Re: [HTCondor-users] Newbie questions about submit

[Samuel Friedman <samf@xxxxxxxxxxx>]

You're pretty close. I would say that you want to change your arguments 
and your list of transfer_input_files.

I would have:

universe                = parallel
executable              = openmpiscript
arguments               = /usr/bin/clustalw-mpi -infile=dataset_11.dat 
-outfile=galaxy_dataset_46.dat -OUTORDER=ALIGNED -SEQNOS=OFF -TYPE=DNA
Getenv                  = True
machine_count           = 4
transfer_input_files    = 
/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat,/usr/bin/clustalw-mpi
should_transfer_files   = yes
when_to_transfer_output = on_exit
Log                     = logs/mpi_$(Process).log
Output                  = logs/mpi_$(Process).out
Error                   = logs/mpi_$(Process).error
notification            = never
queue

Some more information can be found at:
http://research.cs.wisc.edu/htcondor/manual/v7.9/2_9Parallel_Applications.html#SECTION00394000000000000000

You need to give clustalw-mpi all the arguments and you must also 
transfer the executable.

Sam

On 03/29/2013 09:05 AM, leconte wrote:
> hello,
>
>  I'm new to Condor use.
>
>  I try example and make somme code  to explore condor "helloworld" and 
> onther :)  I try ... vanilla universe and MPI.
>
>  all work perfectly ... now I want to make more usefull thing.
>
>  But I have a problem ... I can run a MPI run with mpirun without 
> problem my CLI was like this.
>
> mpirun clustalw-mpi -infile=dataset_11.dat 
> -outfile=galaxy_dataset_46.dat -OUTORDER=ALIGNED -SEQNOS=OFF -TYPE=DNA
>
>
>
> I began to write my submit_file to play with condor_submit command  
> but I don't know where I put my arguments "-OUTORDER=ALIGNED 
> -SEQNOS=OFF -TYPE=DNA "
>
> I try these submit_file without success
>
>
>
> universe                = parallel
> executable              = openmpiscript
> arguments               = /usr/bin/clustalw-mpi
> Getenv                  = True
> machine_count           = 4
> transfer_input_files    = 
> /home/galaxy/galaxy-dist/database/files/000/dataset_11.dat
> should_transfer_files   = yes
> when_to_transfer_output = on_exit
> Log                     = logs/mpi_$(Process).log
> Output                  = logs/mpi_$(Process).out
> Error                   = logs/mpi_$(Process).error
> notification            = never
> queue
>
>
> And this one
>
> universe = MPI
> executable=/usr/bin/clustalw-mpi
> # only with grid and vanilla
> #transfert_executable=True
> log = logfile
> arguments = -OUTORDER=ALIGNED -SEQNOS=OFF -TYPE=DNA
> #input = logs/hooinfile.$(NODE)
> input = /home/galaxy/galaxy-dist/database/files/000/dataset_11.dat
> output = logs/hoooutfile.$(NODE)
> error = logs/hooerrfile.$(NODE)
> machine_count = 4
> should_transfer_files = yes
> when_to_transfer_output = on_exit
> queue
>
>
> And this ... do nothing :( ....
>
> Some advices ?
>
> greetings
> _______________________________________________
> HTCondor-users mailing list
> To unsubscribe, send a message to htcondor-users-request@xxxxxxxxxxx 
> with a
> subject: Unsubscribe
> You can also unsubscribe by visiting
> https://lists.cs.wisc.edu/mailman/listinfo/htcondor-users
>
> The archives can be found at:
> https://lists.cs.wisc.edu/archive/htcondor-users/


--

Dr. Samuel H. Friedman                University of Wisconsin-Madison
Center for High Throughput Computing  Department of Computer Sciences
samf@xxxxxxxxxxx                      1210 W. Dayton St. Rm #4246
Phone: (608) 263-2150                 Madison, WI 53706-1685