[GE users] PVM w/ SGE

Reuti reuti at staff.uni-marburg.de
Wed Dec 14 21:50:58 GMT 2005


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Hi,

Am 13.12.2005 um 20:57 schrieb Raymond Chan:
<snip>
> In the error file (pfam.err), I always get a  ?pvm_spawn: host 1  
> (compute-0-0.local): hmmpfam-pvm not in path? error.
>
>
>
> However, my host file does find this path correctly when I run PVM  
> HMMER standalone w/o SGE.  I thought this error may mean it?s not  
> in my $PATH environment, so that?s why I added the path to the  
> hmmpfam-pvm binary in the submitted script as well (/apps/HMMER/ 
> bin).  Does SGE control of PVM affect the paths and settings in the  
> PVM host file, so that?s why it always gives me that error?  I  
> apologize that this is also a PVM question as well and I know I?m  
> emailing the SGE list, but since I only have problems during SGE, I  
> thought maybe you guys would be more help.  FYI: I?m running this  
> all on a ROCKS 4.0.0 x86_64 cluster.
the default hostfile isn't used by the SGE startup (you mean the file  
which you specify if you start pvm by hand after the pvm command?).

Instead it will be created for each job again. So you could try to  
define in the start_proc_args of your PE as additional option:

-ep /apps/HMMER/bin

which should add "* ep=/apps/HMMER/bin" to this temporary hostfile.

HTH - Reuti
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