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Top Forums UNIX for Dummies Questions & Answers Bsub array problem Post 302893717 by ehj on Thursday 20th of March 2014 05:23:05 PM
Old 03-20-2014
Bsub array problem

I'm trying to run some computations on a cluster and have found that a bsub array is what I need.. So I tried running a simple example I found

Code:
bsub -J "myArray[1-10]" echo "Job \$LSB_JOBINDEX"

This should create 10 jobs that output "Job 1" "Job 2" .. etc. But when I run this from afs space I get the message
"LSB_JOBINDEX: Undefined variable."

LSB_JOBINDEX should be the index of the current array job.. Any ideas what's going on?
 

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ECACCESS-JOB-GET(1p)					User Contributed Perl Documentation				      ECACCESS-JOB-GET(1p)

NAME
ecaccess-job-get - Download a Job Output/Input/Error File SYNOPSIS
ecaccess-job-get -version|-help|-manual ecaccess-job-get [-debug] [-input|-error] [-encrypt] [-binary] [-bufsize length] job-id local-target-file DESCRIPTION
Allow downloading the Job Output/Input/Error Files with identifier job-id. The file is downloaded localy in the local-target-file. ARGUMENTS
job-id The identifier of the ECaccess Job to retrieve. local-target-file The name of the Local Target File. OPTIONS
-input By default the Job Output File is downloaded. Using this option allow downloading the Job Input File instead. -error By default the Job Output File is downloaded. Using this option allow downloading the Job Error File instead. -encrypt By default files are downloaded through the plain text channel (http). Using this option will force the download to occurs through the SSL secure channel (https). -binary By default files are downloaded as text files. This option will download files as binary files (decode_base64 required). Please note that text files can also be downloaded in binary mode but text mode is faster. You should use this option if your job output is containing non-text characters. -bufsize length Specify the length of the buffer (in bytes) which is used to download the file. The larger the buffer the smaller the number of http/s requests. By default a buffer of 524288 bytes(512KB) is used. -version Display version number and exits. -help Print a brief help message and exits. -manual Prints the manual page and exits. -debug Display the SOAP messages exchanged. EXAMPLES
ecaccess-job-get 124356 ./ecaccess-job-124356.output Download the output of the ECaccess Job 124356 in the local ecaccess-job-124356.output file. SEE ALSO
ecaccess-job-delete, ecaccess-job-list, ecaccess-job-restart, ecaccess-job-submit and ecaccess. perl v5.14.2 2012-04-16 ECACCESS-JOB-GET(1p)
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