Question: Custom toolshed tool: job memory requirements
0
gravatar for Jelle Scholtalbers
4.0 years ago by
Germany
Jelle Scholtalbers360 wrote:

Is it possible to add job requirements to (toolshed) tools?

For example, if a tool minimally requires >4gb of ram, ("java -Xmx4g") this will most of the time run fine on a non-cluster enabled galaxy instance. However, when using a cluster this might fail with "PBS: job killed: mem job total 4131052 kb exceeded limit 1048576 kb" due to the default job being specified for a low memory machine.

I understand a galaxy admin is able to add this to his job_conf.xml, and thus have absolute control, but when using the toolshed one might expect the tool just to work without fiddling with any xml configuration files.

toolshed • 1.1k views
ADD COMMENTlink modified 4.0 years ago by jmchilton1.1k • written 4.0 years ago by Jelle Scholtalbers360
1
gravatar for Bjoern Gruening
4.0 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi Jelle,

you can try to see if "_JAVA_OPTIONS" is set during execution of your tool. If it's not set you can provide your default settings. Try to document your tool in a way that gives a hint to the Galaxy admin that indicates that he should use "_JAVA_OPTIONS" to override your settings.

Hope this works for you,

Bjoern

ADD COMMENTlink written 4.0 years ago by Bjoern Gruening5.1k

ow, this might indeed be the solution for the error stated... However, I'm actually more referring to an error similar to "PBS: job killed: mem job total 4131052 kb exceeded limit 1048576 kb". (sorry for the confusion). I updated the question.

ADD REPLYlink written 4.0 years ago by Jelle Scholtalbers360
1
gravatar for jmchilton
4.0 years ago by
jmchilton1.1k
United States
jmchilton1.1k wrote:

It is not possible at this time - I have updated this (https://trello.com/c/HGEYPQf6) Trello card with that suggestion. In general deployers state fixed things about how jobs run that are not informed by the tool - I think finding the right way to templatize what the tool author suggest when the deployer is specifying things such as cluster parameters will be a real challenge - but it would definitely make these things more usable. 

ADD COMMENTlink written 4.0 years ago by jmchilton1.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 113 users visited in the last hour