I am not sure I understand what you mean, but if you are setting the
job to run with a ppn of greater than one but GALAXY_SLOTS is being
evaluated as 1 then you have likely uncovered a bug - maybe in the
runner, your job configuration, or the GALAXY_SLOTS logic for
pbs/torque.

I have created a Galaxy tool for debugging the problem -
https://gist.github.com/jmchilton/9548516. If you could run in your
environment and assign it multiple cores it should spit out some
interesting information relevant to debugging the problem. It will
create Galaxy datasets corresponding to the runtime-computed Galaxy
slots, the contents of PBS_NODEFILE which Galaxy attempts to use to
compute Galaxy slots, and the full contents of your worker node
environment. This last one may contain sensitive information - but if
you could post the first two or send them to me directly it would
hopefully help debug the problem.

-John

On Wed, Mar 12, 2014 at 12:37 PM, Geert Vandeweyer
<geert.vandewey...@uantwerpen.be> wrote:
> How would those statements translate to pbs/torque (pbs_python)
>
> I request resources using the nodes=1:ppn:4 syntax.  The -pe argument is not
> available it seems...
>
> Best,
>
> Geert
>
>
> On 03/12/2014 04:43 PM, Björn Grüning wrote:
>>
>> Hi Geert,
>>
>> you can give every tool a different amount of SLOTS via the job_conf.xml
>> file.
>>
>> https://wiki.galaxyproject.org/Admin/Config/Jobs
>>
>> For example:
>>
>>         <tool
>> id="toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_variant_recalibrator"
>> destination="12cores_24G" />
>>
>>
>> where 12cores_24G is defined with a parallel SGE environment.
>>
>> Cheers,
>> Bjoern
>>
>> Am 12.03.2014 16:32, schrieb Geert Vandeweyer:
>>>
>>> Hi,
>>>
>>> Is there documentation for the proper setup and utilisation of the
>>> \${GALAXY_SLOTS:-4} style options?
>>>
>>> I noticed that tools with this setting, including BWA and GATK run
>>> single threaded, with the following settings respectively:
>>>
>>> BWA  \${GALAXY_SLOTS:-4}"
>>> ===
>>> ps output: python
>>>
>>> /galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/b4427dbb6ced/bwa_wrappers/bwa_wrapper.py
>>> --threads=1 --fileSource=indexed
>>> --ref=/galaxy/galaxy_references/hg19/bwa-0.5.9/base/hg19.fasta
>>> --do_not_build_index
>>> --input1=/galaxy/galaxy-dist/database/files/093/dataset_93021.dat
>>> --input2=/galaxy/galaxy-dist/database/files/093/dataset_93023.dat
>>> --output=/galaxy/galaxy-dist/database/files/000/112/dataset_112301.dat
>>> --genAlignType=paired --params=pre_set --suppressHeader=false
>>>
>>> xml config: --threads="\${GALAXY_SLOTS:-4}"
>>>
>>>
>>> GATK Base Recalibrator \${GALAXY_SLOTS:-8}
>>> ==============
>>> python
>>>
>>> /galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/8bcc13094767/gatk2/gatk2_wrapper.py
>>> --max_jvm_heap 6g --stdout
>>> /galaxy/galaxy-dist/database/files/000/112/dataset_112292.dat -d -I
>>> /galaxy/galaxy-dist/database/files/000/112/dataset_112289.dat bam
>>> gatk_input -d
>>> /galaxy/galaxy-dist/database/files/_metadata_files/012/metadata_12686.dat
>>> bam_index
>>> gatk_input -p           java -jar
>>> "$GATK2_PATH/GenomeAnalysisTK.jar"        -T "BaseRecalibrator"
>>> $GATK2_SITE_OPTIONS      --num_cpu_threads_per_data_thread
>>> ${GALAXY_SLOTS:-8}      --no_standard_covs          -R
>>> "/galaxy/galaxy_references/hg19/srma-0.1.15/hg19.fasta" --out
>>> "/galaxy/galaxy-dist/database/files/000/112/dataset_112291.dat" -cov
>>> "ContextCovariate"             -cov "CycleCovariate"     -d
>>> --knownSites:dbsnp,%(file_type)s
>>> /galaxy/galaxy-dist/database/files/000/101/dataset_101086.dat vcf
>>> input_dbsnp_0 -p --pedigreeValidationType "STRICT" -d --intervals
>>> /galaxy/galaxy-dist/database/files/000/100/dataset_100129.dat bed
>>> input_intervals_0 -p --interval_set_rule "UNION" -p --downsampling_type
>>> "NONE" -p          --baq "OFF" --baqGapOpenPenalty
>>> "40.0"                  --defaultBaseQualities "-1"
>>> --validation_strictness "STRICT" --interval_merging "ALL"
>>>
>>> java -Xmx6g -jar
>>> /galaxy/galaxy-dist/tool-data/shared/jars/gatk2//GenomeAnalysisTK.jar -T
>>> BaseRecalibrator --num_cpu_threads_per_data_thread 1 --no_standard_covs
>>> -R /galaxy/galaxy_references/hg19/srma-0.1.15/hg19.fasta --out
>>> /galaxy/galaxy-dist/database/files/000/112/dataset_112291.dat -cov
>>> ContextCovariate -cov CycleCovariate --pedigreeValidationType STRICT
>>> --interval_set_rule UNION --downsampling_type NONE --baq OFF
>>> --baqGapOpenPenalty 40.0 --defaultBaseQualities -1
>>> --validation_strictness STRICT --interval_merging ALL -I
>>> /tmp/tmp-gatk-fIuncH/gatk_input.bam --knownSites:dbsnp,vcf
>>> /tmp/tmp-gatk-fIuncH/input_dbsnp_0.vcf --intervals
>>> /tmp/tmp-gatk-fIuncH/input_intervals_0.bed
>>>
>>>
>>> Best,
>>>
>>> Geert
>>>
>>>
>>>
>>>
>
>
> --
>
> Geert Vandeweyer, Ph.D.
> Department of Medical Genetics
> University of Antwerp
> Prins Boudewijnlaan 43
> 2650 Edegem
> Belgium
> Tel: +32 (0)3 275 97 56
> E-mail: geert.vandewe...@ua.ac.be
> http://ua.ac.be/cognitivegenetics
> http://www.linkedin.com/in/geertvandeweyer
>
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