sungridengine Questions
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 $...
Ritualist asked 1/2, 2012 at 13:56
9
Solved
How can I get qstat to give me full job names?
I know qstat -r gives detailed information about the task, but it's too much and the resource requirements are included.
The qstat -r output is like...
Tusche asked 29/9, 2014 at 16:2
2
Solved
Why is it not recommended to run squeue in a loop to avoid overloading Slurm, but no such limitations are mentioned for the bjobs tool from LSF or qstat from SGE ?
The man page for squeue states:
...
Actinopod asked 22/6, 2020 at 11:24
2
Solved
From the qstat (Sun Grid Engine) manpage:
mem: The current accumulated memory usage of the job in Gbytes seconds.
What does that mean?
Yongyoni asked 2/12, 2012 at 22:42
1
Solved
If one is running an array job on a slurm cluster, how can one restart a failed worker job?
In a Sun Grid Engine queue, one can add #$ -r y to the job file to indicate the job should be restarted ...
Neuropathy asked 2/6, 2018 at 22:34
4
I am running a program, and it is interrupted by Segmentation fault. The problem is that the core dump file is created, but of size zero.
Have you heard about such a case and how to resolve it?
...
Eared asked 15/11, 2012 at 18:28
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
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
Solved
Is it possible to expand variables in comments inside a bash script?
I want to write a script to feed into SGE. The qsub syntax allows me to pass additional parameters to the grid engine using lin...
Evangelina asked 5/2, 2013 at 17:1
1
Solved
I want to qdel a range of jobs, with consecutive IDs. For example:
qdel 18280 18281 18282 18283 18284 18285
Imagine I had a longer list of consecutive IDs like this. I obviously don't want to have...
Erickaericksen asked 1/12, 2015 at 21:9
1
Solved
In SGE/PBS, I can submit binary executables to the cluster just like I would locally. For example:
qsub -b y -cwd echo hello
would submit a job named echo, which writes the word "hello" to its o...
Hewe asked 28/10, 2015 at 20:14
1
Solved
I am wondering if it is possible to create a virtual cluster with Docker so that I can run scripts that have been designed for HPC clusters using SGE cluster management. These are pretty large/comp...
Markusmarl asked 21/7, 2015 at 2:28
1
I'm trying to submit jobs to SGE. It has been working for me the same way in the past. Now instead, all jobs are stuck in the qw state.
"qstat -g c" output:
> CLUSTER QUEUE CQLOAD USED AVAIL T...
Lavatory asked 3/3, 2015 at 13:14
2
Solved
When qsub-ing a job I want one job to wait to execute until the first one has succeeded. I've been looking at the options -hold_jid_ad and -hold_jid to do this, but can't see a difference in them.
...
Obligation asked 26/6, 2014 at 17:6
3
Solved
I have the need to set up and run "embarrassingly" parallel jobs on Google Compute Engine. I am looking for tools to facilitate this.
On EC2, I was using MIT's Starcluster to set up the cluster, ...
Siltstone asked 20/6, 2013 at 18:43
1
Solved
Is there a way to list the node which executed a Sun Grid Engine job using qstat or other SGE commands?
I have to get this information using a python script. I have figured out how to execute SGE c...
Heelandtoe asked 31/3, 2014 at 18:36
2
Solved
I have an existing qlogin job like this:
job-ID prior name user state submit/start at queue
-------------------------------------------------------------------------
3530770 0.50500 QLOGIN jlsmit...
Hearth asked 3/7, 2013 at 4:46
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
I am trying to list all nodes on the cluster, but don't know the command. I searched if I use qhost it can list part of nodes. Any idea how to list all nodes?
Wireworm asked 13/6, 2013 at 22:50
0
Does anyone know if there is a Starcluster equivalent for GCE? I have been quite happy using Starcluster with EC2 for embarrisingly parallel jobs. Now I want to try out GCE. I would be happy ...
Deodand asked 9/6, 2013 at 5:49
2
Solved
I would like to submit jobs via qsub on Sun Grid Engine (now: Oracle Grid Engine?). I do not wish to use the -sync yes option or qrsh, because I want my controlling program to be single-threaded an...
Elsey asked 22/6, 2010 at 7:37
2
Solved
How to request the number of nodes (not procs), while job submission in SGE?
for e.g. In TORQUE, we can specify qsub -l nodes=3
How to request the nodes by their names in SGE?
for e.g. In TORQUE...
Tavie asked 22/6, 2012 at 9:24
1
I'm running a lot of jobs with Sun Grid Engine. Since these are a jobs (~100000), I would like to use array jobs, which seems to be easier on the queue.
Another problem is that each jobs produces ...
Deathlike asked 14/9, 2010 at 10:44
2
Solved
I have a perl script that prepares files for input to a binary program and submits the execution of the binary program to the SGE queueing system version 6.2u2.
The jobs are submitted with the -sy...
Solanum asked 3/2, 2011 at 6:11
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