Custom Query (87 matches)

The oml2-server-hook.sh script that is attached to the tutorial instructions and installed on emmy9 will only push results to the appropriate account in irods if the slice name and the user's iRODS account username start with gimi[0-9]. It assumes that the zone on the iRODS server is geniRenci.

NAME=${DBFILE:12:6}; FILE=${DBFILE:12}; LENGTH=${#FILE} SLICE=${FILE:0:$LENGTH-4} DATE=date ${IPUT} ${OPTION} ${DBFILE}

if $NAME =~ ^gimi[0-9] ?; then

echo "Entered..."

ichmod -M own $NAME /geniRenci/home/$NAME/$FILE iput -f ${DBFILE} /geniRenci/home/$NAME/$FILE; imeta add -d /geniRenci/home/$NAME/$FILE Date ${DATE} imeta add -d /geniRenci/home/$NAME/$FILE UserName? $NAME imeta add -d /geniRenci/home/$NAME/$FILE SliceName? $SLICE

fi

The hook script is also very specific to the configuration of the OML server in that it assumes the path to the DB file contains 12 characters. It isn't clear in the instructions that the user will need to adjust the hook script if they want to use it on their own OML server.

We would like a wiki page that describes how to run the init script including screen shots. This wiki page could then be referenced by the tutorials.

The production LabWiki (emmy9.casa.umass.edu:4000) is currently being used by students to run experiments. We noticed a few crashes with the same error as below:

DEBUG development::LabWiki::LWWidget: Calling 'on_stop_experiment on 'LabWiki::Plugin::Experiment::ExperimentWidget' widget


DEBUG development::LabWiki::Plugin::Experiment::ExperimentWidget: STOP EXPERIMENT as requested>>> {:action=>"stop_experiment", :col=>"execute", :sid=>"s6751972_4585340"}


DEBUG development::LabWiki::Plugin::Experiment::Experiment: SEND job stop request to http://emmy9.casa.umass.edu:8003/jobs/841cc39d-58ef-471d-aad4-7df138b71e60>>>


DEBUG development::LabWiki::Plugin::Experiment::Util::RetryHandler: canceled - #<Proc:0x00000003cea5d8@/var/lib/omfwebapps/lw_gec19/plugins/labwiki_experiment_plugin/lib/labwiki/plugin/experiment/log_adapter.rb:31>


DEBUG development::LabWiki::Plugin::Experiment::Util::RetryHandler: canceled - #<Proc:0x00000003cea1a0@/var/lib/omfwebapps/lw_gec19/plugins/labwiki_experiment_plugin/lib/labwiki/plugin/experiment/ec_adapter.rb:32>

terminate called after throwing an instance of 'std::runtime_error'

  what():  unable to add new descriptor: Bad file descriptor

Aborted (core dumped)

The maximum file descriptor size for emmy9 seems to be quite high

gimiadmin@emmy9:~$ cat /proc/sys/fs/file-max
1212548

Is there a maximum limit defined in gems used by LabWiki??