[GE users] SGE submission using custom install of OpenMPI

prentice prentice at ias.edu
Mon Apr 26 19:11:52 BST 2010


macmanes wrote:
> Hi All, 
> 
> I am using SGE to submit jobs to one of the TeraGrid sites, specifically TACC-RANGER. The problem, is, that I am using a program that requires OpenMPI version 1.4.1, and the latest install on RANGER is 1.3.1.  I was told that I could install OpenMPI in my home directory, and run jobs using my newer version.. However, I am having problems doing this, getting the error message contained in the attachment. 
> 
> Its seems that the compute nodes are not accessing all the sufficient libraries for the newer version of OpenMPI. 
> 
> Can anybody tell me what I can do to get the jobs running using the newer version of OpenMPI. Thanks!
> 


Your job script is incorrect. Specifically, define your LD_LIBRARY_PATH
6 different times, with each one overwriting the previous definition:

LD_LIBRARY_PATH=/work/01301/mmacmane
LD_LIBRARY_PATH=/work/01301/mmacmane/bin
LD_LIBRARY_PATH=/work/01301/mmacmane/include
LD_LIBRARY_PATH=/work/01301/mmacmane/etc
LD_LIBRARY_PATH=/work/01301/mmacmane/lib
LD_LIBRARY_PATH=/work/01301/mmacmane/openmpi-1.4.1

After these lines, your LD_LIBRARY_PATH is set to

/work/01301/mmacmane/openmpi-1.4.1

This directory pointless to have in your LD_LIBRARY_PATH, too since that
directory itself won't contain any library files.

The correct syntax to define your LD_LIBRARY_PATH with the above
directories would be this:

LD_LIBRARY_PATH=/work/01301/mmacmane:/work/01301/mmacmane/bin:/work/01301/mmacmane/include:/work/01301/mmacmane/etc:/work/01301/mmacmane/openmpi-1.4.1

But that can be simplified significantly, only one of these files
actually contains library files, /work/01301/mmacmane/lib, so you should
only need this:

LD_LIBRARY_PATH=/work/01301/mmacmane/lib

-- 
Prentice

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