Hi Shahzeb, Have you modified the OpenMPI easyconfig to enable LSF support on your production system? https://www.open-mpi.org/faq/?category=building#build-rte-lsf
Also, have you tried building HDF5 by hand and seeing where the problem really arises and if you can find a manual way around it first? You can get everything you need to do that with 'eb -x ...' Alan On 31 March 2017 at 14:09, Siddiqui, Shahzeb <[email protected]> wrote: > I have tried to pass LIBS="-lm" and LDFLAGS="-lm" as part of buildopts and > it did not work. The library libbat.so is something that comes from LSF, I > am not responsible for installing LSF and I don't expect LSF should be > reconfigured just for sake of building HDF5. By the way, HDF5 was building > correctly in a non-LSF environment, it only caused an issue when I am > building software on a production system. In our VM, we don't have LSF > configured as part of startup process so I had no means to configure > OpenMPI with LSF. I let all my builds proceed normally while keeping in > mind, that I would rebuild on a production machine with LSF support. > > The error appeared when I tried to rebuild HDF5. > > I am going to try to build HDF5-1.8.17 -foss-2016b and all its dependency > strickly from EB to see if the issue is an OpenMPI or HDF5 issue. > > > > -----Original Message----- > From: [email protected] [mailto:easybuild-request@ > lists.ugent.be] On Behalf Of Åke Sandgren > Sent: Friday, March 31, 2017 3:01 AM > To: [email protected] > Subject: Re: [easybuild] HDF5 build issue with lsf library libbat.so > > I would say that the error is in the build of your > /hpc/grid/lsfhpc1p/9.1/linux2.6-glibc2.3-x86_64/lib/libbat.so > > If it needs log/ceil, etc then that shared lib should have been built with > a -lm dependency. > > On 03/31/2017 08:52 AM, Markus Geimer wrote: > > Shahzeb, > > > > I have no clue about LSF nor have I ever tried building HDF5, but did > > you try adding > > > > configopts = 'LIBS=-lm' > > > > to the HDF5 easyconfig? > > > > Markus > > > > > > On 03/30/2017 09:21 PM, Siddiqui, Shahzeb wrote: > >> Hello, > >> > >> > >> > >> I would really like if someone can assist me resolve the issue with > >> HDF5 I am facing. It is holding me back in building R. I have tried > >> to rebuild both OpenMPI and HDF5 with multiple version, each > >> combination gets me to the same error which is an LSF related error. > >> I have reached out to HDF5 and they couldn't help much. The error > >> seems trivial, it can't find math library functions though the system > >> has both static/shared libraries /usr/lib/libm.a & /usr/lib64/libm.so. > >> > >> > >> > >> I have tried to tweak the HDF5 easyconfig by passing in LDFLAGS and > >> LIBS value both of them didn't work. I have tried to unset LSF > >> library from my OpenMPI module and that reports an error building a C > >> file. The error seems to be coming from the Makefile in > hdf5-1.8.17/c++/test. > >> > >> > >> > >> > >> > >> Help would be greatly appreciated. > >> > >> > >> > >> Regards, > >> > >> > >> > >> *From:*[email protected] > >> [mailto:[email protected]] *On Behalf Of *Kenneth > >> Hoste > >> *Sent:* Monday, March 20, 2017 3:19 PM > >> *To:* [email protected] > >> *Subject:* Re: [easybuild] HDF5 build issue with lsf library > >> libbat.so > >> > >> > >> > >> Hi Shahzeb, > >> > >> On 17/03/2017 20:20, Siddiqui, Shahzeb wrote: > >> > >> Hello, > >> > >> > >> > >> I am having a problem with building HDF5 that points to a lsf > >> library issue. We install LSF in a non-standard path and source the > >> profile.lsf script. In my OpenMPI script I have set LD_LIBRARY_PATH > >> to LSF_LIBDIR in order for OpenMPI to pick up the libraries. This is > >> needed when you verify OpenMPI is configured with lsf using > >> ompi_info see: https://www.open-mpi.org/faq/?category=building > >> > >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.open-2Dmpi. > >> org_faq_-3Fcategory-3Dbuilding&d=DwMD-g&c=UE1eNsedaKncO0Yl_u8bfw&r=RM > >> JdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=M217HieEKfQ3NeOumjB63h900 > >> BQTyop8eb_dA63Sbts&s=Ogz8DtgLRp4Wx8KDlX4FTxBO7LeJvxwN9myNrrtCPlA&e=> > >> > >> > >> > >> The error seems to be trivial. The reference to pow, ceil, log seems > >> to point to the math library. I would suspect this is provided by > >> GCC and if so it should be picked up. > >> > >> > >> Usually it's sufficient to also include -lm in the set of libraries > >> to link against to resolve these errors. > >> > >> However, maybe this is a sign of something not being 100% correct in > >> the way that OpenMPI was made LFS-aware. > >> > >> Unfortunately I'm clueless about LSF myself... > >> > >> > >> regards, > >> > >> Kenneth > >> > >> > >> > >> [hpcswadm@amrndhl1157 HDF5]$ eb HDF5-1.8.17-foss-2016.03.eb > >> > >> == temporary log file in case of crash > >> /tmp/eb-P1j91T/easybuild-dHe7E3.log > >> > >> == processing EasyBuild easyconfig > >> /hpc/hpcswadm/easybuild/HDF5/HDF5-1.8.17-foss-2016.03.eb > >> > >> == building and installing MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/HDF5/ > 1.8.17... > >> > >> == fetching files... > >> > >> == creating build dir, resetting environment... > >> > >> == unpacking... > >> > >> == patching... > >> > >> == preparing... > >> > >> == configuring... > >> > >> == building... > >> > >> == FAILED: Installation ended unsuccessfully (build directory: > >> /nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1.8.17/foss-2016. > >> 03): build failed (first 300 chars): cmd " make -j 80 > >> CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK" FC="mpifort" " exited with > exitcode 2 and output: > >> > >> Making all in src > >> > >> make[1]: Entering directory > >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1. > 8.17/foss-2016.03/hdf5-1.8.17/src' > >> > >> make all-am > >> > >> make[2]: Entering directory `/nfs/grid/ > >> > >> == Results of the build can be found in the log file(s) > >> /tmp/eb-P1j91T/easybuild-HDF5-1.8.17-20170317.150809.jGPiX.log > >> > >> ERROR: Build of > >> /hpc/hpcswadm/easybuild/HDF5/HDF5-1.8.17-foss-2016.03.eb > >> failed (err: 'build failed (first 300 chars): cmd " make -j 80 > >> CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK" FC="mpifort" " exited > >> with exitcode 2 and output:\nMaking all in src\nmake[1]: Entering > >> directory > >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1.8.17/foss-2016 > >> .03/hdf5-1.8.17/src\'\nmake > >> all-am\nmake[2]: Entering directory `/nfs/grid/') > >> > >> [hpcswadm@amrndhl1157 HDF5]$ vi > >> /tmp/eb-P1j91T/easybuild-HDF5-1.8.17-20170317.150809.jGPiX.log > >> > >> [hpcswadm@amrndhl1157 HDF5]$ tail > >> /tmp/eb-P1j91T/easybuild-HDF5-1.8.17-20170317.150809.jGPiX.log > >> > >> make[1]: *** [all-recursive] Error 1 > >> > >> make[1]: Leaving directory > >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1. > 8.17/foss-2016.03/hdf5-1.8.17/c++' > >> > >> make: *** [all-recursive] Error 1 > >> > >> (at > >> easybuild/software/Core/EasyBuild/3.1.1/lib/python2.7/site-packages/e > >> asybuild_framework-3.1.1-py2.7.egg/easybuild/tools/run.py:446 > >> in parse_cmd_output) > >> > >> == 2017-03-17 15:09:45,763 easyblock.py:2520 WARNING build failed > >> (first > >> 300 chars): cmd " make -j 80 CXXFLAGS="$CXXFLAGS > >> -DMPICH_IGNORE_CXX_SEEK" FC="mpifort" " exited with exitcode 2 and > output: > >> > >> Making all in src > >> > >> make[1]: Entering directory > >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1. > 8.17/foss-2016.03/hdf5-1.8.17/src' > >> > >> make all-am > >> > >> make[2]: Entering directory `/nfs/grid/ > >> > >> == 2017-03-17 15:09:45,764 easyblock.py:276 INFO Closing log for > >> application name HDF5 version 1.8.17 > >> > >> > >> > >> > >> > >> > >> > >> CXX tvlstr.o > >> > >> CXX h5cpputil.o > >> > >> CXX ttypes.o > >> > >> CXXLD testhdf5 > >> > >> /hpc/grid/lsfhpc1p/9.1/linux2.6-glibc2.3-x86_64/lib/libbat.so: error: > >> undefined reference to 'pow' > >> > >> /hpc/grid/lsfhpc1p/9.1/linux2.6-glibc2.3-x86_64/lib/libbat.so: error: > >> undefined reference to 'ceil' > >> > >> /hpc/grid/lsfhpc1p/9.1/linux2.6-glibc2.3-x86_64/lib/libbat.so: error: > >> undefined reference to 'log' > >> > >> collect2: error: ld returned 1 exit status > >> > >> make[2]: *** [testhdf5] Error 1 > >> > >> make[2]: Leaving directory > >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1. > 8.17/foss-2016.03/hdf5-1.8.17/c++/test' > >> > >> make[1]: *** [all-recursive] Error 1 > >> > >> make[1]: Leaving directory > >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1. > 8.17/foss-2016.03/hdf5-1.8.17/c++' > >> > >> make: *** [all-recursive] Error 1 > >> > >> (at > >> easybuild/software/Core/EasyBuild/3.1.1/lib/python2.7/site-packages/e > >> asybuild_framework-3.1.1-py2.7.egg/easybuild/tools/run.py:446 > >> in parse_cmd_output) > >> > >> == 2017-03-17 15:09:45,763 easyblock.py:2520 WARNING build failed > >> (first > >> 300 chars): cmd " make -j 80 CXXFLAGS="$CXXFLAGS > >> -DMPICH_IGNORE_CXX_SEEK" FC="mpifort" " exited with exitcode 2 and > output: > >> > >> Making all in src > >> > >> make[1]: Entering directory > >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1. > 8.17/foss-2016.03/hdf5-1.8.17/src' > >> > >> make all-am > >> > >> make[2]: Entering directory `/nfs/grid/ > >> > >> == 2017-03-17 15:09:45,764 easyblock.py:276 INFO Closing log for > >> application name HDF5 version 1.8.17 > >> > >> > >> > >> Shahzeb Siddiqui > >> > >> HPC Linux Engineer > >> > >> B2220-447.2 > >> > >> Groton, CT > >> > >> > >> > >> > >> > > > > -- > > Dr. Markus Geimer > > Juelich Supercomputing Centre > > Institute for Advanced Simulation > > Forschungszentrum Juelich GmbH > > 52425 Juelich, Germany > > > > Phone: +49-2461-61-1773 > > Fax: +49-2461-61-6656 > > E-Mail: [email protected] > > WWW: http://www.fz-juelich.de/jsc > > > > > > ---------------------------------------------------------------------- > > -------------------------- > > ---------------------------------------------------------------------- > > -------------------------- > > Forschungszentrum Juelich GmbH > > 52425 Juelich > > Sitz der Gesellschaft: Juelich > > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > > Prof. Dr. Sebastian M. Schmidt > > ---------------------------------------------------------------------- > > -------------------------- > > ---------------------------------------------------------------------- > > -------------------------- > > > > -- > Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden > Internet: [email protected] Phone: +46 90 7866134 Fax: +46 90-580 14 > Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se > -- Dr. Alan O'Cais E-CAM Software Manager Juelich Supercomputing Centre Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49 2461 61 5213 Fax: +49 2461 61 6656 E-mail: [email protected] WWW: http://www.fz-juelich.de/ias/jsc/EN
