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Questions tagged [gridengine]

Oracle Grid Engine, previously known as Sun Grid Engine (SGE), CODINE (Computing in Distributed Networked Environments) or GRD (Global Resource Director), is an open source batch-queuing system, developed and supported by Sun Microsystems. Sun once also sold a commercial product based on SGE, known as N1 Grid Engine (N1GE).

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In Dec 2010, Oracle officially passed on the torch for maintaining the Grid Engine open source code base to the Open Grid Scheduler project.

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Konsole works, gnome-terminal doesn't?

I'm running on CentOS 5.7 (in case that matters) I have a program (not my own) that runs fine from Lonsole, but when I run it from xterm, gnome-terminal or rxvt, it just hangs. I'm doing this with a completely fresh account, no .bashrc, no…
Brian Postow
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stdout redirect. sh: resource temporarily unavailable

I have large batches of bash processes. Each bash script invokes executeables which have their stdout redirected to distinct log files. About 5% of the runs end up with: sh: [name of log]: Resource temporarily unavailable I tried to reduce amount of…
lev haikin
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stat meanings of computing nodes

I submitted a job to a Linux cluster which uses SGE job scheduler. The job stat is qw for a long time, so I inspected the stats of computing nodes using "qstat -f". I found that many nodes were labelled with stats "d", "adu" and "E". I wonder what…
Dejian
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Remotely compile and run program using ssh and screen

I'm trying to compile and run a program remotely. However, I'd like to this within a screen and also I'd like to run this using grid engine on another node after I ssh. Currently I have: ssh me@server screen -R session 'qlogin; cd path; mvn…
akobre01
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usr/bin/xterm Xt error: Can't open display: /usr/bin/xterm: DISPLAY is not set?

I'm trying to submit a job to a school server (HPC) with: #!/bin/bash #$ -S /bin/bash #$ -cwd #$ -o ./out_$JOB_ID.txt #$ -e ./err_$JOB_ID.txt #$ -notify #$ -pe orte…
Sibbs Gambling
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what is the difference between qsub and ./

Can anyone tell me the difference between the following ways of submitting a script: $ qsub script_name.sh and ./script_name.sh What are the differences between the above two ways of submitting a job to a cluster? Also how come sometimes I need…
john_w
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Shell Variable Expansion in qsub command through drmaa

I am running a bulk job submission to SGE (Sun Grid Engine) using python drmaa bindings. For the bulk job submission I am submitting a python script that takes in one argument and is command line executable, through a shebang. To properly…
Melendowski
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Determine slot ID for a running job

On a compute node with multiple slots, are the running jobs each explicitly assigned a slot ID as they start, and if so how can the user or submission script see it? To see the job ID, one can use the $JOB_ID environment variable within the…
feedMe
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Qsub to any node with more than n cores available

I have a program that is parallelized using MPI. It thinks that it is able to run across multiple nodes on our (CentOS 6.6)-based HPC grid, when in actual fact it only runs successfully on multiple cores of the same compute node. e.g. If I qsub a…
feedMe
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Stack screen output into columns to make use of screen width and avoid scrolling

I often use gridengine's qstat command on our HPC cluster but since I have many jobs running on the cluster the output is too long to fit on my screen and I end up doing a lot of scrolling to see the upper section of the output. My terminal has…
feedMe
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Generalising Grid Engine qsub job file for multiple programs and input file names

I am using Grid Engine on a Linux cluster. I am running many jobs with different programs and different input files. I don't want to create multiple specific job scripts for each pair of program and input file. Instead I want to be able to specify…
cyuut
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How do I check if a job is running on cluster using job name (CentOS)

I am running a bash script to submit multiple jobs. The submission of a job only happens if such job is not already running. I want to use an if statement inside my bash script to simply check if "job123" is already running or in the queue. I have…
Herman Toothrot
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Allocate Variable Slots For OGE Based on User Needs

On one machine, some users want to submit sets of jobs which will at most use X GB each, while other users want sets of up to Y GB each. Can Open Grid Engine (OGE) create variable amounts of slots based on job load? For example, if Y >> X, and the…
David Robie
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Allocate Total RAM For OGE

Is there a way to set the total amount of usable RAM in Open Grid Engine (OGE), regardless of the number of slots? I have a suspicion that the answer might be "No, but you can set hard limits on each slot, and do the math yourself." However, this…
David Robie
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Small TaskQueue shared on two computers

There are two computers with 12 physical cores each. Computer A should accept jobs and distribute them among A and B I want to setup Computers A and B such that A will accept jobs (via ssh) and distribute them among A and B (more or less…
infinitezero
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