Running Galaxy on a cluster with SLURM ?

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Running Galaxy on a cluster with SLURM ?

Carlos Lijeron
Hello everyone,

I¹m setting up Galaxy to run on our cluster which uses SLURM as the job
manager.   I am wondering if any of you have any expertise in this area,
ideas to share or lessons learned.   I carried out the following steps
listed below, but I can¹t make the final connection just yet.  Any
pointers will be greatly appreciated.

1. Setup Galaxy to run on the head node
2. Setup MySQL and it¹s running well with Galaxy
3. Setup the drmaa-python library inside our Galaxy folder


Main questions:

What would be the next step to take?

Where to setup Galaxy to use an exclusive pool of resources (called
partition in SLURM).



Thank you all !


Carlos.

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Re: Running Galaxy on a cluster with SLURM ?

Sven E. Templer
Hi Carlos,

next steps might include:

* install slurm drmaa


e.g.

tar -xf slurm-drmaa-1.0.7.tar.gz
cd slurm-drmaa-1.0.7
p=$(which srun)
p=${p%/bin/srun}/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH="$p"
./configure #CFLAGS="-g -O0"
make
sudo make install
# rm -r slurm-drmaa*
# Make the config file writeable by group_galaxy:
sudo touch /etc/slurm_drmaa.conf
sudo cp /etc/slurm_drmaa.conf /etc/slurm_drmaa.conf.original
sudo chown :group_galaxy /etc/slurm_drmaa.conf
sudo chmod g+w /etc/slurm_drmaa.conf
# Test the drmaa-run binary by submitting a small job:
export DRMAA_LIBRARY_PATH=/usr/local/lib/libdrmaa.so
echo 'echo "Test executed on host $(hostname) by user $USER"' > test.drmaa
drmaa-run bash test.drmaa


job_categories: {
  default: "-J galaxy -p galaxy_partition",
},

* configure config/job_conf.xml [https://wiki.galaxyproject.org/Admin/Config/Jobs], e.g.

<xml version="1.0"?>
<job_conf>
<plugins workers="10">
<plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner">
<param id="drmaa_library_path">/usr/local/lib/libdrmaa.so</param>
</plugin>
</plugins>
<handlers default="handlers">
<handler id="main" tags="handlers">
<plugin id="slurm"/>
</handler>
</handlers>
<destinations default="slurm_part">
<destination id="slurm_part" runner="slurm">
  </destination>
  <destination id="slurm_part_12" runner="slurm">
    <param id="nativeSpecification">--ntasks=12</param>
</destination>
</destinations>
<tools>
<tool id="flexbar" destination="slurm_part_12"/>
<tool id="tophat2" destination="slurm_part_12"/>
<tool id="bowtie2" destination="slurm_part_12"/>
<tool id="bwa_wrapper" destination="slurm_part_12"/>
  <!-- ... -->
</tools>
</job_conf>

* Have fun!

Sven

On 21 September 2015 at 21:14, Carlos Lijeron <[hidden email]> wrote:
Hello everyone,

I¹m setting up Galaxy to run on our cluster which uses SLURM as the job
manager.   I am wondering if any of you have any expertise in this area,
ideas to share or lessons learned.   I carried out the following steps
listed below, but I can¹t make the final connection just yet.  Any
pointers will be greatly appreciated.

1. Setup Galaxy to run on the head node
2. Setup MySQL and it¹s running well with Galaxy
3. Setup the drmaa-python library inside our Galaxy folder


Main questions:

What would be the next step to take?

Where to setup Galaxy to use an exclusive pool of resources (called
partition in SLURM).



Thank you all !


Carlos.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


On 21 September 2015 at 21:14, Carlos Lijeron <[hidden email]> wrote:
Hello everyone,

I¹m setting up Galaxy to run on our cluster which uses SLURM as the job
manager.   I am wondering if any of you have any expertise in this area,
ideas to share or lessons learned.   I carried out the following steps
listed below, but I can¹t make the final connection just yet.  Any
pointers will be greatly appreciated.

1. Setup Galaxy to run on the head node
2. Setup MySQL and it¹s running well with Galaxy
3. Setup the drmaa-python library inside our Galaxy folder


Main questions:

What would be the next step to take?

Where to setup Galaxy to use an exclusive pool of resources (called
partition in SLURM).



Thank you all !


Carlos.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/