Re: [ESPResSo-users] running on cluster

[Olaf Lenz]

Hi!

You write that it works on the main node, but not on the subordinate nodes. Apparently, the subordinate nodes do not have the same libraries installed, at least not in the same locations as the main node. In this case, fftw3 seems not to exist on the nodes.

A solution to this is either to install fftw3 on the subordinate nodes, or to compiled and install fftw3 and ESPResSo statically, so that the binary contains all code.

Olaf 

2013/11/26 Stefan Kesselheim <address@hidden>

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)

--

Dr. rer. nat. Olaf Lenz

Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart

Phone: +49-711-685-63607