<div dir="ltr">You code failed at the very first step I mentioned below: <div><br></div><div><ul><li>First, make sure that your GATE code runs correctly in non-Server mode and check the output;</li><li>Second, make sure that Condor runs normally. </li><li>Third, try to run your GATE code with Condor. </li></ul><div>Good luck.</div></div><div><br></div><div>Zhengzhi </div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 1:27 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu">zliu36@stanford.edu</a>> wrote:<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 dir="ltr">Hi Xinjie, <div><br></div><div>There is no difference at all between the GATE code running on a single core and the one running on a cluster with tens of cores. There are exactly the same. </div><div>I am using Gate 8.2, there might be some difference. But as far as I know, you don't need to modify condor.script except adding the single line "getenv=true" to the script.</div><div>As the error message, it says you didn't put 'GateMaterials.db' at the right location. Please go your macros to locate where GateMaterials.db is called. It may refer to a location outside your current folder, thus no matter where you put it in your folder running this code, it still can't find it. Also, please do a thorough check before running any code. For Gate, you want to do a visualization check as well and look at all error in the console. </div><div><br></div><div>Zhengzhi</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 12:59 PM Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>> wrote:<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 dir="ltr">Hi Zhengzhi,<div><br><div>Thanks for your immediate response again. I have done almost the same before as you did on environmental variables except the difference on /Path/to/Gate , what I am still confused with cluster running are as follows: </div><div>1. Don't we need to replace the GC_EXEC and GC_MACRO as mentioned in the script comment? Or just adding "getenv=True"?</div></div><div>2. There were no error show when I run every step following the guide, but an error in the output .err file like the following:</div><div>*** G4Exception : GateMDBFile<br> issued by : GateMDBFile::GateMDBFile<br>Could not find material database file 'GateMaterials.db'<br>*** Fatal Exception *** core dump ***<br>[G4-cerr] **** Track information is not available at this moment<br>[G4-cerr] **** Step information is not available at this moment<br>[G4-cerr] <br></div><div><br></div><div>In case that GATE cannot find the material database 'GateMaterials.db', I copied it to any folder related to the cluster running, but it still showed during running. Do I have to configure that database in some special way? Thank you again!</div><div><br></div><div>Best,</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 3:37 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>> wrote:<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 dir="ltr"><div>Hi Xinjie, <br></div><div><br></div><div>DON'T modify condor.script except adding "getenv=True" to its very first line. <br></div><div>If you set up the environment correctly in .bashrc by strictly following the instructions in the user manual, all shall be good to go. <br></div><div><br></div><div>Following is my entire GATE related env setting: <br></div><div><br></div><div style="margin-left:40px">### ROOT ENV ###<br>source /home/zliu/Products/root/bin/thisroot.sh<br>alias root='root -l'</div><div style="margin-left:40px"><br></div><div style="margin-left:40px">### GEANT4 ENV ###<br>source /home/zliu/Products/Geant4/geant4.10.05.p01-install/bin/geant4.sh<br><br>### GATE PATH ###<br>export PATH=/home/zliu/Products/Gate/Gate-8.2-install/bin:$PATH<br><br>### ClusterGATE ENV ###<br>export GC_DOT_GATE_DIR=/home/zliu/Products/Gate/output/<br>export GC_GATE_EXE_DIR=/home/zliu/Products/Gate/Gate-8.2-install/bin/</div><div style="margin-left:40px"><br></div><div><br></div><div>Please note that .Gate is a hidden directory under /home/zliu/Products/Gate/output/ in my case. Hopefully these would help a little bit.<br></div><div><br></div><div>Good luck and have fun with Condor. <br></div><div><br></div><div>Zhengzhi <br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 11:40 AM Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>> wrote:<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 dir="ltr">Hi Zhengzhi,<div><br></div><div>Thanks for your immediate response, I really appreciate that. I have a question about the following condor script, could you help answering it?</div><div>```</div><div>Executable = $GC_EXEC <br>universe = vanilla<br>getenv=True<br><br>#Requirements = Memory >= 512 && Arch =="INTEL" <br>#Rank = Memory >= 512<br>#Image_Size = 28 Meg <br> <br>#GJS PART => DO NOT REMOVE OR CHANGE ANYTHING FROM THIS POINT ON<br>#INCLUDING THESE COMMENT LINES!! <br>Arguments = $GC_MACRO <br>Input = $GC_EXEC.in1<br>Output = $GC_EXEC.out1 <br>Error = $GC_EXEC.err1<br>Log = $GC_EXEC.log1<br>Queue </div><div>```</div><div>For $GC_EXEC, we just replace it with Gate executable directory? Or we need to write a .sh with Gate bash command? Thank you!</div><div><br></div><div>Best,</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 2:31 PM Zhengzhi Liu <<a href="mailto:zliu36@stanford.edu" target="_blank">zliu36@stanford.edu</a>> wrote:<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 dir="ltr">Hi Xinjie, <div><br></div><div>Has it thrown any error message? I also followed the instruction (the second link in your email) step by step. Although I also had some minor issues at the very beginning, I got it to work very well. To me, the only thing I need to add to condor.script to make it work is adding "getenv=true" to the script. </div><div><br></div><div>Here are my suggestions to debug: </div><div><br></div><div><ul><li>First, make sure that your GATE code runs correctly in non-Server mode and check the output;</li><li>Second, make sure that Condor runs normally. </li><li>Third, try to run your GATE code with condor. </li></ul></div><div><br></div><div>If you have further questions, please let me know. </div><div><br></div><div>Good luck,</div><div><br></div><div>Zhengzhi </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Mar 30, 2020 at 7:09 AM Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>> wrote:<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 dir="ltr">Dear all,<div><br></div><div>I am using HTCondor platform for GATE cluster running with the following guides:</div><div>1.<a href="http://www.opengatecollaboration.org/Materials2015/PracticalExercises2015/RunningGATECluster" target="_blank">http://www.opengatecollaboration.org/Materials2015/PracticalExercises2015/RunningGATECluster</a></div><div>2.<a href="https://opengate.readthedocs.io/en/latest/how_to_use_gate_on_a_cluster.html" target="_blank">https://opengate.readthedocs.io/en/latest/how_to_use_gate_on_a_cluster.html</a></div><div><br></div><div>I can run every step but just always get wrong output with 0 byte .out file. I am a rookie to GATE cluster running, any reply will be highly appreciated. Thank you!</div><div><br></div><div>Best,<br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><b><font color="#000000">....................................................</font></b><br></div><div><b><span style="color:rgb(153,0,0);font-family:"arial black",sans-serif;font-size:x-small">Xinjie Cao</span></b><br></div><div><b><font size="1" face="arial black, sans-serif">M.E. / Ph.D. student</font></b></div><div><b><font size="1" face="arial black, sans-serif">Research Project Assistant</font></b></div><div><b><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></b></div><div><b><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></b></div><div><b><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></b></div><div><b><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></b></div><div><b><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></b></div><div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black, sans-serif"><br></font></b></div><div><font size="1" face="arial black, sans-serif"><b>email: </b><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></font></div><div><font size="1" face="arial black, sans-serif"><br></font></div><div><font size="1" face="arial black, sans-serif"> </font><img src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ" width="200" height="28"> <img src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" width="200" height="33"></div><div><div><b><font color="#000000">....................................................</font></b></div><div>It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><b><font color="#000000">....................................................</font></b><br></div><div><b><span style="color:rgb(153,0,0);font-family:"arial black",sans-serif;font-size:x-small">Xinjie Cao</span></b><br></div><div><b><font size="1" face="arial black, sans-serif">M.E. / Ph.D. student</font></b></div><div><b><font size="1" face="arial black, sans-serif">Research Project Assistant</font></b></div><div><b><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></b></div><div><b><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></b></div><div><b><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></b></div><div><b><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></b></div><div><b><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></b></div><div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black, sans-serif"><br></font></b></div><div><font size="1" face="arial black, sans-serif"><b>email: </b><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></font></div><div><font size="1" face="arial black, sans-serif"><br></font></div><div><font size="1" face="arial black, sans-serif"> </font><img src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ" width="200" height="28"> <img src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" width="200" height="33"></div><div><div><b><font color="#000000">....................................................</font></b></div><div>It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><b><font color="#000000">....................................................</font></b><br></div><div><b><span style="color:rgb(153,0,0);font-family:"arial black",sans-serif;font-size:x-small">Xinjie Cao</span></b><br></div><div><b><font size="1" face="arial black, sans-serif">M.E. / Ph.D. student</font></b></div><div><b><font size="1" face="arial black, sans-serif">Research Project Assistant</font></b></div><div><b><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></b></div><div><b><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></b></div><div><b><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></b></div><div><b><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></b></div><div><b><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></b></div><div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black, sans-serif"><br></font></b></div><div><font size="1" face="arial black, sans-serif"><b>email: </b><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></font></div><div><font size="1" face="arial black, sans-serif"><br></font></div><div><font size="1" face="arial black, sans-serif"> </font><img src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ" width="200" height="28"> <img src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" width="200" height="33"></div><div><div><b><font color="#000000">....................................................</font></b></div><div>It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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