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From: | Olaf Lenz |
Subject: | Re: [ESPResSo-users] running on cluster |
Date: | Tue, 26 Nov 2013 13:17:19 +0100 |
Dear guozhicheng222,
please make sure libfftw.so.3 is in /usr/local/lib
Furthermore, you can add /usr/local/lib to you LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
I assume, you get the error 8 times, because you run with mipexec or mpirun -np 8, correct?
Good luck
Stefan
On 11/26/2013 05:59 AM, guozhicheng222 wrote:
Hi:
I find the strange error when I am running the simulation in cluster. It is working on main node of cluster, however, crashed on subordinate node of cluster. I checked the error message on subordinate node as described below:
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
/gpfs/home/lsd001/espresso-3.2.0/bin/Espresso: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
In addition, I used "ldd Espresso" command to check the configuration of 'libfftw3.so.3' and found that it's correct as following. I'm really confused about this matter. Anyone can help me to fix it? Thanks in advance for your suggestion.
linux-vdso.so.1 => (0x00007fffe09fc000)
libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x00002b5cca25f000)
libtk8.6.so => /usr/local/lib/libtk8.6.so (0x00002b5cca51e000)
libtcl8.6.so => /usr/local/lib/libtcl8.6.so (0x00002b5cca764000)
libm.so.6 => /lib64/libm.so.6 (0x00002b5cca9bd000)
libSM.so.6 => /usr/X11R6/lib64/libSM.so.6 (0x00002b5ccab12000)
libICE.so.6 => /usr/X11R6/lib64/libICE.so.6 (0x00002b5ccac1d000)
libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x00002b5ccad38000)
libmpi.so.1 => /gpfs/home/lsd001/openmpi-1.6.5/lib/libmpi.so.1 (0x00002b5ccaf46000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b5ccb263000)
libnuma.so.1 => /usr/lib64/libnuma.so.1 (0x00002b5ccb367000)
librt.so.1 => /lib64/librt.so.1 (0x00002b5ccb46c000)
libnsl.so.1 => /lib64/libnsl.so.1 (0x00002b5ccb576000)
libutil.so.1 => /lib64/libutil.so.1 (0x00002b5ccb68c000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b5ccb78f000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b5ccb89d000)
libc.so.6 => /lib64/libc.so.6 (0x00002b5ccb9b6000)
libXft.so.2 => /usr/X11R6/lib64/libXft.so.2 (0x00002b5ccbbf6000)
libfreetype.so.6 => /usr/lib64/libfreetype.so.6 (0x00002b5ccbd0c000)
libfontconfig.so.1 => /usr/lib64/libfontconfig.so.1 (0x00002b5ccbe87000)
libXrender.so.1 => /usr/X11R6/lib64/libXrender.so.1 (0x00002b5ccbfca000)
libXss.so.1 => /usr/X11R6/lib64/libXss.so.1 (0x00002b5ccc0d4000)
libXext.so.6 => /usr/X11R6/lib64/libXext.so.6 (0x00002b5ccc1d7000)
libz.so.1 => /lib64/libz.so.1 (0x00002b5ccc2e8000)
libimf.so => /gpfs/hpc/intel/Compiler/11.1/064/lib/intel64/libimf.so (0x00002b5ccc3fd000)
libsvml.so => /gpfs/hpc/intel/Compiler/11.1/064/lib/intel64/libsvml.so (0x00002b5ccc78f000)
libintlc.so.5 => /gpfs/hpc/intel/Compiler/11.1/064/lib/intel64/libintlc.so.5 (0x00002b5ccc9a5000)
/lib64/ld-linux-x86-64.so.2 (0x00002b5cca143000)
libexpat.so.1 => /usr/lib64/libexpat.so.1 (0x00002b5cccae3000)
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