Created attachment 555712 [details] build.log 'MAKEOPTS=-j1 emerge -v1 openmpi' fails with: ... libtool: link: x86_64-pc-linux-gnu-gcc -m32 -shared -fPIC -DPIC class/.libs/opal_bitmap.o class/.libs/opal_free_list.o class/.libs/opal_hash_table.o .... /usr/lib64/libltdl.so -ldl -levent -levent_pthreads -m32 -march=broadwell -O2 -pthread -Wl,-O1 -Wl,--as-needed -pthread -Wl,-soname -Wl,libopen-pal.so.40 -o .libs/libopen-pal.so.40.20.0 /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/librt.so when searching for -lrt /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/librt.a when searching for -lrt /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libutil.so when searching for -lutil /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libutil.a when searching for -lutil /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: skipping incompatible /usr/lib64/libz.so when searching for -lz /usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: /usr/lib64/libhwloc.so: error adding symbols: file in wrong format collect2: error: ld returned 1 exit status make[2]: *** [Makefile:2233: libopen-pal.la] Error 1 make[2]: Leaving directory '/var/tmp/portage/sys-cluster/openmpi-4.0.0/work/openmpi-4.0.0-abi_x86_32.x86/opal' root@lynx:/root(120)# emerge -pqv '=sys-cluster/openmpi-4.0.0::science' [ebuild U ] sys-cluster/openmpi-4.0.0 [3.1.3] USE="cxx fortran ipv6 java romio -cma -cuda -heterogeneous -numa" ABI_X86="32 (64) (-x32)" OPENMPI_FABRICS="-knem -ofed -psm" OPENMPI_OFED_FEATURES="-control-hdr-padding -dynamic-sl -rdmacm -udcm" OPENMPI_RM="-pbs -slurm"
Created attachment 555714 [details] Output of "emerge --info '=sys-cluster/openmpi-4.0.0::science' "
I masked >=sys-cluster/openmpi-4.0.0
(In reply to Juergen Rose from comment #2) > I masked >=sys-cluster/openmpi-4.0.0 Ok, but seems silly as it works just fine if you're not using the multibuild stuff. Leaving a comment mainly so anyone who hits the mask and isn't building for more than one arch knows they can safely unmask.
(In reply to Justin Bronder from comment #3) > (In reply to Juergen Rose from comment #2) > > I masked >=sys-cluster/openmpi-4.0.0 > > Ok, but seems silly as it works just fine if you're not using the multibuild > stuff. Leaving a comment mainly so anyone who hits the mask and isn't > building for more than one arch knows they can safely unmask. If I unmask >=sys-cluster/openmpi-4.0.0 and remove the abi_x86_32 USE flag from sys-cluster/openmpi and virtual/mpi I can emerge openmpi-4.0.0::science. But the subsequent 'emerge -vuDN world' fails with: root@lynx:/root(68)# emerge -pvuDN world These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sys-cluster/openmpi-4.0.0::science USE="cxx fortran ipv6 java romio -cma -cuda -heterogeneous -numa" ABI_X86="32* (64) (-x32)" OPENMPI_FABRICS="-knem -ofed -psm" OPENMPI_OFED_FEATURES="-control-hdr-padding -dynamic-sl -rdmacm -udcm" OPENMPI_RM="-pbs -slurm" 0 KiB Total: 1 package (1 reinstall), Size of downloads: 0 KiB ... virtual/mpi:0 (virtual/mpi-2.0-r5:0/0::gentoo, ebuild scheduled for merge) conflicts with >=virtual/mpi-2.0-r4[abi_x86_32(-),abi_x86_64(-),cxx,threads] required by (dev-libs/boost-1.65.0:0/1.65.0::gentoo, installed) =virtual/mpi-2.0-r5[abi_x86_32(-),abi_x86_64(-),cxx,threads] required by (dev-libs/boost-1.65.0:0/1.65.0::gentoo, installed) The following USE changes are necessary to proceed: (see "package.use" in the portage(5) man page for more details) # required by virtual/mpi-2.0-r5::gentoo # required by dev-python/mpi4py-3.0.0::gentoo # required by dev-python/h5py-2.7.1::gentoo[mpi] # required by dev-python/astropy-2.0.1::gentoo # required by sci-visualization/veusz-3.0.1::gentoo[fits] # required by @selected # required by @world (argument) >=sys-cluster/openmpi-4.0.0 abi_x86_32 emerge: there are no ebuilds built with USE flags to satisfy ">=sys-cluster/openmpi-1.10.2-r1[abi_x86_32(-)?,abi_x86_64(-)?,abi_x86_x32(-)?,abi_mips_n32(-)?,abi_mips_n64(-)?,abi_mips_o32(-)?,abi_ppc_32(-)?,abi_ppc_64(-)?,abi_s390_32(-)?,abi_s390_64(-)?,cxx?,fortran?,romio?,threads(+)?]". !!! One of the following packages is required to complete your request: - sys-cluster/openmpi-3.1.3::science (Change USE: +abi_x86_32) - virtual/mpi-2.0-r5::gentoo (Change USE: -abi_x86_32) (dependency required by "virtual/mpi-2.0-r5::gentoo" [installed]) (dependency required by "dev-libs/boost-1.65.0::gentoo[mpi]" [installed]) (dependency required by "virtual/podofo-build-0.9.6::gentoo[boost]" [installed]) (dependency required by "app-text/calibre-3.36.0::gentoo" [installed]) (dependency required by "@selected" [set]) (dependency required by "@world" [argument]) Is there not any patch to emerge openmpi-4.0.0 with the abi_x86_32 USE flag?
(In reply to Juergen Rose from comment #4) > Is there not any patch to emerge openmpi-4.0.0 with the abi_x86_32 USE flag? I need to look into it. Sadly, this came at a busy time for me as my second child was just born so things are pretty busy for me as you can imagine ;)
It still fails with the same error.
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/proj/sci.git/commit/?id=9b561f5c757362a404c9a7505b7344602a649ad3 commit 9b561f5c757362a404c9a7505b7344602a649ad3 Author: Jian Cao <sworden.cao@gmail.com> AuthorDate: 2019-04-04 20:46:56 +0000 Commit: Justin Bronder <jsbronder@gentoo.org> CommitDate: 2019-04-08 21:56:12 +0000 sys-cluster/openmpi: specify external libraries and version bump Closes: https://bugs.gentoo.org/671510 Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Jian Cao <sworden.cao@gmail.com> Signed-off-by: Justin Bronder <jsbronder@gentoo.org> sys-cluster/openmpi/Manifest | 2 +- sys-cluster/openmpi/{openmpi-4.0.0.ebuild => openmpi-4.0.1.ebuild} | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-)
(In reply to Juergen Rose from comment #6) > It still fails with the same error. Luckily you can thank Jian Cao for researching the issue and contributing a fix.
(In reply to Larry the Git Cow from comment #7) > The bug has been closed via the following commit(s): > > https://gitweb.gentoo.org/proj/sci.git/commit/ > ?id=9b561f5c757362a404c9a7505b7344602a649ad3 > > commit 9b561f5c757362a404c9a7505b7344602a649ad3 > Author: Jian Cao <sworden.cao@gmail.com> > AuthorDate: 2019-04-04 20:46:56 +0000 > Commit: Justin Bronder <jsbronder@gentoo.org> > CommitDate: 2019-04-08 21:56:12 +0000 > > sys-cluster/openmpi: specify external libraries and version bump > > Closes: https://bugs.gentoo.org/671510 > Package-Manager: Portage-2.3.62, Repoman-2.3.12 > Signed-off-by: Jian Cao <sworden.cao@gmail.com> > Signed-off-by: Justin Bronder <jsbronder@gentoo.org> > > sys-cluster/openmpi/Manifest | 2 +- > sys-cluster/openmpi/{openmpi-4.0.0.ebuild => openmpi-4.0.1.ebuild} | 6 > +++--- > 2 files changed, 4 insertions(+), 4 deletions(-) Thanks for the patch, it works now for me.
