Custom Query (87 matches)

The initial disk space allocated to OML server was 5GB.

After more experiments ran, the partition filled out (almost fully by the postgres database) and required disk size increase.

The disk size has now been increased to 100GB and the VM is restarted.

I got my experiment running and tried to dump the results to iRODS.

I encountered two problems with this dump. The first is captured in ticket #93. The second problem is that the irodsPath does not seem to be correct. In the oml2-irods-dumper.log file I see:

 INFO    Creating experiment directory first
 irods://irodsHost:irodsPortjo0530
 ............>>>105
 INFO    Pushing
 /tmp/gemini70-jotest7-2014-05-30T19-50-09.2014-05-30_19:52:58+0000.pg.sql
 to irods://irodsHost:irodsPortjo0530

This path only has jo0530. It does not include the project directory. It should have been geni-GIMITesting/jo0530.

The user does not have access to the data they dumped because they do not have permissions to /home/gimiadmin. They only have access to their project directories in /home/gimiadmin.

I got my experiment running and tried to dump the results to iRODS.

I encountered two problems with this dump. The first is that it seems that pg_dump is not installed on gimi1 so it is not properly dumping the database contents to the SQL file.

I saw this in the oml2-irods-dumper.log file:

DEBUG LWWidget: Calling 'on_dump on 'LabWiki::Plugin::Experiment::ExperimentWidg
et' widget
DEBUG ExperimentWidget: DUMP State as requested for Experiment gemini70-jotest7-
2014-05-30T19-50-09
INFO    Dumping PostgreSQL DB gemini70-jotest7-2014-05-30T19-50-09 as /tmp/gemin
i70-jotest7-2014-05-30T19-50-09.2014-05-30_19:52:58+0000.pg.sql and pushing to i
RODS
CMD: pg_dump -O -U oml2 -h gimi2.casa.umass.edu -p 5432 gemini70-jotest7-2014-05
-30T19-50-09 > /tmp/gemini70-jotest7-2014-05-30T19-50-09.2014-05-30_19:52:58+000
0.pg.sql
/home/gimiadmin/oml2-irods-dumper.sh: line 103: pg_dump: command not found
INFO    Creating experiment directory first irods://irodsHost:irodsPortjo0530
............>>>105
INFO    Pushing /tmp/gemini70-jotest7-2014-05-30T19-50-09.2014-05-30_19:52:58+0000.pg.sql to irods://irodsHost:irodsPortjo0530