| Summary: | sci-libs/fftw-3.3.8 : configure: error: could not find mpi library for --enable-mpi | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Toralf Förster <toralf> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED TEST-REQUEST | ||
| Severity: | normal | CC: | jorge.ramos, jstein, preed, zlogene |
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | All | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Bug Depends on: | 733576 | ||
| Bug Blocks: | |||
| Attachments: |
emerge-info.txt
emerge-history.txt environment etc.portage.tbz2 logs.tbz2 sci-libs:fftw-3.3.8:20191109-070937.log temp.tbz2 Fixes fftw-3.3.6_p2 ebuild for systems with no openmpi. |
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Description
Toralf Förster
2019-11-09 09:59:47 UTC
Created attachment 595522 [details]
emerge-info.txt
Created attachment 595524 [details]
emerge-history.txt
Created attachment 595526 [details]
environment
Created attachment 595528 [details]
etc.portage.tbz2
Created attachment 595530 [details]
logs.tbz2
Created attachment 595532 [details]
sci-libs:fftw-3.3.8:20191109-070937.log
Created attachment 595534 [details]
temp.tbz2
I started getting this with latest emerge --sync. I guess something must have stabilized. I ran into this problem starting ~last week myself; it's due to an assumption in the fftw 3.3.6_p2 and 3.3.8 ebuilds. For a reason I don't understand (and I'm sure someone will tell me), MPI functionality which was provided by the openmpi library was replaced by the mpich2 library last week; not sure if this is because the virtual changed, or what, but I have: > 1584881864: >>> emerge (23 of 23) sys-cluster/mpich2-1.5 to / > 1584881864: === (23 of 23) Cleaning (sys-cluster/mpich2-1.5::/usr/portage/sys-cluster/mpich2/mpich2-1.5.ebuild) > 1584881864: === (23 of 23) Compiling/Merging (sys-cluster/mpich2-1.5::/usr/portage/sys-cluster/mpich2/mpich2-1.5.ebuild) > 1584882013: === (23 of 23) Merging (sys-cluster/mpich2-1.5::/usr/portage/sys-cluster/mpich2/mpich2-1.5.ebuild) > 1584882015: >>> AUTOCLEAN: sys-cluster/mpich2:0 > 1584882019: === (23 of 23) Post-Build Cleaning (sys-cluster/mpich2-1.5::/usr/portage/sys-cluster/mpich2/mpich2-1.5.ebuild) > 1584882019: ::: completed emerge (23 of 23) sys-cluster/mpich2-1.5 to / > 1584882019: === Unmerging... (sys-cluster/openmpi-2.0.2) > 1584882025: >>> unmerge success: sys-cluster/openmpi-2.0.2 Anyway, fftw's configure will check for MPI_Init() in both -lmpi (openmpi's implementation) and -lmpich (mpich2's), and seems to happily use either. The problem is: the ebuild calls ./configure with -lmpi, which means it will _always_ try to link with libmpi, which means if you don't have openmpi on your system, then even though the link against -lmpich will succeed, the ./configure (and thus the build) will fail. Attaching a patch for 3.3.6 shortly, but building the patched ebuild locally gives: > make[1]: Leaving directory '/var/tmp/portage/sci-libs/fftw-3.3.6_p2-r1/work/fftw-3.3.6-pl2-longdouble-abi_x86_64.amd64/m4' > >>> Completed installing sci-libs/fftw-3.3.6_p2-r1 into /var/tmp/portage/sci-libs/fftw-3.3.6_p2-r1/image/ > > * Final size of build directory: 104832 KiB (102.3 MiB) > * Final size of installed tree: 9872 KiB ( 9.6 MiB) > > strip: x86_64-pc-linux-gnu-strip --strip-unneeded -N __gentoo_check_ldflags__ -R .comment -R .GCC.command.line -R .note.gnu.gold-version > /usr/lib64/libfftw3f_threads.so.3.5.6 > /usr/lib64/libfftw3f_omp.so.3.5.6 > /usr/lib64/libfftw3f.so.3.5.6 > /usr/lib64/libfftw3f_mpi.so.3.5.6 > /usr/bin/fftwf-wisdom > /usr/lib64/libfftw3.so.3.5.6 > /usr/lib64/libfftw3_threads.so.3.5.6 > /usr/lib64/libfftw3_omp.so.3.5.6 > /usr/lib64/libfftw3_mpi.so.3.5.6 > /usr/bin/fftw-wisdom > /usr/lib64/libfftw3l.so.3.5.6 > /usr/lib64/libfftw3l_threads.so.3.5.6 > /usr/lib64/libfftw3l_omp.so.3.5.6 > /usr/lib64/libfftw3l_mpi.so.3.5.6 > /usr/bin/fftwl-wisdom > > >>> Installing (1 of 1) sci-libs/fftw-3.3.6_p2-r1::localrepo > <<< !needed sym /usr/lib64/libmpi.so.20 > <<< !needed obj /usr/lib64/libmpi.so.20.0.2 > <<< !needed sym /usr/lib64/libopen-pal.so.20 > <<< !needed obj /usr/lib64/libopen-pal.so.20.2.0 > <<< !needed sym /usr/lib64/libopen-rte.so.20 > <<< !needed obj /usr/lib64/libopen-rte.so.20.1.0 > > >>> Recording sci-libs/fftw:3.0 in "world" favorites file... > >>> Auto-cleaning packages... The same patch should work for fftw-3.3.8, but I didn't try it. NOTE: I don't know if it's actually intentional that openmpi got blown away; perhaps that's actually the core issue here? Created attachment 626622 [details, diff]
Fixes fftw-3.3.6_p2 ebuild for systems with no openmpi.
Patch to fftw-3.3.6_p2 ebuild to fix the build on systems that only have mpich2 (and no openmpi) on them.
If I remember correctly that "-lmpi" had something to do with multilib. Have you tried that patch with ABI_X86="32 64"? (In reply to Christoph Junghans from comment #11) > If I remember correctly that "-lmpi" had something to do with multilib. Have > you tried that patch with ABI_X86="32 64"? I have not, and probably won't because doing so causes portage to want to rebuild a bunch of libraries that I'm not super-interested in dealing with. Interestingly enough, asking portage to do this causes a conflict between openmpi and mpich2 in the other opposite direction. > Calculating dependencies... done! > [ebuild R ] dev-libs/libltdl-2.4.6 ABI_X86="32*" > [ebuild R ] dev-libs/libevent-2.1.8 ABI_X86="32*" > [ebuild R ] sys-process/numactl-2.0.12 ABI_X86="32*" > [ebuild R ] sys-apps/pciutils-3.5.6-r1 ABI_X86="32*" > [ebuild R ] x11-libs/libpciaccess-0.16 ABI_X86="32*" > [ebuild R ] sys-apps/hwloc-1.11.2-r1 ABI_X86="32*" > [ebuild N ] sys-cluster/openmpi-2.0.4 USE="fortran ipv6 threads -cma (-cuda) -cxx -heterogeneous -java -mpi-threads -numa -romio" ABI_X86="32 (64) (-x32)" OPENMPI_FABRICS="(-knem) (-ofed) (-psm)" OPENMPI_OFED_FEATURES="(-connectx-xrc) (-control-hdr-padding) (-dynamic-sl) (-failover) (-rdmacm) (-udcm)" OPENMPI_RM="(-pbs) (-slurm)" > [ebuild R ] virtual/mpi-2.0-r4 USE="fortran* -cxx*" ABI_X86="32*" > [ebuild R ] sci-libs/fftw-3.3.6_p2-r1 ABI_X86="32*" > [blocks B ] sys-cluster/mpich2 ("sys-cluster/mpich2" is blocking sys-cluster/openmpi-2.0.4) > [blocks B ] sys-cluster/openmpi ("sys-cluster/openmpi" is blocking sys-cluster/mpich2-1.5) This _looks_ like it may be related to: https://gitweb.gentoo.org/repo/gentoo.git/commit/sys-cluster?id=b287f5f8078ecfc7b222267aa1d590d994bd87b9 There's also weirdness in that portage choose mpich2, as opposed to mpich (see bug 547208) when resolving the upgrade path. Cc'ing the commit author. Finally, it wouldn't surprise me too much if the -lmpi was put in there to solve multilib issues, but it seems like fftw does the right thing when looking for MPI_Init(), so I'm not sure it'd be necessary anymore anyway? Perhaps I'm missing why a force-link to a library would be needed when the ./configure seems to check for it. But even if it is requires, perhaps protecting it by a check for multilib makes sense... The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=67a3fff18cedaf357e1a8cff0eae5f8aaf4824eb commit 67a3fff18cedaf357e1a8cff0eae5f8aaf4824eb Author: Christoph Junghans <junghans@gentoo.org> AuthorDate: 2020-03-29 16:57:10 +0000 Commit: Christoph Junghans <junghans@gentoo.org> CommitDate: 2020-03-29 16:57:28 +0000 sci-libs/fftw: fix build with mpich Closes: https://bugs.gentoo.org/699650 Package-Manager: Portage-2.3.89, Repoman-2.3.20 Signed-off-by: Christoph Junghans <junghans@gentoo.org> sci-libs/fftw/fftw-3.3.8-r1.ebuild | 182 +++++++++++++++++++++++++++++++++++++ sci-libs/fftw/fftw-9999.ebuild | 34 +++---- 2 files changed, 196 insertions(+), 20 deletions(-) *** Bug 717164 has been marked as a duplicate of this bug. *** Regarding to #717164 the bug does still exist. Reopening. It was only fixed in fftw-3.3.8-r1, not fftw-3.3.6_p2. I just don't like to touch stable packages. (In reply to Christoph Junghans from comment #16) > It was only fixed in fftw-3.3.8-r1, not fftw-3.3.6_p2. I just don't like to > touch stable packages. Oh, that's why. Let me know if you need anything. Please check 3.3.9. fftw-3.3.9 Compiles for me |
