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If I do a qsub on the script I get the same error message:
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">job_number: 6597054</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">exec_file: job_scripts/6597054</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">submission_time: Sun May 3 21:15:23 2015</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">owner: tcrnma3</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">uid: 147447</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">group: users</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">gid: 1002</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">sge_o_home: /home/tcrnma3/</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">sge_o_log_name: tcrnma3</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">sge_o_path: /shared/ucl/apps/mrxvt/0.5.4/bin:/shared/ucl/apps/nedit/5.6/bin:/shared/ucl/apps/gerun/i:/usr/mpi/qlogic//sbin:/usr/mpi/qlogic//bin:/usr/lib64/qt-3.3/bin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/sbin:/usr/sbin:/shared/ucl/apps/bin:/cm/shared/apps/intel/toolkit/Compiler/11.1/072//bin:/cm/shared/apps/intel/toolkit/Compiler/11.1/072//bin/intel64:/cm/shared/apps/sge/6.2u3/bin/lx26-amd64:/home/tcrnma3//bin</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">sge_o_shell: /bin/bash</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">sge_o_workdir: /imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">sge_o_host: login06</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">account: ucl_jsv4h;S=0;T=1.0;W=1.0;X=1.0;Y=1.0;V=0;Z=1.0;U=1.0</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">stderr_path_list: NONE:NONE:/imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit.stderr</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">hard resource_list: batch=true,bonus=0,h_rt=540,jcs=0,jct=1,jcu=1,jcv=0,jcw=1,jcx=1,jcy=1,jcz=1,maxversion=2,memory=1M,penalty=604801,s_rt=530</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">mail_list:
<a href="mailto:tcrnma3@login06.data.legion.ucl.ac.uk">tcrnma3@login06.data.legion.ucl.ac.uk</a></div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">notify: FALSE</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">job_name: B0503-3707460-0</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">stdout_path_list: NONE:NONE:/imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit.stdout</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">jobshare: 0</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">restart: n</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">shell_list: NONE:/bin/ksh</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">env_list: WORKER_LOGGING_LEVEL=NONE,XAUTHORITY=/scratch/scratch/tcrnma3/.Xauthority,PAID=0,GPU=0,OMP_NUM_THREADS=1,MICCOUNT=0,SCRATCH_SPACE=10737418240,MEMPERSLOT=1048576,SGE_SHARENODE=1,IFS=<span class="Apple-tab-span" style="white-space:pre">
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">script_file: SGE7948718974736431209.submit</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">project: AllUsers</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">error reason 1: 05/03/2015 21:15:57 [147447:18805]: error: can't open output file "/imports/home1/tcrnma3/Scratch/Ur</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">scheduling info: (Collecting of scheduler job information is turned off)</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Mark</div>
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<div>On May 3, 2015, at 9:06 PM, Mihael Hategan <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">It seems that it is more likely that the error message gets truncated<br>
rather than the path itself. After all, stdout_path_list does contain<br>
what seems to be the correct path.<br>
<br>
There should be a<br>
script: /imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit<br>
(or similar) that should be available while a swift run is in progress. <br>
<br>
I think one way to troubleshoot things would be to copy that script and<br>
submit it manually.<br>
<br>
Mihael<br>
<br>
On Sun, 2015-05-03 at 19:20 +0000, Altaweel, Mark wrote:<br>
<blockquote type="cite">Yes so I do import swift in the shell script that gets distributed. However, same conclusion it seems. I don’t understand why it truncates the path, unless it is there but only writes a certain number of the characters.<br>
<br>
This is added to the script:<br>
<br>
export PATH=$PATH:~/Scratch/swift-0.96-sge-mod/bin<br>
module load java/1.7.0_45<br>
<br>
So java is included. If I remove it same thing happens though.<br>
<br>
Mark<br>
<br>
<br>
<br>
On May 3, 2015, at 8:07 PM, Mihael Hategan <<a href="mailto:hategan@mcs.anl.gov">hategan@mcs.anl.gov</a><<a href="mailto:hategan@mcs.anl.gov">mailto:hategan@mcs.anl.gov</a>>> wrote:<br>
<br>
On Sun, 2015-05-03 at 18:43 +0000, Altaweel, Mark wrote:<br>
error reason 1: 05/03/2015 19:38:15 [147447:22761]: error: can't open output file "/imports/home1/tcrnma3/Scratch/Ur<br>
<br>
... aaand my PE suggestion had little to do with the problem.<br>
<br>
Is /imports mounted on compute nodes?<br>
<br>
Mihael<br>
<br>
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</blockquote>
<br>
<br>
</blockquote>
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