVXOPT-1.2.1-fix-setup-py.patch
./c/CVXOPT/CVXOPT-1.3.1-foss-2022a.eb
./c/CVXOPT/CVXOPT-1.3.1_fix-setup-py.patch
./d/DOLFIN/DOLFIN-2018.1.0.post1-foss-2018a-Python-3.6.4.eb
./d/DOLFIN/DOLFIN-2019.1.0.post0-foss-2019b-Python-3.7.4.eb
./d/DOLFIN/DOLFIN-1.6.0_fix-SuiteSparse-4.3.patch
./y/Yade/Yade-2018.02b-intel-2018a-Python-2.7.14.eb
./p/PETSc/PETSc-3.12.4-foss-2020a-Python-3.8.2.eb
./p/PETSc/PETSc-3.7.2-intel-2016a-Python-2.7.11.eb
./p/PETSc/PETSc-3.12.4-intel-2019b-Python-2.7.16.eb
./p/PETSc/PETSc-3.18.4-intel-2021b.eb
./p/PETSc/PETSc-3.7.5-intel-2016b-downloaded-deps.eb
./p/PETSc/PETSc-3.9.3-foss-2018a.eb
./p/PETSc/PETSc-3.11.1-intel-2019a-Python-3.7.2.eb
./p/PETSc/PETSc-3.12.4-foss-2019b-Python-3.7.4.eb
./p/PETSc/PETSc-3.15.1-intel-2021a.eb
./p/PETSc/PETSc-3.11.0-foss-2018b-downloaded-deps.eb
./p/PETSc/PETSc-3.8.3-foss-2017b-downloaded-deps.eb
./p/PETSc/PETSc-3.12.4-intel-2020a-Python-3.8.2.eb
./p/PETSc/PETSc-3.9.3-intel-2018a.eb
./p/PETSc/PETSc-3.19.2-foss-2022b.eb
./p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb
./p/PETSc/PETSc-3.9.1-foss-2018a-downloaded-deps.eb
./p/PETSc/PETSc-3.14.4-foss-2020b.eb
./p/PETSc/PETSc-3.14.4-intel-2020b.eb
./p/PETSc/PETSc-3.11.1-foss-2019a-Python-3.7.2.eb
./p/PETSc/PETSc-3.15.1-foss-2021a.eb
./p/PETSc/PETSc-3.17.4-foss-2022a.eb
./p/PETSc/PETSc-3.12.4-intel-2019b-Python-3.7.4.eb
./p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb
./p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb
@appolloford Updating any easyconfigs using a deprecated toolchain is a useless effort, since those are archived in the 5.0.x branch already.
Now that we have the 2023b version of the common toolchains set in stone, anything older than 2021a (GCC 10.3.0) is deprecated; see also https://docs.easybuild.io/policies/toolchains
Are these the easyconfigs that have a dependency on SuiteSparse?
No changes are needed for PETSc-3.19.2-foss-2022b.eb imho, installing that works just fine with the updated PETSc easyblock?
CVXOPT is definitely broken, fails with:
cc1: fatal error: /software/SuiteSparse/5.13.0-foss-2022a-METIS-5.1.0/SuiteSparse_config/SuiteSparse_config.c: No such file or directory
Yes, the list is simply showing the easyconfigs with SuiteSparse dependency. PETSc and Trilinos easyconfigs should work fine with the new easyblock. I had a quick look on igraph, AUGUSTUS, Octave, and CVXOPT easyconfigs, which having toolchain later than 2021a, and it seems CVXOPT is the only one need updates. I will test them to make sure them work and probably also modify the CVXOPT easyblock.