| Summary: | sci-mathematics/petsc-3.15.0: fails with USE="fftw -mpi" | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Fabio Rossi <rossi.f> |
| Component: | Current packages | Assignee: | Matthias Maier <tamiko> |
| Status: | RESOLVED FIXED | ||
| Severity: | normal | CC: | sam, sci-mathematics |
| Priority: | Normal | Keywords: | PATCH, PullRequest |
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| URL: | https://lists.mcs.anl.gov/pipermail/petsc-users/2021-November/044955.html | ||
| See Also: |
https://gitlab.com/petsc/petsc/-/merge_requests/4604 https://github.com/gentoo/gentoo/pull/23136 |
||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
emerge-info.txt.gz
petsc-3.15.0:20211124-192815.log.gz |
||
Created attachment 756109 [details]
emerge-info.txt.gz
Created attachment 756112 [details]
petsc-3.15.0:20211124-192815.log.gz
reported upstream in https://lists.mcs.anl.gov/pipermail/petsc-users/2021-November/044955.html, it seems is possible to patch petsc to avoid mandatory dep on fftw[mpi] (In reply to Fabio Rossi from comment #3) > reported upstream in > https://lists.mcs.anl.gov/pipermail/petsc-users/2021-November/044955.html, > it seems is possible to patch petsc to avoid mandatory dep on fftw[mpi] thank you! I have tested upstream merge request backporting to latest 3.16.0 which is not in portage yet. What do you prefer to do? A new bug for updating petsc first? repoman still complains about too large patch The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2c0aea17b396af99413234f7a84607817f31dbd3 commit 2c0aea17b396af99413234f7a84607817f31dbd3 Author: Fabio Rossi <rossi.f@inwind.it> AuthorDate: 2021-12-01 18:04:37 +0000 Commit: Sam James <sam@gentoo.org> CommitDate: 2021-12-01 21:25:12 +0000 sci-mathematics/petsc: version bump to 3.16.0 and bugfix The latest release is needed to backport the patch from upstream to solve the issue of Gentoo bug #827185 (build issue with USE="fftw -mpi"). Upstream fix is at https://gitlab.com/petsc/petsc/-/merge_requests/4604 Closes: https://bugs.gentoo.org/827185 Signed-off-by: Fabio Rossi <rossi.f@inwind.it> Closes: https://github.com/gentoo/gentoo/pull/23136 Signed-off-by: Sam James <sam@gentoo.org> sci-mathematics/petsc/Manifest | 2 + .../files/petsc-3.16.0-fix_sandbox_violation.patch | 15 ++ sci-mathematics/petsc/petsc-3.16.0.ebuild | 192 +++++++++++++++++++++ 3 files changed, 209 insertions(+) (In reply to Fabio Rossi from comment #5) > I have tested upstream merge request backporting to latest 3.16.0 which is > not in portage yet. What do you prefer to do? A new bug for updating petsc > first? Thank you! New version was fine but no new bug was needed (as you figured) (In reply to Fabio Rossi from comment #7) > repoman still complains about too large patch I compressed it and uploaded it to my devspace, thank you |
I am trying to emerge: [ebuild N ~] sci-mathematics/petsc-3.15.0::gentoo USE="X boost fftw fortran metis threads -afterimage -complex-scalars -cxx -debug -hdf5 -hypre -mpi -mumps -scotch -sparse -superlu" 0 KiB where [ebuild R ] sci-libs/fftw-3.3.9:3.0/3::gentoo USE="fortran openmp threads -doc -mpi -test (-zbus)" ABI_X86="(64) -32 (-x32)" CPU_FLAGS_X86="sse sse2 -avx -avx2 -fma3 -fma4" 0 KiB but I get the following error: ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Did not find package MPI needed by fftw. Enable the package using --with-mpi ******************************************************************************* * ERROR: sci-mathematics/petsc-3.15.0::gentoo failed (configure phase): * econf failed * * Call stack: * ebuild.sh, line 127: Called src_configure * environment, line 2790: Called econf 'scrollOutput=1' 'FFLAGS=-O2 -pipe -fPIC' 'CFLAGS=-march=core2 -O2 -pipe -fPIC' 'CXXFLAGS=-march=core2 -O2 -pipe -fPIC' 'LDFLAGS=-Wl,-O1 -Wl,--as-needed' '--prefix=/usr/lib64/petsc' '--with-shared-libraries' '--with-single-library' '--with-clanguage=c' '--with-petsc-arch=linux-gnu-c-opt' '--with-precision=double' '--with-gnu-compilers' '--with-blas-lapack-lib=-lblas -llapack ' '--with-debugging=0' '--with-mpi=0' '--with-cc=x86_64-pc-linux-gnu-gcc' '--with-cxx=x86_64-pc-linux-gnu-g++' '--with-fortran=1' '--with-fc=x86_64-pc-linux-gnu-gfortran' '--with-mpi-compilers=0' '--with-scalar-type=real' '--with-windows-graphics=0' '--with-matlab=0' '--with-cmake:BOOL=1' '--with-pthread=1' '--with-afterimage=0' '--without-hdf5' '--with-hypre=0' '--without-suitesparse' '--with-superlu=0' '--with-x' '--with-x11' '--with-ptscotch=0' '--with-scalapack=0' '--without-mumps' '--with-imagemagick=0' '--with-python=0' '--with-boost' '--with-fftw' * phase-helpers.sh, line 711: Called __helpers_die 'econf failed' * isolated-functions.sh, line 112: Called die * The specific snippet of code: * die "$@" * * If you need support, post the output of `emerge --info '=sci-mathematics/petsc-3.15.0::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-mathematics/petsc-3.15.0::gentoo'`. * The complete build log is located at '/var/log/portage/build/sci-mathematics/petsc-3.15.0:20211124-192815.log.gz'. * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-mathematics/petsc-3.15.0/temp/build.log.gz'. * The ebuild environment file is located at '/var/tmp/portage/sci-mathematics/petsc-3.15.0/temp/environment'. * Working directory: '/var/tmp/portage/sci-mathematics/petsc-3.15.0/work/petsc-3.15.0' * S: '/var/tmp/portage/sci-mathematics/petsc-3.15.0/work/petsc-3.15.0'