Hi,
I'm having a problem with the subroutine "h5pset_fapl_mpio_f"
to set up the file access property list. Calling this
subroutine giving me an error message
"undefined symbol: h5fdmpio_mp_h5pset_fapl_mpio_f_"
I'm using the intel fortran compiler version 12.1.
I also checked in libhdf5.settings that the parallel
feature is enabled.
Anybody has any idea how to fix this problem?
Thank you very much in advance.
best regards,
Annop Wongwathanarat
Hi Annop,
Is Fortran enabled too? Which version of HDF5 are you using? Did you build the HDF5 library? It will be very helpful if you show the content of the libhdf5.settings file. If Fortran is enabled, but Fortran compiler version is different, it may cause the problems too.
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Feb 14, 2013, at 1:03 PM, annop@MPA-Garching.MPG.DE wrote:
Hi,
I'm having a problem with the subroutine "h5pset_fapl_mpio_f"
to set up the file access property list. Calling this
subroutine giving me an error message"undefined symbol: h5fdmpio_mp_h5pset_fapl_mpio_f_"
I'm using the intel fortran compiler version 12.1.
I also checked in libhdf5.settings that the parallel
feature is enabled.Anybody has any idea how to fix this problem?
Thank you very much in advance.
best regards,
Annop Wongwathanarat_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
Hi Elena,
I'm not the one who built the library. It's the version 1.8.9.
Here is the content in libhdf5.settings
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.9
Configured on: Fri Nov 16 13:49:47 CET 2012
Configured by: wwn@hydra02
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux hydra02 3.0.42-0.7-default #1 SMP Tue Oct 9 11:58:45
UTC 2012 (a8dc443) x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /u/system/SLES11/soft/hdf5/1.8.9/intel12.1/pe1209
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /opt/ibmhpc/pe1209/ppe.poe/bin/mpiicc ( Intel(R) C Intel(R)
64 Compiler Version 12.1 Build 20120928)
CFLAGS: -fPIC
H5_CFLAGS: -std=c99 -O3
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: yes
Fortran Compiler: /opt/ibmhpc/pe1209/ppe.poe/bin/mpiifort ( Intel(R) Fortran
Intel(R) 64 Compiler Version 12.1 Build 20120928)
Fortran 2003 Compiler: yes
Fortran Flags: -fPIC
H5 Fortran Flags: -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yes
C++: no
Features:
---------
Parallel HDF5: yes
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE:
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
I'm using the same fortran compiler as the one used for building the
library.
The code runs without problem on my personal laptop with HDF5 1.8.8
built with GNU fortran compiler.
Thanks.
Annop
Hi Annop,
Is Fortran enabled too? Which version of HDF5 are you using? Did you build the HDF5 library? It will be very helpful if you show the content of the libhdf5.settings file. If Fortran is enabled, but Fortran compiler version is different, it may cause the problems too.
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Annop Wongwathanarat |
Max-Planck-Institut f�r Astrophysik |
Karl-Schwarzschild-Str. 1 |
85741 Garching, Germany |
Tel: +49-89-30000-2206 |
Fax: +49-89-30000-2235 |
E-mail: annop@mpa-garching.mpg.de |
==========================================
Summary looks good. Could you please try to compile your program with the h5pfc script that should be the "bin" directory of the HDF5 installation directory?
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
On Feb 15, 2013, at 4:36 AM, Annop Wongwathanarat wrote:
Hi Elena,
I'm not the one who built the library. It's the version 1.8.9.
Here is the content in libhdf5.settingsSUMMARY OF THE HDF5 CONFIGURATION
=================================General Information:
-------------------
HDF5 Version: 1.8.9
Configured on: Fri Nov 16 13:49:47 CET 2012
Configured by: wwn@hydra02
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux hydra02 3.0.42-0.7-default #1 SMP Tue Oct 9 11:58:45
UTC 2012 (a8dc443) x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /u/system/SLES11/soft/hdf5/1.8.9/intel12.1/pe1209Compiling Options:
------------------
Compilation Mode: production
C Compiler: /opt/ibmhpc/pe1209/ppe.poe/bin/mpiicc ( Intel(R) C Intel(R)
64 Compiler Version 12.1 Build 20120928)
CFLAGS: -fPIC
H5_CFLAGS: -std=c99 -O3
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: noLanguages:
----------
Fortran: yes
Fortran Compiler: /opt/ibmhpc/pe1209/ppe.poe/bin/mpiifort ( Intel(R) Fortran
Intel(R) 64 Compiler Version 12.1 Build 20120928)
Fortran 2003 Compiler: yes
Fortran Flags: -fPIC
H5 Fortran Flags: -O3
AM Fortran Flags:
Shared Fortran Library: yes
Static Fortran Library: yesC++: no
Features:
---------
Parallel HDF5: yes
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE:
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yesI'm using the same fortran compiler as the one used for building the
library.The code runs without problem on my personal laptop with HDF5 1.8.8
built with GNU fortran compiler.Thanks.
Annop
Hi Annop,
Is Fortran enabled too? Which version of HDF5 are you using? Did you build the HDF5 library? It will be very helpful if you show the content of the libhdf5.settings file. If Fortran is enabled, but Fortran compiler version is different, it may cause the problems too.
Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--
> Annop Wongwathanarat |
> Max-Planck-Institut für Astrophysik |
> Karl-Schwarzschild-Str. 1 |
> 85741 Garching, Germany |
> Tel: +49-89-30000-2206 |
> Fax: +49-89-30000-2235 |
> E-mail: annop@mpa-garching.mpg.de |_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
