[gridengine users] Details on some terminologies of Sun Grid Engine cluster

I am working on SGE and I need some precise definition of some terms. These are the terms I often hear about, but does not really understand them. These are Head Node Login Node Compute Node Submit Host Cluster Nodes Master Host Any insight would be helpful Thanks Varun ___

[gridengine users] All commands in one script

Hello Everyone, Till now I have been writing simple scripts to do my work. Now I want to automate my task. I have no idea about submitting array jobs So here is the explanation of what I want to do and then you can help me how to design the script. In a directory I have these 4 fastq files A-122

Re: [gridengine users] All commands in one script

ld2] fail to open the BAM file.[E::main_mem] fail to open file `_P1_'.Usage: samtools sort [-on] [-m ] [main_samview] fail to open "sam" for reading.open: No such file or directory[bam_index_build2] fail to open the BAM file.* Sorry for troubling you on this Help!! Regards Varun

[gridengine users] Basic information working on cluster

HI Everyone, I have been using SGE for some time but I still have lots of doubts. I hope to find my solution here. When I submit my job using qsub and using arguments like -l mf=8G does -l mf=8G provides me 8GB ram for that job to run?? This job which i Submit runs on one computer or several comp

[gridengine users] command for finding available nodes and associated memory with those nodes

Hi, I am working on SGE. I want to find out the available nodes on my cluster and associated memory with each node so that I can submit my jobs accordingly. What command should I use Regards Varun ___ users mailing list users@gridengine.org https://grid

[gridengine users] Information on compute nodes

Hi Everyone, I have started to understand the basics of SGE, but still I am pretty new in this cluster computation. When I qsub an application, and use qstat to check the status of my submitted job I see that my job has been submitted to a compute node something like this *biology@compute-0-18.loc

Re: [gridengine users] Information on compute nodes

Thanks for the reply, I am looking at qhost command now. Also a compute node *biology@compute-0-18.local* would mean one of the several computers on the cluster?? Regards On Tue, May 6, 2014 at 11:48 AM, Jesse Becker wrote: > On Tue, May 06, 2014 at 11:34:50AM -0400, VG wrote: >

[gridengine users] to find number of available processors on a host machine(compute node)

Hi, I am working on SGE. When I ssh to connect to cluster it connects me to the head node. Then I use qlogin to get onto one of the compute nodes/ or lets say one of the host machine. To my understanding I think when I qlogin, the compute node which is provided to me , I can use all the resources

[gridengine users] Running an array job on SGE not giving expected output

HI everyone, I am trying to make a job array script. I have 2 files in my working directory namely abc.fastq and def.fastq I want to run one command on these 2 files(later on I will include more .fastq files) on different compute nodes. So I made this array script, but it only produces output for

Re: [gridengine users] Running an array job on SGE not giving expected output

Reuti wrote: > Hi, > > Am 02.09.2015 um 19:17 schrieb VG: > > > HI everyone, > > > > I am trying to make a job array script. I have 2 files in my working > directory namely abc.fastq and def.fastq > > > > I want to run one command on these 2 files(later o

[gridengine users] running failed array jobs in UGE

Hi Everyone, I submitted 200 array jobs on the cluster using -t option. My command line looks like this: qsub -t 1-200 -cwd -j y -b y -N jobs -l h_vmem=30G ./script.sh After this, job numbered 3,10,45,56,98,134 failed to finish. What can I do to only run the failed job now? Can I use -t option i

[gridengine users] different results on terminal and on submission via qsub

Hi, I am trying to run a command on the terminal and also submit it to the cluster but I am getting different results. When I type on the terminal this : for i in *_1.fastq.gz; do echo $i >> t.txt; zcat $i | grep "GCTGGCAGAAGGTAACATG" >> t.txt ; echo >> t.txt ; done I get the output like

Re: [gridengine users] different results on terminal and on submission via qsub

t; > > > > > On Mon, Jul 9, 2018 at 1:23 PM, VG wrote: > >> Hi, >> I am trying to run a command on the terminal and also submit it to the >> cluster but I am getting different results. >> >> When I type on the terminal this : >> >> for i

[gridengine users] scripting help with per user job submit restrictions

I have a scripting question regarding submitting jobs to the cluster. There is a limitation per user of 1000 jobs only. Let's say I have 1200 tar.gz files I tried to submit all the jobs together but after 1000 jobs it gave me an error message saying per user limit is 1000 and after that it did n

Re: [gridengine users] scripting help with per user job submit restrictions

or >> per-project basis. I don't know that you can limit on jobs in RQSs but you >> certainly can on slots; the sge_resource_quota(5) man page has some >> examples. >> >> On Thu, Jun 13, 2019 at 12:32:51PM -0400, VG wrote: >> > I have a scripting

Re: [gridengine users] scripting help with per user job submit restrictions

ar -xzf >> $i" >> done >> >> On Thu, Jun 13, 2019 at 12:39 PM Skylar Thompson wrote: >> >>> We've used resource quota sets to accomplish that on a per-queue or >>> per-project basis. I don't know that you can limit on jobs in RQSs but >&g

Re: [gridengine users] scripting help with per user job submit restrictions

Hi, Where should I put my qsub command? On Thu, Jun 13, 2019 at 12:54 PM VG wrote: > Hi Daniel, > Will give it a try. If I am not mistaken, there should be another *done *in > the code snippet. > > Regards > Varun > > On Thu, Jun 13, 2019 at 12:45 PM Daniel Povey

Re: [gridengine users] scripting help with per user job submit restrictions

t all the tar.gz in one folder and run array script as you told, other wise is there a work around where everything runs and also remains in the respective directories. Thanks for your help. Regards Varun On Thu, Jun 13, 2019 at 1:11 PM Joshua Baker-LePain wrote: > On Thu, 13 Jun 2019 a

Re: [gridengine users] scripting help with per user job submit restrictions

VARUN On Thu, Jun 13, 2019 at 1:46 PM Feng Zhang wrote: > You can try to write the script to first scan all the files to get their > full path names and then run the Array jobs. > > > On Jun 13, 2019, at 1:20 PM, VG wrote: > > HI Joshua, > I like the array job option be