[Swift-user] hung submission

[Altaweel, Mark]

If I do a qsub on the script I get the same error message:

job_number:                 6597054
exec_file:                  job_scripts/6597054
submission_time:            Sun May  3 21:15:23 2015
owner:                      tcrnma3
uid:                        147447
group:                      users
gid:                        1002
sge_o_home:                 /home/tcrnma3/
sge_o_log_name:             tcrnma3
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
sge_o_shell:                /bin/bash
sge_o_workdir:              /imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts
sge_o_host:                 login06
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
stderr_path_list:           NONE:NONE:/imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit.stderr
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
mail_list:                  tcrnma3 at login06.data.legion.ucl.ac.uk<mailto:tcrnma3 at login06.data.legion.ucl.ac.uk>
notify:                     FALSE
job_name:                   B0503-3707460-0
stdout_path_list:           NONE:NONE:/imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit.stdout
jobshare:                   0
restart:                    n
shell_list:                 NONE:/bin/ksh
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=
script_file:                SGE7948718974736431209.submit
project:                    AllUsers
error reason    1:          05/03/2015 21:15:57 [147447:18805]: error: can't open output file "/imports/home1/tcrnma3/Scratch/Ur
scheduling info:            (Collecting of scheduler job information is turned off)

Mark

On May 3, 2015, at 9:06 PM, Mihael Hategan <hategan at mcs.anl.gov<mailto:hategan at mcs.anl.gov>> wrote:

It seems that it is more likely that the error message gets truncated
rather than the path itself. After all, stdout_path_list does contain
what seems to be the correct path.

There should be a
script: /imports/home1/tcrnma3/Scratch/UrbanModel/run005/scripts/SGE7948718974736431209.submit
(or similar) that should be available while a swift run is in progress.

I think one way to troubleshoot things would be to copy that script and
submit it manually.

Mihael

On Sun, 2015-05-03 at 19:20 +0000, Altaweel, Mark wrote:
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.

This is added to the script:

export PATH=$PATH:~/Scratch/swift-0.96-sge-mod/bin
module load java/1.7.0_45

So java is included. If I remove it same thing happens though.

Mark



On May 3, 2015, at 8:07 PM, Mihael Hategan <hategan at mcs.anl.gov<mailto:hategan at mcs.anl.gov><mailto:hategan at mcs.anl.gov>> wrote:

On Sun, 2015-05-03 at 18:43 +0000, Altaweel, Mark wrote:
error reason    1:          05/03/2015 19:38:15 [147447:22761]: error: can't open output file "/imports/home1/tcrnma3/Scratch/Ur

... aaand my PE suggestion had little to do with the problem.

Is /imports mounted on compute nodes?

Mihael

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