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Old 05-21-2010, 04:31 AM   #1
Registered: Oct 2005
Location: Italy
Distribution: Gentoo
Posts: 83

Rep: Reputation: 17
Parallel mpirun non interactive run uses wrong lib on cluster nodes

I am having this issue with Intel compiled version of openMpi which apparently prevents parallel running on home made cluster nodes:
Here below is the output of ldd command on the program which is on shared nfs dir:

On the Master

pier@mindthegap /mnt/sda4/WRFiFort/WRFV3/test/em_real $ ldd /mnt/sda4/WRFiFort/WRFV3/test/em_real/wrf.exe => (0x00007fffa43ff000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46f7f9e000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46f7d14000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46f7b10000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46f78d4000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46f7605000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46f7383000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46f7108000) => /lib/ (0x00007f46f6f04000) => /lib/ (0x00007f46f6cec000) => /lib/ (0x00007f46f6ae9000) => /lib/ (0x00007f46f6866000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46f8293000) => /lib/ (0x00007f46f664a000) => /lib/ (0x00007f46f62f1000) => /lib/ (0x00007f46f60da000) => /usr/lib/ (0x00007f46f5ea7000) => /usr/lib/ (0x00007f46f5c80000) => /usr/lib/ (0x00007f46f5a2f000) => /usr/lib/ (0x00007f46f56a5000) => /lib/ (0x00007f46f549c000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46f5108000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46f4ef2000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46f4db4000) => /usr/lib/ (0x00007f46f4b7b000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46f4a42000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46f47cb000)
/lib64/ (0x00007f46f8247000) => /lib/ (0x00007f46f45b5000)

non interactively on node1

pier@mindthegap /mnt/sda4/WRFiFort/WRFV3/test/em_real $ ssh node1 ldd /mnt/sda4/WRFiFort/WRFV3/test/em_real/wrf.exe
Warning: untrusted X11 forwarding setup failed: xauth key data not generated
Warning: No xauth data; using fake authentication data for X11 forwarding. => (0x00007fff73ae2000) => /usr/lib/ (0x00007f178d2f5000) => /usr/lib/ (0x00007f178d09b000) => /usr/lib/ (0x00007f178ce97000) => /usr/lib/ (0x00007f178cc62000) => /usr/lib/ (0x00007f178c9c9000) => /usr/lib/ (0x00007f178c76b000) => /usr/lib/ (0x00007f178c50a000) => /lib/ (0x00007f178c306000) => /lib/ (0x00007f178c0ee000) => /lib/ (0x00007f178beeb000) => /lib/ (0x00007f178bc68000) => /lib64/ (0x00007f178d589000) => /lib/ (0x00007f178ba4c000) => /lib/ (0x00007f178b6f3000) => /lib/ (0x00007f178b4dc000) => /lib/ (0x00007f178b2d3000) => /usr/lib/ (0x00007f178b082000) => /usr/lib/ (0x00007f178acf8000) => /lib/ (0x00007f178aae2000) => /usr/lib/ (0x00007f178a8a9000) => /usr/lib/gcc/x86_64-pc-linux-gnu/4.3.4/ (0x00007f178a5ce000)
/lib64/ (0x00007f178d53d000)

interactively on node1:

pier@node1 /mnt/sda4/WRFiFort/WRFV3/test/em_real $ ldd /mnt/sda4/WRFiFort/WRFV3/test/em_real/wrf.exe => (0x00007fffafcce000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46d7f79000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46d7cef000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46d7aeb000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46d78af000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46d75e0000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46d735e000) => /mnt/sda4/WRFiFort/lib/ (0x00007f46d70e3000) => /lib/ (0x00007f46d6edf000) => /lib/ (0x00007f46d6cc7000) => /lib/ (0x00007f46d6ac4000) => /lib/ (0x00007f46d6841000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46d826e000) => /lib/ (0x00007f46d6625000) => /lib/ (0x00007f46d62cc000) => /lib/ (0x00007f46d60b5000) => /usr/lib/ (0x00007f46d5e82000) => /usr/lib/ (0x00007f46d5c5b000) => /usr/lib/ (0x00007f46d5a0a000) => /usr/lib/ (0x00007f46d5680000) => /lib/ (0x00007f46d5477000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46d50e3000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46d4ecd000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46d4d8f000) => /usr/lib/ (0x00007f46d4b56000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46d4a1d000) => /opt/intel/Compiler/11.1/072/lib/intel64/ (0x00007f46d47a6000)
/lib64/ (0x00007f46d8222000) => /lib/ (0x00007f46d4590000)

How to make the program use the "right" intel libs (preventing mixing of mpi intel-gnu compiled libs) when run non interactively by mpirun?

Thanks for any hint on this,

Last edited by Pier; 05-21-2010 at 04:49 AM.
Old 05-21-2010, 08:28 AM   #2
Registered: Oct 2005
Location: Italy
Distribution: Gentoo
Posts: 83

Original Poster
Rep: Reputation: 17
Well, it seems I got over with writing a wrap script:


# initialize intel environment
. /mnt/sda4/WRFiFort/

ulimit -s unlimited

Yet I don't know whether a solution as such is a bad slimy workaround.


cluster, noninteractive

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