[Hdf-forum] run-time error help
Elena Pourmal
epourmal at hdfgroup.org
Sat Oct 31 21:03:42 EDT 2009
Could you please try to remove ":" in your "set LD_lIBRARY_PATH ..."
command?
Elena
On Oct 31, 2009, at 4:18 PM, winthan wrote:
> 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 = ( ${LD_LIBRARY_PATH}: /apps/rhel5/graphics/
> x86_64/intel/11.1.038/szip/lib/ )
> i attempted to copy to the lib where hdf5 lib is located but since
> it's read only file system and i'm only a client of that
> supercomputer so i don't have access to it.
> any help or suggestion wouldbe appreciated. or reinstalling on my
> local drive will help?
> thanks again
> winthan
> On Sat, Oct 31, 2009 at 3:25 AM, winthan <keshunli at gmail.com> wrote:
> line 2036 of configure.in in /hdf5-1.8.1
> LD_LIBRARY_PATH="$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 at 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;
>>
>> }
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> Hdf-forum at hdfgroup.org
>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum at hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum at hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
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