Problem with parallel-hdf5 not including symbols needed for MOAB

Hdf-forum archives
1

Hi all,

I recently have had some issues compiling a parallel hdf5 version
1.8.12 that includes parallel mpi symbols needed by MOAB.

I get this message from MOAB out of the configure process with this message

configure: WARNING:

···

*************************************************************************
* MOAB has been configured with parallel and HDF5 support
* but the configured HDF5 library does not support parallel IO.
* Some parallel IO capabilities will be disabled.
************************************************************************

I however did build hdf5 with the parallel flag.

CC='mpicc -w -m64 -fPIC' ./configure --prefix=/soft/hdf5/test
--enable-gpfs --enable-parallel --disable-shared

The nm output for the hdf5 library

$ nm -g -A /soft/hdf5/test/lib/libhdf5.a | grep fapl_mpio
/soft/hdf5/test/lib/libhdf5.a:H5FDmpio.o:0000000000000260 T H5Pget_fapl_mpio
/soft/hdf5/test/lib/libhdf5.a:H5FDmpio.o:0000000000000010 T H5Pset_fapl_mpio

For the mpicc I used mvapich2 compiled with intel compilers with
support for the PSM (Qlogic) interface

$ mpichversion
MVAPICH2 Version: 1.9
MVAPICH2 Release date: Mon May 6 12:25:08 EDT 2013
MVAPICH2 Device: ch3:psm
MVAPICH2 configure: --prefix=/soft/mvapich2/1.9-intel-13.1-psm
--with-device=ch3:psm --enable-shared --with-romio --enable-f77
--enable-fc --enable-cxx --with-psm-include=/usr --with-psm=/usr
MVAPICH2 CC: icc -DNDEBUG -DNVALGRIND -O2
MVAPICH2 CXX: icpc -DNDEBUG -DNVALGRIND -O2
MVAPICH2 F77: ifort -O2
MVAPICH2 FC: ifort -O2

Any suggestions or guidance would be greatly appreciated.

Thanks,
John

2

John,

Please send configure output, config.log, make, and make check output for HDF5 to help@hdfgroup.org

Thanks,
Mohamad

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of John
Sent: Thursday, March 05, 2015 11:41 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Problem with parallel-hdf5 not including symbols needed for MOAB

Hi all,

I recently have had some issues compiling a parallel hdf5 version
1.8.12 that includes parallel mpi symbols needed by MOAB.

I get this message from MOAB out of the configure process with this message

configure: WARNING:
*************************************************************************
* MOAB has been configured with parallel and HDF5 support
* but the configured HDF5 library does not support parallel IO.
* Some parallel IO capabilities will be disabled.
************************************************************************

I however did build hdf5 with the parallel flag.

CC='mpicc -w -m64 -fPIC' ./configure --prefix=/soft/hdf5/test --enable-gpfs --enable-parallel --disable-shared

The nm output for the hdf5 library

$ nm -g -A /soft/hdf5/test/lib/libhdf5.a | grep fapl_mpio
/soft/hdf5/test/lib/libhdf5.a:H5FDmpio.o:0000000000000260 T H5Pget_fapl_mpio
/soft/hdf5/test/lib/libhdf5.a:H5FDmpio.o:0000000000000010 T H5Pset_fapl_mpio

For the mpicc I used mvapich2 compiled with intel compilers with support for the PSM (Qlogic) interface

$ mpichversion
MVAPICH2 Version: 1.9
MVAPICH2 Release date: Mon May 6 12:25:08 EDT 2013
MVAPICH2 Device: ch3:psm
MVAPICH2 configure: --prefix=/soft/mvapich2/1.9-intel-13.1-psm
--with-device=ch3:psm --enable-shared --with-romio --enable-f77 --enable-fc --enable-cxx --with-psm-include=/usr --with-psm=/usr
MVAPICH2 CC: icc -DNDEBUG -DNVALGRIND -O2
MVAPICH2 CXX: icpc -DNDEBUG -DNVALGRIND -O2
MVAPICH2 F77: ifort -O2
MVAPICH2 FC: ifort -O2

Any suggestions or guidance would be greatly appreciated.

Thanks,
John

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

3

John, do you have other HDF5 installations on the build machine?
MOAB seems to be prone to picking up HDF5 installations for example
from default locations (/usr/local & friends) or the LD_LIBRARY_PATH.
(Temporarily) Adjusting your LD_LIBRARY_PATH might help.

G.

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of John
Sent: Thursday, March 5, 2015 11:41 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Problem with parallel-hdf5 not including symbols needed for MOAB

Hi all,

I recently have had some issues compiling a parallel hdf5 version
1.8.12 that includes parallel mpi symbols needed by MOAB.

I get this message from MOAB out of the configure process with this message

configure: WARNING:
*************************************************************************
* MOAB has been configured with parallel and HDF5 support
* but the configured HDF5 library does not support parallel IO.
* Some parallel IO capabilities will be disabled.
************************************************************************

I however did build hdf5 with the parallel flag.

CC='mpicc -w -m64 -fPIC' ./configure --prefix=/soft/hdf5/test --enable-gpfs --enable-parallel --disable-shared

The nm output for the hdf5 library

$ nm -g -A /soft/hdf5/test/lib/libhdf5.a | grep fapl_mpio
/soft/hdf5/test/lib/libhdf5.a:H5FDmpio.o:0000000000000260 T H5Pget_fapl_mpio
/soft/hdf5/test/lib/libhdf5.a:H5FDmpio.o:0000000000000010 T H5Pset_fapl_mpio

For the mpicc I used mvapich2 compiled with intel compilers with support for the PSM (Qlogic) interface

$ mpichversion
MVAPICH2 Version: 1.9
MVAPICH2 Release date: Mon May 6 12:25:08 EDT 2013
MVAPICH2 Device: ch3:psm
MVAPICH2 configure: --prefix=/soft/mvapich2/1.9-intel-13.1-psm
--with-device=ch3:psm --enable-shared --with-romio --enable-f77 --enable-fc --enable-cxx --with-psm-include=/usr --with-psm=/usr
MVAPICH2 CC: icc -DNDEBUG -DNVALGRIND -O2
MVAPICH2 CXX: icpc -DNDEBUG -DNVALGRIND -O2
MVAPICH2 F77: ifort -O2
MVAPICH2 FC: ifort -O2

Any suggestions or guidance would be greatly appreciated.

Thanks,
John

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5