Hello Barbara, Did you check the Makefile in the https://github.com/hpcugent/easybuild-easyconfigs/issues/4377
EasyBuild uses LD_LIBRARY_PATH and LIBS is set accordingly. The library /usr/lib/libm.a is system library and that is probably compatible with GCC-4. We are running RHEL7 and default GCC is 4.8.5. I am building HDF5 with GCC 5.4.0, OpenMPI-2.0.0 I checked that /usr/lib/libm.a is provided by glibc-static, is this something that would be provided by any application such as GCC. LD = /nfs/grid/software/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/binutils/2.27/bin/ld -m elf_x86_64 LDFLAGS = -L/nfs/grid/software/RHEL7/easybuild/software/Core/GCCcore/5.4.0/lib64 -L/nfs/grid/software/RHEL7/easybuild/software/Core/GCCcore/5.4.0/lib -L/nfs/grid/software/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/OpenBLAS/0.2.19-LAPACK-3.6.0/lib -L/nfs/grid/software/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/ScaLAPACK/2.0.2-OpenBLAS-0.2.19-LAPACK-3.6.0/lib -L/nfs/grid/software/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/FFTW/3.3.4/lib -L/nfs/grid/software/RHEL7/easybuild/software/MPI/GCC/5.4.0-2.27/OpenMPI/2.0.0/Szip/2.1/lib -L/nfs/grid/software/RHEL7/easybuild/software/Compiler/GCCcore/5.4.0/zlib/1.2.8/lib LIBS = -lsz -lz -ldl -lm -lm -lpthread -----Original Message----- From: [email protected] [mailto:[email protected]] Sent: Wednesday, March 29, 2017 2:20 PM To: Siddiqui, Shahzeb Subject: RE: HDF5 math library issue with LSF library in path Hi Shaahzeb, Oh.. I did so those errors (ceil, pow, log) at one point. Your LDFLAGS uses "-lm" which expects a path to go with it. Maybe that path is getting lost when the options are passed to python?? Can you try adding an absolute path and library name to LDFLAGS? For example: LD_FLAGS="/usr/lib/libm.a $LDFLAGS" I'm just guessing. -Barbara ======================================================== Barbara Jones, The HDF Group Helpdesk, [email protected] Support Services: https://www.hdfgroup.org/support/ ======================================================== On Wed, 29 Mar 2017, Siddiqui, Shahzeb wrote: > Hello Barbara, > > Easybuild is a configuration file that passes config opts to a backend > python script that feeds the option for the build. Originally I didn't specify LDFLAGS="-lm" but I tried this because the error indicated it was not able to find the math libraries. The error seems to be something with respect to libbat.so (LSF library) causing issues, I am not sure why this is a problem. > > We are running LSF so OpenMPI module dynamically loads LSF_LIBDIR so > that OpenMPI is configured with LSF. This is causing some issue with HDF5 since its built with OpenMPI. > > Are you setting this or does ezbuild do this? The error "build failed > (first > 300 chars)" makes me wonder if the command line specified is too long..??? > > This is a generic error output from EasyBuild, ignore this and check the log > file. > > -----Original Message----- > From: [email protected] [mailto:[email protected]] > Sent: Wednesday, March 29, 2017 1:35 PM > To: Siddiqui, Shahzeb > Subject: Re: HDF5 math library issue with LSF library in path > > Hi Shahzeb, > > I am not familiar with ezbuild, so I'm not sure I can help, but I'll try. > > I looked at issue 4377. The error occurring near the end is this: > > ...8.16-foss-2016.03.eb failed (err: 'build failed (first 300 chars): cmd " > make -j 80 CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK" LDFLAGS="-lm $LDFLAGS" > .. > > Are you setting this or does ezbuild do this? The error "build failed > (first > 300 chars)" makes me wonder if the command line specified is too long..??? > > With HDF5 you can set environment variables and HDF5 will use those > preferentially. You do not need to specify them on the command line. > > If you type "./configure -help" from the top of the HDF5 source code > directory you will see which environment variables can influence HDF5. I have > included them below: > > CC C compiler command > CFLAGS C compiler flags > LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a > nonstandard directory <lib dir> > LIBS libraries to pass to the linker, e.g. -l<library> > CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I<include dir> if > you have headers in a nonstandard directory <include dir> > FC Fortran compiler command > FCFLAGS Fortran compiler flags > CXX C++ compiler command > CXXFLAGS C++ compiler flags > CXXCPP C++ preprocessor > LT_SYS_LIBRARY_PATH > User-defined run-time library search path. > CPP C preprocessor > > Use these variables to override the choices made by `configure' or to help it > to find libraries and programs with nonstandard names/locations. > > -Barbara > > ======================================================== > Barbara Jones, The HDF Group Helpdesk, [email protected] Support > Services: https://www.hdfgroup.org/support/ > ======================================================== > > On Tue, 28 Mar 2017, Siddiqui, Shahzeb wrote: > >> Hello, >> >> I would like to bring to your attention issue: >> https://github.com/hpcugent/easybuild-easyconfigs/issues/4377 >> >> I am using EasyBuild to install HDF5 and it was working properly on a build >> VM, now when I tried to rebuild on a different machine which has LSF, I am >> running into an issue. We are using environment modules and I have OpenMPI >> configured in modules to pick up LSF_LIBDIR using LD_LIBRARY_PATH but for >> some reason that is causing HDF5 to break. >> >> LSF library needs to be part of LD_LIBRARY_PATH in order for >> ompi_info to pick up LSF library as means to check if OpenMPI is >> configured with LSF properly see: >> https://www.open-mpi.org/faq/?category=building#build-rte-lsf >> >> I would like to get your assistance in resolving this issue. >> >> Regards, >> >> >> Shahzeb Siddiqui >> HPC Linux Engineer >> B2220-447.2 >> Groton, CT >> >> > > --
