i attached the wrong hdf5.settings file
here is the right now
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.3
Configured on: Fri Sep 11 18:12:02 EDT 2009
Configured by:@steele-adm.rcac.purdue.edu
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux steele-adm.rcac.purdue.edu 2.6.18-157.el5 #1 SMP Mon Jul 6 18:12:07 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /apps/rhel5/graphics/x86_64/intel/11.1.038/hdf5-1.8.3p
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /apps/rhel5/mpich2-1.1.1p1/64/nemesis-intel-11.1.038/bin/mpicc (icc-11.1)
CFLAGS/H5_CFLAGS: /-std=c99 -O2 -Wl,-s
CPPFLAGS/H5_CPPFLAGS: -I/apps/rhel5/graphics/x86_64/intel/11.1.038/szip/include -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
Shared Libraries: yes
Static Libraries: yes
Statically Linked Executables: yes
Extra libraries: -L/apps/rhel5/graphics/x86_64/intel/11.1.038/szip/lib -lsz -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
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),szip(encoder)
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
Linux Large File Support (LFS): yes
in the Extra libraries: it's linked to where szip is located. i tried adding the szip path to LD_LIBRARY_PATH as follow
set LD_LIBRARY_PATH = ( ${LD_LIBRARY_PATH}: /apps/rhel5/graphics/x86_64/intel/11.1.038/szip/lib/ )
i attempted to copy to the lib where hdf5 lib is located but since it's read only file system and i'm only a client of that supercomputer so i don't have access to it.
any help or suggestion wouldbe appreciated. or reinstalling on my local drive will help?
thanks again
winthan
On Sat, Oct 31, 2009 at 3:25 AM, winthan <keshunli@gmail.com> wrote:
line 2036 of configure.in in /hdf5-1.8.1
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`
Content of libhdf5.settings
General Information:
-------------------
HDF5 Version: 1.8.1
Configured on: Wed Jul 30 15:22:25 EDT 2008
Configured by:
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux haha.edu 2.6.9-42.0.10.EL_SFS2.2_1.8smp #1 SMP Tue May 20 07:51:23 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Parallel support: no
Installation point: /home/sth
Compiler: /opt/gcc-4.1.1/bin/gcc (gcc-4.1.1)
Compiler switches: -m32 -m32 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE
Extra libraries: -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /opt/gcc-4.1.1/bin/gcc (gcc-4.1.1)
CFLAGS/H5_CFLAGS: -m32/-std=c99 -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wmultichar -Wformat-nonliteral -Wformat-security -Wformat-y2k -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wmissing-field-initializers -Wvariadic-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -O -fomit-frame-pointer -finline-functions
CPPFLAGS/H5_CPPFLAGS: -m32 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE / -DNDEBUG -UH5_DEBUG_API
LDFLAGS:
Debug Mode:
Shared Libraries: no
Static Libraries: yes
Statically Linked Executables: no
Default Public Symbols Version: v18
With Deprecated Public Symbols: yes
Tracing: no
Clear file buffers before write: yes
Using memory checker: no
Optimization Instrumentation: no
Languages:
----------
Fortran: no
C++: no
Features:
---------
dmalloc: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Default API Mapping: v18
I/O filters (external):
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
Linux Large File Support (LFS): yes
MPE: no
Parallel HDF5: no
Direct VFD: no
Threadsafety: no
High Level library: yes
----------------------------------
since it's installed by other persons, i have no clue how to check whether it's installed with szip. should i download the packet szip and add the path to
line 2036 of configure.in in /hdf5-1.8.1
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`
?will that work?
thanks
On Fri, Oct 30, 2009 at 2:52 PM, Elena Pourmal > <epourmal@hdfgroup.org> wrote:
It sounds like parallel HDF5 library was built using szip library. (to confirm, please check libhdf5.settings file in the directory where hdf5 library is installed).
If so, add location of the szip library to LD_LIBRARY_PATH.
Elena
On Oct 30, 2009, at 3:05 PM, winthan wrote:
module load mpich2-intel
module load hdf5-1.8.3/intel-parallel
h5pcc sth.c -o sth
mpirun -np 2 ./sth
i got the error below
./file: error while loading shared libraries: libsz.so.2: cannot open shared object file: No such file or directory
./file: error while loading shared libraries: libsz.so.2: cannot open shared object file: No such file or directory
./file: error while loading shared libraries: libsz.so.2: cannot open shared object file: No such file or directory
before that,i run through the mpio.c at ftp://ftp.hdfgroup.org/HDF5/current/src/unpacked/release_docs/INSTALL_parallel to make sure myI compilers and the parallel file system. any help would be great.thanks
sth.c
--------
#include "hdf5.h"
#define H5FILE_NAME "SDS_row.h5"
int
main (int argc, char **argv)
{
/*
* HDF5 APIs definitions
*/
hid_t file_id; /* file and dataset identifiers */
hid_t plist_id; /* property list identifier( access template) */
herr_t status;
/*
* MPI variables
*/
int mpi_size, mpi_rank;
MPI_Comm comm = MPI_COMM_WORLD;
MPI_Info info = MPI_INFO_NULL;
/*
* Initialize MPI
*/
MPI_Init(&argc, &argv);
MPI_Comm_size(comm, &mpi_size);
MPI_Comm_rank(comm, &mpi_rank);
/*
* Set up file access property list with parallel I/O access
*/
plist_id = H5Pcreate(H5P_FILE_ACCESS);
H5Pset_fapl_mpio(plist_id, comm, info);
/*
* Create a new file collectively.
*/
file_id = H5Fcreate(H5FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
/*
* Close property list.
*/
H5Pclose(plist_id);
/*
* Close the file.
*/
H5Fclose(file_id);
MPI_Finalize();
return 0;
}
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_______________________________________________
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_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@hdfgroup.org
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