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
