qsub Questions
4
Solved
I have a program that usually runs inside a conda environmet in Linux, because I use it to manage my libraries, with this instructions:
source activate my_environment
python hello_world.py
How c...
6
Solved
I have the following shellscript:
#!/bin/sh
cd /sw/local/bin/
export LD_LIBRARY_PATH=/sw/local/lib:/usr/local/Trolltech/Qt-4.7.2/lib:$LD_LIBRARY_PATH
./FeatureFinderRaw -in /homes/JG-C1-18.mzML -o...
Piloting asked 8/5, 2012 at 10:21
8
Solved
I have an SGE script to execute some python code, submitted to the queue using qsub. In the python script, I have a few print statements (updating me on the progress of the program). When I run the...
Strident asked 26/3, 2012 at 17:40
3
Solved
I have a qsub script as
#####----submit_job.sh---#####
#!/bin/sh
#$ -N job1
#$ -t 1-100
#$ -cwd
SEEDFILE=/home/user1/data1
SEED=$(sed -n -e "$SGE_TASK_ID p" $SEEDFILE)
/home/user1/run.sh $...
Ritualist asked 1/2, 2012 at 13:56
3
Solved
Is there a way to directly pass parameters to a .pbs script before submitting a job? I need to loop over a list of files indicated by different numbers and apply a script to analyze each file.
The...
9
I have a batch script which starts off a couple of qsub jobs, and I want to trap when they are all completed.
I don't want to use the -sync option, because I want them to be running simultaneously...
Heavyhanded asked 17/7, 2012 at 14:52
2
Solved
From the qstat (Sun Grid Engine) manpage:
mem: The current accumulated memory usage of the job in Gbytes seconds.
What does that mean?
Yongyoni asked 2/12, 2012 at 22:42
1
Solved
I have a script job.bin for executing a code in python (pythoncode.py) on a cluster, submitting jobs via qsub. In job.bin:
cd /path/to/my/python/code
python pythoncode.py
What happens if:
a) wh...
3
Solved
When I submit a job using
qsub script.sh
is $@ setted to some value inside script.sh? That is, are there any command line arguments passed to script.sh?
2
I want to submit a a bunch of jobs using qsub - the jobs are all very similar. I have a script that has a loop, and in each instance it rewrites over a file tmpjob.sh and then does qsub tmpjob.sh ....
Storer asked 6/2, 2012 at 22:0
4
Solved
how can I parametrize a shell script that is executed on a grid (started with qsub) ? I have a shell script, where I use getopts to read the parameters.
When I start (qsub script.sh -r firstparam...
Phelloderm asked 17/8, 2010 at 15:22
1
I have a python script main_script.py that looks like this:
import os
Files = os.listdir(os.path.join(path, "."))
FilesNumber = len(Files)
for fileID in range (0,FilesNumber):
filename = Files[...
2
I'm having an issue passing variables to a Bash script using QSub.
Assume I have a Bash script named example. The format of example is the following:
#!/bin/bash
# (assume other variables have be...
Rotation asked 20/9, 2013 at 20:12
2
Solved
I am using a cluster. I will use qsub command to distribute my job, what I want is I can get back the job id so that I can monitor the job.
Basically, I want some thing like this:
#!/bin/bash
JOB...
Lexicon asked 6/4, 2014 at 11:56
3
Solved
There are some commands I'd like to run on a grid using qsub (SGE 8.1.3, CentOS 5.9) that need to use a pipe (|) or a redirect (>). For example, let's say I have to parallelize the command
echo...
Judiciary asked 19/8, 2013 at 20:12
1
I'm trying to submit a torque job that is dependent on an array completing.
FIRST=`qsub -q hep -t 1-5 foo.sh`
qsub -q hep -W depend=afterok:$FIRST bar.sh
The FIRST job array submits and complete...
Rambler asked 7/11, 2016 at 18:36
3
Currently, I have a driver program that runs several thousand instances of a "payload" program and does some post-processing of the output. The driver currently calls the payload program directly, ...
Corrody asked 12/5, 2011 at 18:46
1
Solved
Hopefully this is not a dublicate and also not just a problem of our cluster's configuration...
I am submitting a job array to a cluster using qsub with the following command:
qsub -q QUEUE -N JO...
Langton asked 9/6, 2016 at 10:44
3
I am having an issue where if I have 2000 jobs queued and try to delete them with qdel all, it'll keep trying to delete the running jobs first. This means I have to wait a long time for the jobs to...
Jada asked 16/1, 2014 at 1:27
2
Solved
I'm using PBSPro and am trying to use qsub command line to submit a job but can't seem to get the output and error files to be named how I want them. Currently using:
qsub -N ${subjobname_short} ...
4
Solved
To get myscript.R to run on a cluster slave node using a job scheduler (specifically, PBS)
Currently, I submit an R script to a slave node using the following command
qsub -S /bin/bash -p -1 -cwd...
Dodge asked 30/10, 2012 at 15:55
2
Solved
Assume that you start running the script. What happens when you change that file when it is being executed? It seems that MATLAB takes a copy of the file and then starts executing it. I want to mak...
4
Solved
I have a function (neural network model) which produces figures. I wish to test several parameters, methods and different inputs (meaning hundreds of runs of the function) from python using PBS on ...
Heywood asked 22/7, 2010 at 10:43
3
Solved
I have more than 200 jobs I need to submit to and sge cluster. I'll be submitting them into two ques. One of the ques have a machine that I don't want to submit jobs to. How can I exclude that mach...
Walkon asked 13/12, 2012 at 13:48
1
Solved
I am trying to adjust some bash scripts to make them run on a (pbs) cluster.
The individual tasks are performed by several script thats are started by a main script.
So far this main scripts start...
Surpass asked 26/8, 2013 at 10:43
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