Re: [Condor-users] Parallel submission issue

[Si Hammond <simon.hammond@xxxxxxxxx>]

On 31 Aug 2007, at 16:23, Nicolas GUIOT wrote:

> Please people, I REALLY need help : I'm leaving this lab very soon,  
> and if I can't get this to work for MPI, it's quite sure people  
> will give up using condor, even for mono-cpu jobs, which would be  
> very sad...
>
> News :
>
> I tested MPI with an other program, and I have exactly the same  
> symptoms : 1 computer stores the output files, and each process  
> that runs on this computer finds the file, but the 2nd computer  
> can't find them.
>
> I would like to make a test and put the EXECUTE directory on the  
> same nfs folder. So, I tried to do this :
> condor_config_val -rset EXECUTE=/nfs/scratch-condor/execute
>
> but it failed, whether I run it as root or as condor user :
> Attempt to set configuration "EXECUTE=/nfs/scratch-condor/execute"  
> on master calisto.my.domain.fr <XXX.XXX.XXX.XXX:55829> failed.
>
> So :
> 1- what's the correct solution to have files see-able by all the  
> computers
> 2- for my tests, how can I change the EXECUTE directory to be nfs- 
> shared

Nicolas, have you tried specifying the execute in the machine's  
configuration file (i.e. making every machine use the NFS-shared space)?


> ++
> Nicolas
>
> ----------------
> On Thu, 30 Aug 2007 12:36:08 +0200
> Nicolas GUIOT wrote:
>
> > Hi
> >
> > I'm trying to sumbit an MPI job to my condor pool.
> >
> > The problem is that when I ask it to run on 2 cpus (ie 1  
> > computer), it's fine, but when I ask for 4 CPU (ie 2 computer),  
> > one seems not to find the file to write the output.
> >
> > Here is the submission script :
> > $ cat sub-cond.cmd
> > universe = parallel
> > executable = mp2script
> > arguments = /nfs/opt/amber/amber9/exe/sander.MPI -O -i md.in -o  
> > TGA07.1.out -p TGA07.top  -c TGA07.0.rst -r TGA07.1.rst -x  
> > TGA07.1.trj -e TGA07.1.ene
> > machine_count = 4
> > should_transfer_files = yes
> > when_to_transfer_output = on_exit_OR_EVICT
> > transfer_input_files = /nfs/opt/amber/amber9/exe/ 
> > sander.MPI,md.in,TGA07.top,TGA07.0.rst
> > Output  = sanderMPI.out
> > Error   = sanderMPI.err
> > Log     = sanderMPI.log
> > queue
> >
> > I'm starting the script from a directory that is nfs-shared :
> >
> > (/nfs/test-space/amber)$ ls
> > blu.sh  clean.sh  md.in  mdinfo  mp2script  mpd.hosts  run_MD.sh   
> > sub-cond.cmd  TGA07.0.rst  TGA07.top
> >
> > The error is a typical amber error when it can't find the result  
> > file (TGA07.1.out is an output file, doesn't exist before runnning  
> > the progam.:
> >
> > $ more sanderMPI.err
> > 0:
> > 0:   Unit    6 Error on OPEN: TGA07.1.out
> >
> > 0: [cli_0]: aborting job:
> > 0: application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> > $
> >
> > So, where is my problem ? NFS ? file transfer ?
> >
> > Any help would be greatly appreciated :)
> >
> > Nicolas
>
>
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