undefined reference to `H5Pset_fapl_mpiposix'

Hdf-forum archives
1

HDF Forum,

I’m actually trying to build NETCDF-4 (with parallel I/O) but I keep running into the following link error which appears to be related to HDF5 v1.8.13:

libtool: link: mpicc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgentab.o -L/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/ ../liblib/.libs/libnetcdf.a /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5_hl.so /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so -lz -ldl -lm -lcurl -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib
../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4file.o): In function `nc4_open_file':
/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174: undefined reference to `H5Pset_fapl_mpiposix’

I have built HDF5 v1.8.13 using MPICH v3 and GCC v4.4.7 on a RHEL6 Linux system. My HDF5 configure options are as follows:

./configure --prefix=/my/install/path CC=mpicc FC=mpif90 CXX=mpicxx --enable-static --enable-shared --enable-parallel

Is there something I am doing wrong that prevents H5Pset_fapl_mpiposix from being built?

Thanks in advance,

Tim.

2

MPI POSIX VFD was removed from HDF5 1.8.13. We submitted a patch to netCDF folks.

See https://github.com/Unidata/netcdf-c/commit/435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8

Elena

···

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 2:09 PM, Timothy Stitt <Timothy.Stitt.9@nd.edu> wrote:

HDF Forum,

I’m actually trying to build NETCDF-4 (with parallel I/O) but I keep running into the following link error which appears to be related to HDF5 v1.8.13:

libtool: link: mpicc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgentab.o -L/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/ ../liblib/.libs/libnetcdf.a /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5_hl.so /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so -lz -ldl -lm -lcurl -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib
../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4file.o): In function `nc4_open_file':
/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174: undefined reference to `H5Pset_fapl_mpiposix’

I have built HDF5 v1.8.13 using MPICH v3 and GCC v4.4.7 on a RHEL6 Linux system. My HDF5 configure options are as follows:

./configure --prefix=/my/install/path CC=mpicc FC=mpif90 CXX=mpicxx --enable-static --enable-shared --enable-parallel

Is there something I am doing wrong that prevents H5Pset_fapl_mpiposix from being built?

Thanks in advance,

Tim.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

3

Thanks Elena, the git version did the trick. Much appreciated.

···

______________________________________________
Tim Stitt PhD
User Support Manager (CRC)
Research Assistant Professor (Computer Science & Engineering)
Room 108, Center for Research Computing, University of Notre Dame, IN 46556
Email: tstitt@nd.edu<mailto:tstitt@nd.edu>

From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Thursday, May 15, 2014 at 3:45 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] undefined reference to `H5Pset_fapl_mpiposix'

MPI POSIX VFD was removed from HDF5 1.8.13. We submitted a patch to netCDF folks.

See https://github.com/Unidata/netcdf-c/commit/435d8a03ed28bb5ad63aff12cbc6ab91531b6bc8

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 2:09 PM, Timothy Stitt <Timothy.Stitt.9@nd.edu<mailto:Timothy.Stitt.9@nd.edu>> wrote:

HDF Forum,

I’m actually trying to build NETCDF-4 (with parallel I/O) but I keep running into the following link error which appears to be related to HDF5 v1.8.13:

libtool: link: mpicc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgentab.o -L/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/<http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/> ../liblib/.libs/libnetcdf.a /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5_hl.so<http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5_hl.so> /afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so<http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib/libhdf5.so> -lz -ldl -lm -lcurl -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib<http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib> -Wl,-rpath -Wl,/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib<http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/hdf5-1.8.13/RELEASE/gcc/lib>
../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4file.o): In function `nc4_open_file':
/afs/crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174:<http://crc.nd.edu/user/t/tstitt/Projects/GenomeMapper/genomemapper/utilties/netcdf-4.3.2/libsrc4/nc4file.c:2174:> undefined reference to `H5Pset_fapl_mpiposix’

I have built HDF5 v1.8.13 using MPICH v3 and GCC v4.4.7 on a RHEL6 Linux system. My HDF5 configure options are as follows:

./configure --prefix=/my/install/path CC=mpicc FC=mpif90 CXX=mpicxx --enable-static --enable-shared --enable-parallel

Is there something I am doing wrong that prevents H5Pset_fapl_mpiposix from being built?

Thanks in advance,

Tim.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org