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Thanks Yadu.
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<div>Yes I did check and digging in it seems to fail :</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">6596817 2.69388 B0503-3707 tcrnma3 Eqw 05/03/2015 19:37:48 </div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">And then if I look at the reason (qstat -j) I get this (basically the error reason shows a truncated version of my file submitted):</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Seems odd that it shortens the path or at least indicates that it does this.</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Mark</div>
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<div style="margin: 0px;">job_number: 6596817</div>
<div style="margin: 0px;">exec_file: job_scripts/6596817</div>
<div style="margin: 0px;">submission_time: Sun May 3 19:37:48 2015</div>
<div style="margin: 0px;">owner: tcrnma3</div>
<div style="margin: 0px;">uid: 147447</div>
<div style="margin: 0px;">group: users</div>
<div style="margin: 0px;">gid: 1002</div>
<div style="margin: 0px;">sge_o_home: /home/tcrnma3/</div>
<div style="margin: 0px;">sge_o_log_name: tcrnma3</div>
<div style="margin: 0px;">sge_o_path: /shared/ucl/apps/Java/64/jdk1.7.0_45/bin:/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:/home/tcrnma3//Scratch/swift-0.96-sge-mod/bin:/sbin</div>
<div style="margin: 0px;">sge_o_shell: /bin/bash</div>
<div style="margin: 0px;">sge_o_workdir: /imports/home1/tcrnma3/Scratch/UrbanModel</div>
<div style="margin: 0px;">sge_o_host: login08</div>
<div style="margin: 0px;">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;">stderr_path_list: NONE:NONE:/imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit.stderr</div>
<div style="margin: 0px;">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;">mail_list: <a href="mailto:tcrnma3@login08.data.legion.ucl.ac.uk">
tcrnma3@login08.data.legion.ucl.ac.uk</a></div>
<div style="margin: 0px;">notify: FALSE</div>
<div style="margin: 0px;">job_name: B0503-3707460-0</div>
<div style="margin: 0px;">stdout_path_list: NONE:NONE:/imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit.stdout</div>
<div style="margin: 0px;">jobshare: 0</div>
<div style="margin: 0px;">restart: n</div>
<div style="margin: 0px;">shell_list: NONE:/bin/ksh</div>
<div style="margin: 0px;">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">
</span></div>
<div style="margin: 0px;">script_file: /imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit</div>
<div style="margin: 0px;">project: AllUsers</div>
<div style="margin: 0px;">error reason 1: 05/03/2015 19:38:15 [147447:22761]: error: can't open output file "/imports/home1/tcrnma3/Scratch/Ur</div>
<div style="margin: 0px;">scheduling info: (Collecting of scheduler job information is turned off)</div>
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<div>On May 3, 2015, at 2:32 PM, Yadu Nand Babuji <<a href="mailto:yadunand@uchicago.edu">yadunand@uchicago.edu</a>> wrote:</div>
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<div bgcolor="#FFFFFF" text="#000000">Hi Mark,<br>
<br>
What you are seeing is progress reports from swift at an interval of 30s, and all this<br>
indicates is that your jobs were submitted to the queue for execution. Until the local resource<br>
manager, in this case the SGE scheduler starts the execution of jobs swift will have to wait.<br>
>From you description all I can gather is that you are seeing long wait times, with no indications<br>
of a any failure.<br>
<br>
Could you check if you can spot the jobs submitted by swift to the queue ? For this, open<br>
a separate terminal on the login node while your swift run is waiting in submitted state,<br>
and use qstat to see your jobs.<br>
<br>
[coursa1@login06 part05]$ qstat <br>
job-ID prior name user state submit/start at queue slots ja-task-ID
<br>
-----------------------------------------------------------------------------------------------------------------<br>
6593408 0.00000 B0503-2802 coursa1 qw 05/03/2015 14:28:40 1
<br>
6593409 0.00000 B0503-2802 coursa1 qw 05/03/2015 14:28:41 1
<br>
<br>
The qw state indicates that your jobs are waiting in the queue.<br>
<br>
Thanks,<br>
Yadu<br>
<br>
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<div class="moz-cite-prefix">On 05/03/2015 01:11 AM, Altaweel, Mark wrote:<br>
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<blockquote cite="mid:20A806EE-399C-47ED-84EE-39F240C6CFFD@live.ucl.ac.uk" type="cite">
Hi,
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<div>I tried executing Swift on our institutions’s sge-based cluster and the submission seems hung or not executing properly. It has the following message:</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Swift 0.96-RC1 git-rev: c7a1dc478a40865f5639f186284697d53978bd48 heads/release-0.96-swift 6274 (modified locally)</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">RunID: run002</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:00:29+0100</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Number of parameter combinations: 2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Stride: 1</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Begin: 1, End: 1</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Begin: 2, End: 2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:00:30+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Error: No parallel environment specified</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:01:00+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:01:30+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:02:00+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:02:30+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:03:00+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:03:30+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:04:00+0100 Submitted:2</div>
<div style="margin: 0px; font-size: 11px; font-family: Menlo;">Progress: Sun, 03 May 2015 07:04:30+0100 Submitted:2</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">This is just repeated and does not seem to stop</div>
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<div style="margin: 0px; font-size: 11px; font-family: Menlo;">The log file has the following messages, which also repeat:</div>
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<div style="margin: 0px;">2015-05-03 07:08:22,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64559392, JVMThreads: 52</div>
<div style="margin: 0px;">2015-05-03 07:08:23,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64559432, JVMThreads: 52</div>
<div style="margin: 0px;">2015-05-03 07:08:23,709+0100 INFO AbstractQueuePoller Actively monitored: 1, New: 0, Done: 0</div>
<div style="margin: 0px;">2015-05-03 07:08:24,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64584080, JVMThreads: 52</div>
<div style="margin: 0px;">2015-05-03 07:08:25,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64584120, JVMThreads: 52</div>
<div style="margin: 0px;">2015-05-03 07:08:26,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64584160, JVMThreads: 52</div>
<div style="margin: 0px;">2015-05-03 07:08:27,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64584200, JVMThreads: 52</div>
<div style="margin: 0px;">2015-05-03 07:08:28,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64584240, JVMThreads: 52</div>
<div style="margin: 0px;">2015-05-03 07:08:29,401+0100 INFO RuntimeStats$ProgressTicker HeapMax: 954728448, CrtHeap: 378535936, UsedHeap: 64584280, JVMThreads: 52</div>
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<div style="margin: 0px;">I did run this locally to see if anything is wrong with the submission and it worked fine with proper output.</div>
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<div style="margin: 0px;">Thank you.</div>
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<div style="margin: 0px;">Mark</div>
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<pre wrap="">_______________________________________________
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