<div dir="ltr"><div>THank you Ashok for your time and for sharing the script,<br></div><div><br></div><div>Effectively, I'm getting the same output as you when typing 'gjs' alone, so I think the gjs installation was successful,</div><div><br></div><div>I mention here that I'm running this job splitting command on my PC (6 cores intel i7 CPU) and not a (real) cluster, and that my .mac file is separated to many .mac files (geometry, output, source, etc) and all linked in the main.mac that I'm referring to in the command,</div><div><br></div><div>I will try to regroup all .mac files in one and retype the command.<br></div><div><br></div><div>Martin<br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le ven. 23 oct. 2020 à 22:03, Ashok Tiwari <<a href="mailto:tiwarias@yahoo.com">tiwarias@yahoo.com</a>> a écrit :<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-size:16px"><div></div>
<div dir="ltr">Hi Martin, </div><div dir="ltr"><br></div><div dir="ltr">I am wondering whether your gjs is working fine. What do you see when you run gjs command? Do you see the following usage message: </div><div dir="ltr"><div><div> +-------------------------------------------+</div><div> | gjs -- The GATE cluster job macro spliter |</div><div> +-------------------------------------------+</div><div><br></div><div> Usage: gjs [-options] your_file.mac</div><div><br></div><div> Options (in any order):</div><div> -a value alias : use any alias</div><div> -numberofsplits, -n n : the number of job splits; default=1</div><div> -clusterplatform, -c name : the cluster platform, name is one of the following:</div><div> openmosix - condor - openPBS - SGE - xgrid</div><div> This executable is compiled with SGE as default</div><div><br></div><div> -openPBSscript, -os script : template for an openPBS script</div><div> see the example that comes with the source code (script/openPBS.script)</div><div> overrules the environment variable below</div><div><br></div><div> -SGEscript, -ss script : template for an SGE script</div><div> see the example that comes with the source code (script/SGE.script)</div><div> overrules the environment variable below</div><div><br></div><div> -condorscript, -cs script : template for a condor submit file</div><div> see the example that comes with the source code (script/condor.script)</div><div> -v : verbosity 0 1 2 3 - 1 default</div><div><br></div></div></div><div dir="ltr">.............................etc?</div><div dir="ltr"><br></div><div dir="ltr">I think if you see this message then it should run in principle, if not then there might be something wrong with the installation or job submission! I am not familiar with the HT condor cluster, so I cannot give you the specific information but in the SGE cluster, I normally submit the job using the following script: (this is the copy-paste of the script)</div><div dir="ltr"><br></div><div dir="ltr"><div><div><font color="#4c76a2">#!/bin/bash</font></div><div><font color="#4c76a2">#<br></font></div><div><font color="#4c76a2"># Queue to submit job</font></div><div><font color="#4c76a2">#$ -q CCOM,UI </font></div><div><font color="#4c76a2"><br></font></div><div><font color="#4c76a2"># batch job stderr and stdout</font></div><div><font color="#4c76a2">#$ -o GC_WORKDIR/GC_LOG</font></div><div><font color="#4c76a2">#$ -e GC_WORKDIR/GC_ERR</font></div><div><font color="#4c76a2"><br></font></div><div><font color="#4c76a2"># Job name</font></div><div><font color="#4c76a2">#$ -N GC_JOBNAME</font></div><div><span style="color:rgb(76,118,162)"># Use current working directory</span><br></div><div><font color="#4c76a2">#$ -cwd</font></div><div><font color="#4c76a2"><br></font></div><div><font color="#4c76a2"># print date and time</font></div><div><font color="#4c76a2">date</font></div><div><font color="#4c76a2"><br></font></div><div><font color="#4c76a2"># I want SGE cluster to send me an email</font></div><div><font color="#4c76a2"># when the job begins and when it ends</font></div><div><font color="#4c76a2">#$ -M <a href="mailto:ashok-tiwari@uiowa.edu" target="_blank">ashok-tiwari@uiowa.edu</a></font></div><div><font color="#4c76a2">#$ -m be</font></div><div><font color="#4c76a2"><br></font></div><div><font color="#4c76a2"># -l h_vmem=20G</font></div><div><span style="color:rgb(76,118,162)"># Set simulation time</span><br></div><div><font color="#4c76a2"># -l h_rt=24:00:00</font></div><div><span style="color:rgb(76,118,162)">#$ -pe smp 8</span><br></div></div><div dir="ltr"><div><div><font color="#4c76a2">## -l mf=20G<br></font></div><div><font color="#4c76a2"><br></font></div><div><font color="#4c76a2"># executable</font></div><div><font color="#4c76a2">GC_GATE</font></div></div><br></div>To use the jobsplitter functionality I submit the job using the following command in the command line:</div><div dir="ltr">$ <span>gjs -numberofsplits 10 -clusterplatform SGE ../somedir/script/main.mac</span></div><div dir="ltr"><span><br></span></div><div dir="ltr">After I hit enter in the command line, it will generate the main.submit file in the same directory within ~seconds. Also at the same time, 10 split macros will be created in the GC_DOT_GATE directory. Then you are supposed to run the main.submit executable file using: ./main.submit to perform a simulation.</div><div dir="ltr"><br></div><div dir="ltr">Hope this is a little bit helpful.</div><div dir="ltr"><br></div><div dir="ltr">Best, </div><div dir="ltr">Ashok</div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div><br></div>
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On Friday, 23 October 2020, 02:46:04 pm GMT-4, Martin Sower <<a href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>> wrote:
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<div><div id="gmail-m_2933884138761872452yiv3409850666"><div><div dir="ltr"><div>Thank you Ashok for your response,</div><div><br clear="none"></div><div>effectively, I had a .split file with one of the expected .mac files (mysim1.mac but no mysim2.mac !) in the DOT_GATE directory but no .submit file in the current directory (where gjs is launched),</div><div><br clear="none"></div><div>I will appreciate if you could share with me your scripts so that I can compare with mines,</div><div><br clear="none"></div><div>thank you for your help.</div><div>Martin<br clear="none"></div></div><br clear="none"><div id="gmail-m_2933884138761872452yiv3409850666yqt62556"><div><div dir="ltr">Le ven. 23 oct. 2020 à 19:17, Ashok Tiwari <<a rel="nofollow" shape="rect" href="mailto:tiwarias@yahoo.com" target="_blank">tiwarias@yahoo.com</a>> a écrit :<br clear="none"></div><blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div style="font-family:Helvetica Neue,Helvetica,Arial,sans-serif;font-size:16px"><div dir="ltr">Hi Martin,</div><div dir="ltr"><br clear="none"></div><div dir="ltr">I don't have experience with the HT condor platform but after running the gjs command you should have a .split file in the current directory where you ran the gjs command and split macros in your .GC_DOT_GATE directory based on your installation. It should not take such a long time, I think it is a matter of ~secs (based on my experience). I don't have an idea about why it is taking too much time, but I suggest you to check the condor script based on available scripts in GATE. I am happy to send you my SGE cluster setting files if you want to compare the scripts to find out the culprit.</div><div dir="ltr"><br clear="none"></div><div dir="ltr">Thanks,</div><div dir="ltr">Ashok Tiwari</div><div dir="ltr"><br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr"><br clear="none"></div><div id="gmail-m_2933884138761872452yiv3409850666gmail-m_-6576721512889142596yahoo_quoted_3530959185">
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On Friday, 23 October 2020, 06:41:19 am GMT-4, Martin Sower <<a rel="nofollow" shape="rect" href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>> wrote:
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<div><div id="gmail-m_2933884138761872452yiv3409850666gmail-m_-6576721512889142596yiv0999134001"><div dir="ltr"><div>Hi,</div><div><br clear="none"></div><div>I installed the gjs (job splitter) and gjm (job merger) as in the Gate User's guide and installed a Personal HTcondor as in <a rel="nofollow" shape="rect" href="https://htcondor.readthedocs.io/en/stable/cloud-computing/using-annex-first-time.html#install-a-personal-htcondor" target="_blank">https://htcondor.readthedocs.io/en/stable/cloud-computing/using-annex-first-time.html#install-a-personal-htcondor</a> with the tests passed successfully, and now I'm trying to split my simulation to 2 jobs, with the command gjs -numberofsplits 2 -clusterplatform condor -condorscript /home/..../Gate-8.2/cluster_tools/jobsplitter/script/condor.script mysim.mac, I'm getting the .split and mysim1.mac in the .GATE directory but nothing else, and the problem is that this command take too much long (1h before I force them to stop), so my question is: is it normal that this gjs command take such a long time? and what can be the origin of this problem?</div><div><br clear="none"></div><div>thank you in advance for your help.</div><div>Martin<br clear="none"></div></div></div>_______________________________________________<br clear="none">Gate-users mailing list<br clear="none"><a rel="nofollow" shape="rect" href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br clear="none"><a rel="nofollow" shape="rect" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></div>
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