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:*easybuild-requ...@lists.ugent.be >> [mailto:easybuild-requ...@lists.ugent.be] *On Behalf Of *Kenneth Hoste >> *Sent:* Monday, March 20, 2017 3:19 PM >> *To:* easybuild@lists.ugent.be >> *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=RMJdCm7m5fiPWhajwKUnEW5yn4eK2YdUWW-MLVShghg&m=M217HieEKfQ3NeOumjB63h900BQTyop8eb_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/easybuild_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="$CXXFLAGS >> -DMPICH_IGNORE_CXX_SEEK" FC="mpifort" " exited with exitcode 2 and output: >> >> Making all in src >> >> make[1]: Entering directory >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1.8.17/foss-2016.03/hdf5-1.8.17/src' >> >> make all-am >> >> make[2]: Entering directory `/nfs/grid/ >> >> == 2017-03-17 15:09:45,764 easyblock.py:276 INFO Closing log for >> application name HDF5 version 1.8.17 >> >> >> >> >> >> >> >> CXX tvlstr.o >> >> CXX h5cpputil.o >> >> CXX ttypes.o >> >> CXXLD testhdf5 >> >> /hpc/grid/lsfhpc1p/9.1/linux2.6-glibc2.3-x86_64/lib/libbat.so: error: >> undefined reference to 'pow' >> >> /hpc/grid/lsfhpc1p/9.1/linux2.6-glibc2.3-x86_64/lib/libbat.so: error: >> undefined reference to 'ceil' >> >> /hpc/grid/lsfhpc1p/9.1/linux2.6-glibc2.3-x86_64/lib/libbat.so: error: >> undefined reference to 'log' >> >> collect2: error: ld returned 1 exit status >> >> make[2]: *** [testhdf5] Error 1 >> >> make[2]: Leaving directory >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1.8.17/foss-2016.03/hdf5-1.8.17/c++/test' >> >> make[1]: *** [all-recursive] Error 1 >> >> make[1]: Leaving directory >> `/nfs/grid/software/RHEL7-BUILD/easybuild/build/HDF5/1.8.17/foss-2016.03/hdf5-1.8.17/c++' >> >> make: *** [all-recursive] Error 1 >> >> (at >> easybuild/software/Core/EasyBuild/3.1.1/lib/python2.7/site-packages/easybuild_framework-3.1.1-py2.7.egg/easybuild/tools/run.py:446 >> in parse_cmd_output) >> >> == 2017-03-17 15:09:45,763 easyblock.py:2520 WARNING build failed (first >> 300 chars): cmd " make -j 80 CXXFLAGS="$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: m.gei...@fz-juelich.de > 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: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
