Hi Andrew:
Andrew Stewart wrote:
> Hi all,
>
> I am working with an Orion DT-12, which is basically a $20,000 piece of
> junk that my lab bought god knows why and it collects dust like none
> other. Oh yeah, the company that made it went out of business too. It
> has twelve single-processor nodes, each with a gig of ram.
>
> Anyways, it came with mpiblast pre-installed and I've been trying to get
> it to work to little avail. I set up my env variables, ran mpiformatdb
> on my blast targets, and issued the command
>
> % mpirun -np 12 mpiblast - -p blastp -d mydb -i myinput -o myoutput -e
> 0.00001 -m 8 -F F
>
> Hit enter, and I simply return to a command line prompt as though the
> program ran to completion. However, there is no activity on qstat and
> no further information is reported. At some point I'll probably ask if
This might be due to the fact that you are not submitting it to SGE.
mpirun runs the subsequent mpi program with the options you give it. I
might suggest using
mpirun -v -np 12 /path/to/mpiblast ...
> anyone on here knows what might be going wrong, but I'd like to take a
> stab at it myself first.. what I'd like to ask the list is if anyone can
> tell me how I can get some more information out of the run. I don't see
> any options for a --verbose mode in mpirun, etc. What logs can I check
> to see whether the job was actually submitted to SGE and how far it
> actually made it if in fact it ever arrived at all?
We have a run_mpiblast script which handles all of the SGE bits if
you need it.
Joe
>
> Any advice would be appreciated.
>
> Thanks,
> Andrew
>
>
> --
> Andrew Stewart
> Research Assistant, Genomics Team
> Navy Medical Research Center (NMRC)
> Biological Defense Research Directorate (BDRD)
> BDRD Annex
> 12300 Washington Avenue, 2nd Floor
> Rockville, MD 20852
>
> email: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
> phone: 301-231-6700 Ext 270
>
>
>
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--
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: [EMAIL PROTECTED]
web : http://www.scalableinformatics.com
phone: +1 734 786 8423
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-------------------------------------------------------------------------
Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier.
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
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