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From: Warner Yuen (wyuen_at_[hidden])
Date: 2006-02-06 17:25:34


Brian help!!!!!! :-)

On Feb 5, 2006, at 9:00 AM, users-request_at_[hidden] wrote:

>> If this is the case, my next question is, how do I supply the usual
>> xgrid options, such as working directory, standard input file, etc?
>> Or is that simply not possible?
>> Do I simply have to have some other way (eg ssh) to get files to/
>> from agent machines, like I would for a batch system like PBS?
>
> It looks like I never implemented those options (shame on me). I've
> added that to my to-do list, although I can't give an accurate time-
> table for implementation at this point. One thing to note is that
> rather than using XGrid's standard input/output forwarding services,
> we use Open MPI's services. So if you do:
>
> mpirun -np 2 ./myapp < foo.txt
>

Under Xgrid with Open MPI, I'm trying to run applications that
require more than just reading standard input/output but also the
creation and writing of other intermediate files. For an application
that like HP Linpack that just reads and writes one file, things work
fine. My guess is that this is where things are getting hung up.
Below, my application was trying to write out a file called
"testrun.nex.run1.p" and failed. The MrBayes application writes out
two files for each mpi process.

Initial log likelihoods for run 1:
Chain 1 -- -429.987779
Chain 2 -- -386.761468
Could not open file "testrun.nex.run1.p"
Memory allocation error on at least one processor
Error in command "Mcmc"
There was an error on at least one processor
Error in command "Execute"
Will exit with signal 1 (error) because quitonerror is set to yes

Am I just misunderstanding how to set up Open MPI to work with Xgrid?

Warner Yuen
Research Computing Consultant
Apple Computer
email: wyuen_at_[hidden]
Tel: 408.718.2859
Fax: 408.715.0133