Hello Ole,
the issue is here:
ld: cannot find -lpciaccess
ld: cannot find -lxml2
to solve this you can either install OS packages (.rpm, .deb, etc.) for
libpciaccess and libxml2, and perhaps add them as OS dependencies.
Alternatively you can put in dependencies for ('libxml2', '2.9.8') and
('libpciaccess', '0.13.4'), where you would need to install libpciaccess
using GCCcore instead of an intel or foss toolchain.
Regards,
Bart
On Mon, 30 Apr 2018 at 05:31, Ole Holm Nielsen <[email protected]>
wrote:
> When we build on nodes with Intel Omni-Path software installed, the
> build of "iomkl" fails:
>
> $ eb iomkl-2018.02.eb -r
> == temporary log file in case of crash /tmp/eb-MDUNmr/easybuild-UxI3tr.log
> == resolving dependencies ...
> == processing EasyBuild easyconfig
>
> /home/modules/software/EasyBuild/3.6.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.0-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb
> == building and installing
> OpenMPI/2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28...
> == fetching files...
> == creating build dir, resetting environment...
> == unpacking...
> == patching...
> == preparing...
> == configuring...
> == building...
> == FAILED: Installation ended unsuccessfully (build directory:
> /home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28):
> build failed (first 300 chars): cmd " make -j 48 " exited with exit code
> 2 and output:
> Making all in config
> make[1]: Entering directory
> `/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/config'
>
> Intel Omni-Path systems
> make[1]: Nothing to be done for `all'.
> make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.3/icc
> == Results of the build can be found in the log file(s)
> /tmp/eb-MDUNmr/easybuild-OpenMPI-2.1.3-20180430.105741.vWNYR.log
> ERROR: Build of
> /home/modules/software/EasyBuild/3.6.0/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.0-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb
>
> failed (err: 'build failed (first 300 chars): cmd " make -j 48 " exited
> with exit code 2 and output:\nMaking all in config\nmake[1]: Entering
> directory
> `/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/config\'\nmake[1]:
>
> Nothing to be done for `all\'.\nmake[1]: Leaving directory
> `/home/modules/build/OpenMPI/2.1.3/icc')
>
> The OpenMPI error log file contains near the end:
>
> CCLD libopen-pal.la
> ld: cannot find -lpciaccess
> ld: cannot find -lxml2
> make[2]: *** [libopen-pal.la] Error 1
> make[2]: Leaving directory
>
> `/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/opal'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory
>
> `/home/modules/build/OpenMPI/2.1.3/iccifort-2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/opal'
> make: *** [all-recursive] Error 1
> (at easybuild/tools/run.py:501 in parse_cmd_output)
> == 2018-04-30 11:03:17,152 easyblock.py:2702 WARNING build failed (first
> 300 chars): cmd " make -j 48 " exited with exit code 2 and output:
> Making all in config
> make[1]: Entering directory `/home/modules/build/OpenMPI/2.1.3/iccifort-
> Intel Omni-Path systems2018.2.199-GCC-6.4.0-2.28/openmpi-2.1.3/config'
> make[1]: Nothing to be done for `all'.
> make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.3/icc
> == 2018-04-30 11:03:17,152 easyblock.py:280 INFO Closing log for
> application name OpenMPI version 2.1.3
>
>
> Question: Can anyone point to the cause of this error? Did OpenMPI
> 2.1.3 introduce this error?
>
>
> Extra information: The issue
> https://github.com/easybuilders/easybuild-easyconfigs/issues/5805 is
> fixed with EB 3.6.0 and OpenMPI 2.1.3. On our systems with Mellanox
> Infiniband software installed, the line in
> OpenMPI-2.1.3-iccifort-2018.2.199-GCC-6.4.0-2.28.eb *does* fix the issue
> 5805 on this platform:
>
> configopts += '--without-ucx ' # hard disable UCX, to dance around bug
> (https://github.com/open-mpi/ompi/issues/4345)
>
> On the Intel Omni-Path system I tried to comment out this line, but the
> build still fails with the same error.
>
> /Ole
>
>
> On 03/05/2018 03:44 PM, Åke Sandgren wrote:
> > To clarify, it's a bug in the OpenMPI configure script when dealing with
> > UCX which they haven't fixed.
> >
> > On 03/05/2018 03:36 PM, Balázs Hajgató wrote:
> >> Dear Ole,
> >>
> >> use
> >> configopts += '--without-ucx '
> >>
> >> in the OpenMPI easyconfig
> >>
> >> Sincerely,
> >>
> >> Balazs
> >>
> >>>>>
> >>> Thanks for any suggestions!
> >>>
> >>
> >
> --
> Ole Holm Nielsen
> PhD, Senior HPC Officer
> Department of Physics, Technical University of Denmark,
> Building 307, DK-2800 Kongens Lyngby, Denmark
> E-mail: [email protected]
> Homepage: http://dcwww.fysik.dtu.dk/~ohnielse/
> Tel: (+45) 4525 3187 / Mobile (+45) 5180 1620
> >> On 05/03/2018 15:27, Ole Holm Nielsen wrote:
> >>> Using EB 3.5.2 I'm trying to build the latest iomkl:
> >>>
> >>> eb iomkl-2018a.eb -r
> >>>
> >>> This works like a charm on 2 of our 3 binary architectures, but on our
> >>> Sandy Bridge nodes with Mellanox Infiniband the build aborts:
> >>>
> >>> # eb iomkl-2018a.eb -r
> >>> == temporary log file in case of crash
> >>> /tmp/eb-Dnjmix/easybuild-6WeIK9.log
> >>> == resolving dependencies ...
> >>> == processing EasyBuild easyconfig
> >>>
> /home/modules/software/EasyBuild/3.5.2/lib/python2.7/site-packages/easybuild_easyconfigs-3.5.2-py2.7.egg/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28.eb
> >>>
> >>> == building and installing
> >>> OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28...
> >>> == fetching files...
> >>> == creating build dir, resetting environment...
> >>> == unpacking...
> >>> == patching...
> >>> == preparing...
> >>> == configuring...
> >>> == building...
> >>> == FAILED: Installation ended unsuccessfully (build directory:
> >>> /home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28):
> >>> build failed (first 300 chars): cmd " make -j 16 " exited with exit
> >>> code 2 and output:
> >>> Making all in config
> >>> make[1]: Entering directory
> >>>
> `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/config'
> >>>
> >>> make[1]: Nothing to be done for `all'.
> >>> make[1]: Leaving directory `/home/modules/build/OpenMPI/2.1.2/icc
> >>> ...
> >>>
> >>> The end of the log file
> >>> /tmp/eb-Dnjmix/easybuild-OpenMPI-2.1.2-20180305.144907.SAFtP.log
> >>> contains:
> >>>
> >>> libtool: error: require no space between '-L' and '-lrt'
> >>> make[2]: *** [libmca_pml_ucx.la] Error 1
> >>> make[2]: Leaving directory
> >>>
> `/home/modules/build/OpenMPI/2.1.2/iccifort-2018.1.163-GCC-6.4.0-2.28/openmpi-2.1.2/ompi/mca/pml/ucx'
> >>>
> >>> make[1]: *** [all-recursive] Error 1
> >>>
> >>> I can't make out what's causing this. Perhaps the build server has a
> >>> library installed triggering an error?
>
--
Dr. Bart E. Oldeman | [email protected] | [email protected]
Scientific Computing Analyst / Analyste en calcul scientifique
McGill HPC Centre / Centre de Calcul Haute Performance de McGill |
http://www.hpc.mcgill.ca
Calcul Québec | http://www.calculquebec.ca
Compute/Calcul Canada | http://www.computecanada.ca
Tel/Tél: 514-396-8926 | Fax/Télécopieur: 514-396-8934
