<div dir="ltr">Hi Hadi,<div><br></div><div>Is that command line absolutely the same as the command you input in your terminal? Or you use ROOT_FILE to replace your real .root file? If you input the real .root output file name from GATE and get that error, maybe you could describe it much more specifically. </div><div><br></div><div>I think the second error is due to your clean of ROOT_FILE alias and that makes the command chaos. Once you input the right .root file it will not be an issue so do not worry about that. </div><div><br></div><div>Also, if all files that gjs command needs and gjs exe file are in the same directory, you do not need to input those long paths in your command and that makes your command look better clear.</div><div><br></div><div>PS: You'd better reply to us two and the gate-mailing list at the same time so other guys who met the same problem could take advantage of it.</div><div><br></div><div>Best,</div><div>Xinjie</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 9, 2020 at 5:27 PM Hadi Rezaei <<a href="mailto:hrezaei.m.ph@gmail.com">hrezaei.m.ph@gmail.com</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 and Ville-Veikko<div>many thanks to you for your reply<br><div>After I copied gjs execute file and type ./gjs I saw some help commands and I think the first problem is resolved. When I enter my parameters the .Gate folder is generated that only contains one macro file with number (1) and one .split file.</div><div>./gjs -numberofsplits 5 -clusterplatform openmosix -a /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/nTBNECR175 ROOT_FILE /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/TBNECR175.mac<br>Summary of all outputs:<br> ROOT output is enabled<br> ASCII output is disabled<br> ARF output is disabled<br> PROJECTION output is disabled<br> ECAT7 output is disabled<br> SINOGRAM output is disabled<br> SINOACCEL output is disabled<br> LMF output is disabled<br> CT output is disabled<br> GPUSPECT output is disabled<br>Summary of all actors:<br> ~~~<br>Number of enabled output: 1<br>Number of enabled actors: 0<br>Could not use the following aliases from the command line:<br> ROOT_FILE<br>Floating point exception (core dumped)<br></div><div><br></div><div>Also when I clean ROOT_FILE I saw this error "**** Your macro file given in parameter does not have any extension. Please give it the .mac extension."</div><div><br></div><div>Best,</div><div><br></div><div> </div><div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 9, 2020 at 8:14 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"><div>Hi Hadi,</div><div><br></div>I think Ville-Veikko's way is the most basic way to solve this problem, if you do not know how to export the path or source your exe file. Also, copy the exe file into your current folder could help you get rid of that long path typing, but either one should work. Thanks for Ville-Veikko's remind!<div><br></div><div>Best,</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 9, 2020 at 11:37 AM Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi" target="_blank">ville-veikko.wettenhovi@uef.fi</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">
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Hi,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Have you tried running /media/rezaei/Data/GATE_v9/gate/Gate/cluster_tools/jobsplitter/gjs -numberofsplits 5 -clusterplatform openmosix -a /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/example1.root ROOT_FILE example.mac ?</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Regards,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Ville-Veikko Wettenhovi<br>
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<div id="gmail-m_-879121648463618001gmail-m_-2020697537894386666gmail-m_5717434183101851946appendonsend"></div>
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<div id="gmail-m_-879121648463618001gmail-m_-2020697537894386666gmail-m_5717434183101851946divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> on behalf of Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Sent:</b> Thursday, July 9, 2020 18:17<br>
<b>To:</b> Hadi Rezaei <<a href="mailto:hrezaei.m.ph@gmail.com" target="_blank">hrezaei.m.ph@gmail.com</a>>; <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> Re: [Gate-users] cluster run on GATE_v9</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Hadi,
<div><br>
</div>
<div>Did you copy the gjs or gjm executable icon into your current folder? I think after the installation of the gjs or gjm in your GATE folder, where the path should be /PATH/TO/cluster_tools/jobsplitter, you could see an executable icon in purple named gjs.
Wherever you want to use the gjs command, you need to copy one into the folder you want to run it, or you have to export the path to its original location in your .bashrc file. Let me know whether it works for you, good luck!</div>
<div><br>
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<div>Best,</div>
</div>
<br>
<div>
<div dir="ltr">On Thu, Jul 9, 2020 at 11:08 AM Hadi Rezaei <<a href="mailto:hrezaei.m.ph@gmail.com" target="_blank">hrezaei.m.ph@gmail.com</a>> wrote:<br>
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<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div>Hi Xinjie</div>
<div>Thank you for your reply.<br>
</div>
<div>I have ubuntu 20.04</div>
<div>After type ./gjs I found "bash: ./gjs: No such file or directory"</div>
<div>indeed it can not find gjs. But I installed it.</div>
<div>Best,<br>
</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Jul 8, 2020 at 10:57 PM Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>> wrote:<br>
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<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Sorry, "./gjs".</div>
<br>
<div>
<div dir="ltr">On Wed, Jul 8, 2020 at 2:26 PM Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>> wrote:<br>
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<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">You should type ./jgs for some linux system. The "gjs>" is another system default command.
<div><br>
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<div>Best,</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Jul 8, 2020 at 1:52 PM Hadi Rezaei <<a href="mailto:hrezaei.m.ph@gmail.com" target="_blank">hrezaei.m.ph@gmail.com</a>> wrote:<br>
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<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Hi,
<div>Thank you for responding.</div>
<div>after type gjs in terminal I get "gjs>".</div>
<div>Also, I installed gjs and gjm as follow:</div>
<div>
<pre style="overflow:auto hidden;font-family:Consolas,Menlo,"DejaVu Sans Mono","Bitstream Vera Sans Mono",monospace;font-size:0.9em;background:none 0% 0% repeat scroll rgb(238,238,238);padding:7px 30px;margin-top:15px;margin-bottom:15px;line-height:1.3em;color:rgb(62,67,73)"><span style="color:rgb(0,0,0)">cd</span> <span style="color:rgb(0,0,0)">jobsplitter</span>
<span style="color:rgb(0,0,0)">make</span></pre>
<pre style="overflow:auto hidden;font-family:Consolas,Menlo,"DejaVu Sans Mono","Bitstream Vera Sans Mono",monospace;font-size:0.9em;background:none 0% 0% repeat scroll rgb(238,238,238);padding:7px 30px;margin-top:15px;margin-bottom:15px;line-height:1.3em;color:rgb(62,67,73)"><span style="color:rgb(0,0,0)">
<pre style="overflow:auto hidden;font-family:Consolas,Menlo,"DejaVu Sans Mono","Bitstream Vera Sans Mono",monospace;font-size:0.9em;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;padding:7px 30px;margin-top:15px;margin-bottom:15px;line-height:1.3em;color:rgb(62,67,73)"><span style="color:rgb(0,0,0)">cd</span> <span style="color:rgb(0,0,0)">filemerger</span>
<span style="color:rgb(0,0,0)">make</span></pre>
</span></pre>
</div>
<div>Thank you.</div>
<div>Best,</div>
</div>
<br>
<div>
<div dir="ltr">On Wed, Jul 8, 2020 at 7:17 PM Ville-Veikko Wettenhovi <<a href="mailto:ville-veikko.wettenhovi@uef.fi" target="_blank">ville-veikko.wettenhovi@uef.fi</a>> wrote:<br>
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<blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Hi,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
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<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
If you simply type gjs in terminal, what do you get? You may have the gjs-package installed (<a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpackages.ubuntu.com%2Ffocal%2Fgjs&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012590849&sdata=X7EdJbGSOR6ldnkb%2FDI3bs3FZFKou0R2hD5qBezCXfc%3D&reserved=0" id="gmail-m_-879121648463618001gmail-m_-2020697537894386666gmail-m_5717434183101851946x_gmail-m_-4646928177222841846gmail-m_-4504249880547815026gmail-m_4427500910174240694gmail-m_7068887562058322880gmail-m_-6673201964482323382LPlnk442175" target="_blank">https://packages.ubuntu.com/focal/gjs</a>)
that probably takes precedence over the GATE gjs in which case you need to call the GATE gjs with the full path.</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Regards,</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0);background-color:rgb(255,255,255)">
Ville-Veikko Wettenhovi<br>
</div>
<div id="gmail-m_-879121648463618001gmail-m_-2020697537894386666gmail-m_5717434183101851946x_gmail-m_-4646928177222841846gmail-m_-4504249880547815026gmail-m_4427500910174240694gmail-m_7068887562058322880gmail-m_-6673201964482323382appendonsend">
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<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Gate-users <<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>> on behalf of Hadi Rezaei
<<a href="mailto:hrezaei.m.ph@gmail.com" target="_blank">hrezaei.m.ph@gmail.com</a>><br>
<b>Sent:</b> Wednesday, July 8, 2020 14:48<br>
<b>To:</b> <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">
gate-users@lists.opengatecollaboration.org</a> <<a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a>><br>
<b>Subject:</b> [Gate-users] cluster run on GATE_v9</font>
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<div>Dear all</div>
<div>I am trying to run cluster GATE_v9 but after type "gjs -numberofsplits 5 -clusterplatform openmosix -a /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/example1.root ROOT_FILE example.mac" I found "<b>Unknown option -numberofsplits</b>"</div>
<div><br>
</div>
<div>I enter in .bashrc:</div>
<div>export GC_DOT_GATE_DIR=/media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI<br>
export GC_GATE_EXE_DIR=/media/rezaei/Data/GATE_v9/gate/Gate/cluster_tools/jobsplitter/gjs</div>
<div>and also in mac file I added the command : /gate/cluster/setTimeSplitHalflife 6586.2 s</div>
<div>I used this link guidance step by step: </div>
<div>
<pre><a href="https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fhow_to_use_gate_on_a_cluster.html&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012590849&sdata=9AzECfVha8MnvLpOFb3M%2F4uiWJmas1Eaz5Tx4gGR3C4%3D&reserved=0" target="_blank">https://opengate.readthedocs.io/en/latest/how_to_use_gate_on_a_cluster.html</a><br><br></pre>
<pre><span style="font-family:arial,sans-serif"><font size="2">How can I fix this problem?<br>any help will be highly appreciated. Thank you</font><br></span><br></pre>
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<div><b><span style="color:rgb(153,0,0);font-family:"arial black",sans-serif;font-size:x-small">Xinjie Cao</span></b><br>
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<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>
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<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://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyou.stonybrook.edu%2Fgoldan%2Fpeople%2F&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012610838&sdata=2j7xH4RMgjHnklirrp2dMktD%2FbPS%2BP2d9H9dHRUlics%3D&reserved=0" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black, sans-serif"><br>
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<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>
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<div><b><span style="color:rgb(153,0,0);font-family:"arial black",sans-serif;font-size:x-small">Xinjie Cao</span></b><br>
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<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>
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<a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a><br>
<a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" rel="noreferrer" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></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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