Re: [HTCondor-users] Condor & Bosco submissions

[Guillermo Marco Puche <guillermo.marco@xxxxxxxxxxxxxxxxxxxxx>]

On 03/06/2013 10:04 AM, Guillermo Marco Puche wrote:

Hello Derek,

At this moment i'm submiting jobs to remote SGE in this way.

I've a Condor Job file which specifies Grid Universe, remote cluster user and host etc...
Executable specified in this Condor file is a bash script that starts a small workflow.

Problem is that all SGE parameters inside my bash script are being ignored. And I'm in need of different SGE configuration for each different Workflow (select different queue, slot number, max memory, etc..)

Here's my bash script called by Condor job file:

#!/bin/bash
## select env.var
#$ -V
## job name
#$ -N aln_bosco
## current work directory
#$ -cwd
## merge outputs
#$ -j y 
## select all.q queue
#$ -q all.q

cd /home/mastablasta
bwa aln /home/mastablasta/ref/hg19.fa /home/mastablasta/input/HapMap_2.fastq -t 8 > /home/mastablasta/output/tmp/HapMap.right.sai

If custom scripts are being echoed I don't understand why this isn't working.

Are custom submit properties simple variables? I don't understand the concept with the example in manual.

+remote_cerequirements = NumJobs == 100

Can i pass my script a custom submit property like this for SGE?

+remote_cerequirements = Queue = all.q

I've also trying editing ~/bosco/glite/bin/sge_local_submit_attributes.sh on SGE cluster with no success. After submiting job through Bosco Condor the execution on SGE cluster runs with default queue, 1 slot etc..
It should be using 8 slots with this config file.

#!/bin/bash
$ -V
$ -cwd
$ -j y
$ -q all.q
$ -pe orte 8

Thank you.

Best regards,
Guillermo.

On 03/05/2013 05:49 PM, Derek Weitzel wrote:

Hi Guillermo,

Are you using the configuration described here:
https://twiki.grid.iu.edu/bin/view/CampusGrids/BoscoInstall#7_3_Custom_submit_properties

I'm not sure what you are referring to when you say: "SGE job file configuration".

-Derek




On Mar 5, 2013, at 10:42 AM, Guillermo Marco Puche <guillermo.marco@xxxxxxxxxxxxxxxxxxxxx> wrote:

Hello again,

My setup to remote SGE cluster is finally working !

However Bosco (Condor) is still ignoring my SGE job file configuration. Bosco submits a job to a remote SGE cluster using a Condor job file. 

Executable inside Condor file points to a wrapper script which has SGE configuration inside (number of processors, selected queue, job name, current working directory) but Condor completly ignores them when submiting the job.

Thank you.

Best regards,
Guillermo.

On 03/02/2013 02:22 PM, Guillermo Marco Puche wrote:

Hello, 

That's exactly what i thought. I'll stick to Bosco then ;) 

Thanks. 

Best regards, 
Guillermo. 

El 01/03/2013 18:53, Jaime Frey escribió: 

On Mar 1, 2013, at 5:00 AM, Guillermo Marco Puche <guillermo.marco@xxxxxxxxxxxxxxxxxxxxx> wrote: 

I've been trying Bosco lately and seems to work pretty well for me to submit to another lan cluster SGE cluster. 

For example: 

$ condor_q 
-- Submitter: brugal : <192.168.6.2:11000?sock=3072_dcd9_3> : brugal 
  ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD 
   62.0   gmarco          3/1  04:43   0+00:14:32 R  0   0.0  bwa.sh 


I was then trying to achieve the same but with my local Condor installation and not with condor pool inside Bosco. I'm having no success when trying to submit exactly the same condor job file: 

As root i start condor with "condor_master". 
ps -ef | grep condor 
condor    3850     1  0 05:05 ?        00:00:00 condor_master 
condor    3851  3850  0 05:05 ?        00:00:00 condor_collector -f 
condor    3853  3850  0 05:05 ?        00:00:00 condor_negotiator -f 
condor    3854  3850  0 05:05 ?        00:00:00 condor_schedd -f 
condor    3855  3850  0 05:05 ?        00:00:00 condor_startd -f 
root      3856  3854  0 05:05 ?        00:00:00 condor_procd -A /var/run/condor/procd_pipe.SCHEDD -L /var/log/condor/ProcLog.SCHEDD -R 10000000 -S 60 -C 498 
condor    3907  3855 87 05:05 ?        00:00:03 mips 
root      3924  3758  0 05:05 pts/0    00:00:00 grep condor 
I try to submit my job and holds on Idle state forever, with Bosco I don't have that problem: 

condor_q 

-- Submitter: brugal : <192.168.6.2:41257> : brugal 
  ID      OWNER            SUBMITTED     RUN_TIME ST PRI SIZE CMD 
   26.0   gmarco          3/1  05:07   0+00:00:00 I  0   0.0  bwa.sh 


That's my job file: 

universe = grid 
grid_resource = batch sge gmarco@cacique 
executable = bwa.sh 
output = bwa.out 
error = bwa.err 
log = bwa.log 
should_transfer_files = YES 
transfer_output = true 
stream_output = true 
when_to_transfer_output = ON_EXIT_OR_EVICT 
queue 

Submitting jobs to a remote cluster using a regular installation of HTCondor requires some manual configuration steps, which we don't have documented currently. This is one of the advantages of Bosco. Over time, we may make this kind of job submission easier to do with a regular HTCondor installation. 

Thanks and regards, 
Jaime Frey 
UW-Madison HTCondor Project 

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-- 
<1MjpCpe.png> G.MARCO: Informatician at Sistemas Genómicos S.L
phone: 0034635197460
web: www.sistemasgenomicos.com
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--

g.marco: Informatician at Sistemas Genómicos S.L
phone: 0034635197460
web: www.sistemasgenomicos.com

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