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Re: [HTCondor-users] Newbie questions about submit
- Date: Fri, 29 Mar 2013 10:44:37 -0500
- From: Samuel Friedman <samf@xxxxxxxxxxx>
- Subject: Re: [HTCondor-users] Newbie questions about submit
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
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--
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