<div dir="ltr"><div>Hi Ashok, thank you for your help,<br></div><div><br></div><div>I can finally split successfully my simulation, after realizing that the issue comes from a very long comment line in my .mac file, and after deleting it the job splitting was completed in a few seconds,<br></div><div><br></div><div>Now I have another issue: I submitted my .submit file using condor_submit mysim.submit command and that seems fine and the jobs are successfully submitted, but when I look at my CPU monitoring, the percentage CPU usage does not increase compared to normal PC working, After 2h of jobs running (my whole simulation takes 1 min without splitting), I am getting juste two .out files and two .root output files (the two .root files are fine), and from stat.txt files (actors) I knew that the time between this two completed jobs is about 1h (1h between the Gate acquisitions, and 20 s duration each acquisition ), then I forced the remaining job to stop using condor_rm job_ID. <br></div><div><br></div><div>I will greatly appreciate your suggestions.<br></div><div>Martin<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le sam. 24 oct. 2020 à 04:49, 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 think linking multiple macros in one main file should yield the same thing! But let me know if it works, and if not try to demystify between how the personal HT condor and real condor cluster works.</div><div dir="ltr"> </div><div dir="ltr">Best, </div><div dir="ltr">Ashok</div><div><br></div>
</div><div id="gmail-m_8252577200528153120yahoo_quoted_4286059923">
<div style="font-family:"Helvetica Neue",Helvetica,Arial,sans-serif;font-size:13px;color:rgb(38,40,42)">
<div>
On Friday, 23 October 2020, 06:23:47 pm GMT-4, Martin Sower <<a href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>> wrote:
</div>
<div><br></div>
<div><br></div>
<div><div id="gmail-m_8252577200528153120yiv1216997956"><div><div dir="ltr"><div>THank you Ashok for your time and for sharing the script,<br clear="none"></div><div><br clear="none"></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 clear="none"></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 clear="none"></div><div>I will try to regroup all .mac files in one and retype the command.<br clear="none"></div><div><br clear="none"></div><div>Martin<br clear="none"></div><div><br clear="none"></div><div><br clear="none"></div></div><br clear="none"><div id="gmail-m_8252577200528153120yiv1216997956yqt00267"><div><div dir="ltr">Le ven. 23 oct. 2020 à 22:03, 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></div>
<div dir="ltr">Hi Martin, </div><div dir="ltr"><br clear="none"></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 clear="none"></div><div> Usage: gjs [-options] your_file.mac</div><div><br clear="none"></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 clear="none"></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 clear="none"></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 clear="none"></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 clear="none"></div></div></div><div dir="ltr">.............................etc?</div><div dir="ltr"><br clear="none"></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 clear="none"></div><div dir="ltr"><div><div><font color="#4c76a2">#!/bin/bash</font></div><div><font color="#4c76a2">#<br clear="none"></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 clear="none"></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 clear="none"></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 clear="none"></div><div><font color="#4c76a2">#$ -cwd</font></div><div><font color="#4c76a2"><br clear="none"></font></div><div><font color="#4c76a2"># print date and time</font></div><div><font color="#4c76a2">date</font></div><div><font color="#4c76a2"><br clear="none"></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 rel="nofollow" shape="rect" 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 clear="none"></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 clear="none"></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 clear="none"></div></div><div dir="ltr"><div><div><font color="#4c76a2">## -l mf=20G<br clear="none"></font></div><div><font color="#4c76a2"><br clear="none"></font></div><div><font color="#4c76a2"># executable</font></div><div><font color="#4c76a2">GC_GATE</font></div></div><br clear="none"></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 clear="none"></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 clear="none"></div><div dir="ltr">Hope this is a little bit helpful.</div><div dir="ltr"><br clear="none"></div><div dir="ltr">Best, </div><div dir="ltr">Ashok</div><div dir="ltr"><br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr"><br clear="none"></div><div dir="ltr"><br clear="none"></div><div><br clear="none"></div>
</div><div id="gmail-m_8252577200528153120yiv1216997956gmail-m_2933884138761872452yahoo_quoted_3834609265">
<div style="font-family:Helvetica,Arial,sans-serif;font-size:13px;color:rgb(38,40,42)">
<div>
On Friday, 23 October 2020, 02:46:04 pm GMT-4, Martin Sower <<a rel="nofollow" shape="rect" href="mailto:melkatib1@gmail.com" target="_blank">melkatib1@gmail.com</a>> wrote:
</div>
<div><br clear="none"></div>
<div><br clear="none"></div>
<div><div id="gmail-m_8252577200528153120yiv1216997956gmail-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_8252577200528153120yiv1216997956gmail-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_8252577200528153120yiv1216997956gmail-m_2933884138761872452yiv3409850666gmail-m_-6576721512889142596yahoo_quoted_3530959185">
<div style="font-family:Helvetica,Arial,sans-serif;font-size:13px;color:rgb(38,40,42)">
<div>
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:
</div>
<div><br clear="none"></div>
<div><br clear="none"></div>
<div><div id="gmail-m_8252577200528153120yiv1216997956gmail-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>
</div>
</div></div></div></blockquote></div></div></div></div></div>
</div>
</div></div></blockquote></div></div></div></div></div>
</div>
</div></div></blockquote></div>