Problem loading modules on blacklight Annalise Marie Nawrocki https://conferences.xsede.org/c/message_boards/find_message?p_l_id=&messageId=390783 2012-09-25T22:29:06Z 2012-09-25T22:29:06Z

I recently submitted a Trinity job on Blacklight, but it failed:<br /><br />PBS Job Id: 200001.tg-login1.blacklight.psc.teragrid.org<br />Job Name: Nawrocki3_qsub.txt<br />Exec host: bl1.psc.teragrid.org<br />Aborted by PBS Server<br />Job cannot be executed<br />See Administrator for help<br /><br />I checked the log file and it says the following:<br /><br />module load trinity<br />module: Command not found<br />module load java<br />Module: Command not found<br />ulimit -u unlimited<br />ulimit: Command not found<br />Trinity.pl &lt;my trinity command was here but that&#039;s not the problem.&gt;<br />Trinity.pl: Command not found<br /><br />I am not sure how to get it to properly load the modules. It works fine outside of my qsub script when I do it in the command line. <br /><br />This is the qsub file I am using to execute the program:<br /><br /><br />#!/bin/csh<br /># combine stderr and stout into one stream<br />#PBS -N Trinity<br />#PBS -l ncpus=32<br />#PBS -l walltime=48:00:00<br />#PBS -j oe<br />#PBS -q batch<br />set echo<br /># output<br />#PBS cd $SCRATCH<br />#PBS -o trinity.log<br /><br /><br />$SCRATCH/Ectopleura_files<br /><br />load module java<br />load module trinity/r2011-08-20cd<br />load module trinity<br />ulimit -s unlimited<br />Trinity.pl --seqType fq --kmer_method meryl --cpu 64 --left old_cat_Forward_all.fastq --right old_cat_Reverse_all.fastq --output $SCRATCH --min_contig_length 200 --paired_fragment_length 175 --CPU 32--bflyCPU 32 --bflyGCThreads 32 --bflyHeapspaceInit 8G<br /><br /><br /><br />Thanks for any help<br /><br />AM Nawrocki

Annalise Marie Nawrocki 2012-09-25T22:29:06Z