Re: error while loading shared libraries: libhdf5.so.0

From: Haijun Tian <hjtian2000_at_gmail.com>
Date: Fri, 7 May 2010 08:52:50 +0800

On Fri, May 7, 2010 at 1:32 AM, Florian Bürzle <
florian.buerzle_at_uni-konstanz.de> wrote:

> Hi!
>
> Am 06.05.2010 um 18:26 schrieb Haijun Tian:
>
> > Hi guys,
> >
> > After installing the gadget2, I tried to get started following
> users-guide,
> >
> > mpirun -m mpihost -np 4 ./Gadget2 parameterfiles/cluster.param
> >
> > but I always get the following errors:
> >
> > /home/hjtian/myworks/gadget2/Gadget-2.0.6/Gadget2/./Gadget2: error while
> loading shared libraries: libhdf5.so.0: cannot open shared object file: No
> such file or directory
> >
> >
> > and then I used
> > locate libhdf5.so.0
> >
> > find libhdf5.so.0 file locates in /usr/lib/libhdf5.so.0
> >
> > so I modified my .bashrc file to add the enviroment variable like
> following,
> >
> > export LD_LIBRARY_PATH=/usr/lib/libhdf5.so.0:$LD_LIBRARY_PATH
>
>
> Maybe this is not sensible, since a PATH environment variable should point
> to a directory, not to an individual file - so set it to /usr/lib, and it
> should work. If not, please post the output of the following commands
>
> ldd Gadget2
>

$ ldd Gadget2
libhdf5.so.0 => /usr/lib64/libhdf5.so.0 (0x0000003b3d800000)
libz.so.1 => /usr/lib64/libz.so.1 (0x0000003011800000)
libgsl.so.0 => /usr/lib64/libgsl.so.0 (0x00000039cfa00000)
libgslcblas.so.0 => /usr/lib64/libgslcblas.so.0 (0x00000039cfe00000)
libimf.so => /usr/site/intel_cpp-11.0.074/lib/intel64/libimf.so
(0x00002acec1787000)
libm.so.6 => /lib64/libm.so.6 (0x0000003010c00000)
libsrfftw_mpi.so.2 => /usr/lib64/libsrfftw_mpi.so.2 (0x00002acec1b0a000)
libsfftw_mpi.so.2 => /usr/lib64/libsfftw_mpi.so.2 (0x00002acec1d0c000)
libsrfftw.so.2 => /usr/lib64/libsrfftw.so.2 (0x00002acec1f13000)
libsfftw.so.2 => /usr/lib64/libsfftw.so.2 (0x00002acec2143000)
libmpich.so.2 => /usr/lib64/libmpich.so.2 (0x00002acec2379000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003016800000)
libc.so.6 => /lib64/libc.so.6 (0x0000003010800000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003011000000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003011400000)
libmpi_infinipath.so.1 => /usr/lib64/libmpi_infinipath.so.1
(0x0000003010400000)
/lib64/ld-linux-x86-64.so.2 (0x000000300f800000)
librt.so.1 => /lib64/librt.so.1 (0x0000003015000000)
libinfinipath.so.4 => /usr/lib64/libinfinipath.so.4 (0x000000300fc00000)
libpsm_infinipath.so.1 => /usr/lib64/libpsm_infinipath.so.1
(0x0000003010000000)


I located the libhdf5.so.0 file, this file exists in the
directory /usr/lib64/.

so I added the /usr/lib64 into $PATH or $LD_LIBRARY_PATH, but the errors are
still there.


> echo $LD_LIBRARY_PATH
>

 /usr/lib64:/usr/local/lib/:/usr/local/lib64/:/usr/site/intel_cpp-11.0.074/mkl/lib/em64t:/usr/site/intel_cpp-11.0.074/tbb/em64t/cc3.4.3_libc2.3.4_kernel2.6.9/lib:/usr/site/intel_cpp-11.0.074/lib/intel64:/usr/site/intel_fortan-11.0.074/mkl/lib/em64t:/usr/site/intel_fortan-11.0.074/lib/intel64:/usr/local/lib/:/usr/local/lib64/:/usr/site/intel_cpp-11.0.074/mkl/lib/em64t:/usr/site/intel_cpp-11.0.074/tbb/em64t/cc3.4.3_libc2.3.4_kernel2.6.9/lib:/usr/site/intel_cpp-11.0.074/lib/intel64:/usr/site/intel_fortan-11.0.074/mkl/lib/em64t:/usr/site/intel_fortan-11.0.074/lib/intel64:/usr/local/lib/:/usr/local/lib64/:/usr/site/intel_cpp-11.0.074/mkl/lib/em64t:/usr/site/intel_cpp-11.0.074/tbb/em64t/cc3.4.3_libc2.3.4_kernel2.6.9/lib:/usr/site/intel_cpp-11.0.074/lib/intel64:/usr/site/intel_fortan-11.0.074/mkl/lib/em64t:/usr/site/intel_fortan-11.0.074/lib/intel64:/usr/local/lib/:/usr/local/lib64/:/usr/site/intel_cpp-11.0.074/mkl/lib/em64t:/usr/site/intel_cpp-11.0.074/tbb/em64t/cc3.4.3_libc2.3.4_kernel2.6.9/lib:/usr/site/intel_cpp-11.0.074/lib/intel64:/usr/site/intel_fortan-11.0.074/mkl/lib/em64t:/usr/site/intel_fortan-11.0.074/lib/intel64:/usr/local/lib/:/usr/local/lib64/:/usr/site/intel_cpp-11.0.074/mkl/lib/em64t:/usr/site/intel_cpp-11.0.074/tbb/em64t/cc3.4.3_libc2.3.4_kernel2.6.9/lib:/usr/site/intel_cpp-11.0.074/lib/intel64:/usr/site/intel_fortan-11.0.074/mkl/lib/em64t:/usr/site/intel_fortan-11.0.074/lib/intel64:/usr/local/lib/:/usr/local/lib64/:/usr/lib64:/usr/site/intel_cpp-11.0.074/mkl/lib/em64t:/usr/site/intel_cpp-11.0.074/tbb/em64t/cc3.4.3_libc2.3.4_kernel2.6.9/lib:/usr/site/intel_cpp-11.0.074/lib/intel64:/usr/site/intel_fortan-11.0.074/mkl/lib/em64t:/usr/site/intel_fortan-11.0.074/lib/intel64



and


$ echo $PATH
/usr/lib64:/usr/site/intel_cpp-11.0.074/bin/intel64:/usr/site/intel_fortan-11.0.074/bin/intel64:/usr/lib64:/usr/site/intel_cpp-11.0.074/bin/intel64:/usr/site/intel_fortan-11.0.074/bin/intel64:/usr/lib64:/usr/site/intel_cpp-11.0.074/bin/intel64:/usr/site/intel_fortan-11.0.074/bin/intel64:/usr/lib64:/usr/site/intel_cpp-11.0.074/bin/intel64:/usr/site/intel_fortan-11.0.074/bin/intel64:/usr/lib:/usr/site/intel_cpp-11.0.074/bin/intel64:/usr/site/intel_fortan-11.0.074/bin/intel64:/usr/lib:/usr/site/intel_cpp-11.0.074/bin/intel64:/usr/site/intel_fortan-11.0.074/bin/intel64:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/site/intel_cpp-11.0.074/bin/intel64:/usr/site/intel_fortan-11.0.074/bin/intel64:/usr/local/bin:/bin:/usr/bin:/usr/X11R6/bin:/sbin:/usr/sbin:/usr/local/sbin:/opt/dell/srvadmin/bin:/opt/bin:/opt/maui/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin:/opt/xcat/contrib/bin:/opt/xcat/contrib/sbin:/opt/xcat/contrib/x86_64/bin:/opt/xcat/contrib/x86_64/sbin:/opt/bin:/opt/maui/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin:/opt/xcat/contrib/bin:/opt/xcat/contrib/sbin:/opt/xcat/contrib/x86_64/bin:/opt/xcat/contrib/x86_64/sbin:/opt/bin:/opt/maui/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin:/opt/xcat/contrib/bin:/opt/xcat/contrib/sbin:/opt/xcat/contrib/x86_64/bin:/opt/xcat/contrib/x86_64/sbin:/opt/bin:/opt/maui/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin:/opt/xcat/contrib/bin:/opt/xcat/contrib/sbin:/opt/xcat/contrib/x86_64/bin:/opt/xcat/contrib/x86_64/sbin:/opt/bin:/opt/maui/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin:/opt/xcat/contrib/bin:/opt/xcat/contrib/sbin:/opt/xcat/contrib/x86_64/bin:/opt/xcat/contrib/x86_64/sbin:/opt/bin:/opt/maui/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin:/opt/xcat/contrib/bin:/opt/xcat/contrib/sbin:/opt/xcat/contrib/x86_64/bin:/opt/xcat/contrib/x86_64/sbin:/opt/bin:/opt/maui/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/x86_64/bin:/opt/xcat/x86_64/sbin:/opt/xcat/contrib/bin:/opt/xcat/contrib/sbin:/opt/xcat/contrib/x86_64/bin:/opt/xcat/contrib/x86_64/sbin



thanks,
Haijun


>
> Cheers
> Florian
>
>
>
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Received on 2010-05-07 02:52:52

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