[GE users] lam tight integration scripts

Reuti reuti at staff.uni-marburg.de
Thu Apr 7 00:05:25 BST 2005


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Mark,

what is the definition of your PE? As line 32 is a done in the script, there 
must be already before an error. Are you using $pe_hostfile in your PE, which 
has the format necessary for this routine to function?

Supplying a hostlist on your own will not work, as SGE grants only qrsh to the 
nodes it selected for this job.

Cheers - Reuti

Quoting mark garey <garey at biostat.ucsf.edu>:

> hello,
> 
> i am trying to implement the lam tight qrsh integration scripts, but 
> the PeHostfile2MachineFile
> function in the startlam.sh script fails with this error when parsing 
> each node in the lamhost file:
> 
> /export/sge/default/lam_tight_qrsh/startlam.sh: line 32: [: head: 
> integer expression expected
> 
> where 'head' is a node in the list of nodes in the lamhosts file. this 
> error  results in an empty
> machines file ( after the lamosts file is read ). as recommended the 
> lamhost file format is
> node1
> node1
> node2
> node2
> etc...
> 
> if this function is commented out and a vaild list is used from 
> /tmp/machines, the job ( tester_mpi.sh
> in this case ) migrates out to the number of slots specified in the pe, 
> but the equivalent
> lam daemons fail to boot on all the nodes and the tester job aborts.
> 
> i using the patched hboot and lam 7.1.1.
> 
> --
> mark garey
> ucsf department of epidemiology and biostatistics
> 500 parnassus ave, mu420w
> san francisco, ca. 94143
> 415-502-8870
> 
> 
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