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<div>Dear Maxime,</div>
<div><br>
</div>
<div>No problem. I found the answer. I post it here, in case anybody else needs it.
<br>
</div>
<div><br>
</div>
<div>It is possible to run the container in one command line inside a batch script. It doesn't necessarily have to be in detached mode (with -d flag).</div>
<div><br>
</div>
<div>After pulling the container:</div>
<div>
<p align="justify"><font face="Courier, monospace"><font style="font-size: 8pt" size="1">$shifterimg pull opengatecollaboration/gate</font></font></p>
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<div>One can run it as follows:</div>
<div>
<p align="justify"><font face="Courier, monospace"><font style="font-size: 8pt" size="1">$srun shifter --image=opengatecollaboration/gate:latest bash -c 'source /root/.bashrc; Gate conditions1.mac'</font></font></p>
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<div>I use slurm to submit jobs, that's why I start the command with srun.</div>
<div>This could be easily used inside a batch script to run multiple simulations in parallel on an HPC.</div>
<div><br>
</div>
<div>Kind regards,</div>
<div>Parisa<br>
</div>
<div style="font-family: Times New Roman; color: #000000; font-size: 16px">
<hr tabindex="-1">
<div id="divRpF597866" style="direction: ltr;"><font size="2" face="Tahoma" color="#000000"><b>From:</b> Maxime Chauvin [maxime.chauvin@inserm.fr]<br>
<b>Sent:</b> 29 October 2018 15:59<br>
<b>To:</b> Parisa Khateri<br>
<b>Cc:</b> gate-users@lists.opengatecollaboration.org<br>
<b>Subject:</b> Re: [Gate-users] GATE Docker container now available !<br>
</font><br>
</div>
<div></div>
<div>Dear Parisa,
<div class=""><br class="">
</div>
<div class="">I am sorry I dont know about that.</div>
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class=""> Maxime<br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 29 Oct 2018, at 15:51, Parisa Khateri <<a href="mailto:parisa.khateri@cern.ch" class="" target="_blank" rel="noopener noreferrer">parisa.khateri@cern.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; direction:ltr; font-family:Tahoma; font-size:10pt">
<div class="">Dear Maxime,</div>
<div class=""><br class="">
</div>
<div class="">Thanks, I didn't know about this option of dockers. Actually, I use "shifter" to run containers on an HPC. I searched to find a similar option for shifter but couldn't find it. Do you know if it is possible to run shifter in background as you
did with docker?</div>
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class="">Parisa<br class="">
</div>
<div class="" style="font-family:"Times New Roman"; font-size:16px">
<hr tabindex="-1" class="">
<div id="divRpF242585" class="" style="direction:ltr"><font class="" size="2" face="Tahoma"><b class="">From:</b><span class="Apple-converted-space"> </span>Maxime Chauvin [<a href="mailto:maxime.chauvin@inserm.fr" class="" target="_blank" rel="noopener noreferrer">maxime.chauvin@inserm.fr</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>24 October 2018 17:34<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Parisa Khateri<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" class="" target="_blank" rel="noopener noreferrer">gate-users@lists.opengatecollaboration.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Gate-users] GATE Docker container now available !<br class="">
</font><br class="">
</div>
<div class=""></div>
<div class="">Dear Parisa,
<div class=""><br class="">
</div>
<div class="">you can run the GATE Docker container non-interactively like this (-d for daemon):</div>
<span class=""><font class="" face="Courier">docker run -id opengatecollaboration/gate:latest<br class="">
</font></span><span class=""><br class="">
</span>
<div class="">then you can copy data to it:</div>
<div class=""><font class="" face="Courier">docker cp /data $container_id:/data</font></div>
<div class=""><br class="">
</div>
<div class="">then execute a script inside the container:</div>
<div class=""><font class="" face="Courier">docker exec $container_id bash /data/gate.sh</font></div>
<div class="">with gate.sh a script of your own that will set the environment variables and run Gate main.mac</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class=""> Maxime Chauvin</div>
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 24 Oct 2018, at 15:49, Parisa Khateri <<a href="mailto:parisa.khateri@cern.ch" class="" rel="noopener noreferrer" target="_blank">parisa.khateri@cern.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; direction:ltr; font-family:Tahoma; font-size:10pt">
<div class="">Dear Maxime, dear gate-users,</div>
<div class=""><br class="">
</div>
<div class="">It's me again.. I would like to know if it is possible to run the Gate container non-interactively. In order to run Gate, first one needs to get into the container using:<font class="" face="Courier, monospace"><font class="" style="font-size:8pt" size="1"><br class="">
</font></font></div>
<div class=""><font class="" face="Courier, monospace"><font class="" style="font-size:8pt" size="1"><br class="">
</font></font></div>
<div class=""><font class="" face="Courier, monospace"><font class="" style="font-size:8pt" size="1">docker run -it opengatecollaboration/gate:latest bash</font></font></div>
<div class=""></div>
<div class=""><br class="">
</div>
<div class="">Then environmental variables:</div>
<div class="">
<div class="" style="margin-top:0px; margin-bottom:0.1in; line-height:16px"><font class="" face="Courier, monospace"><font class="" style="font-size:8pt" size="1">source /root/.bashrc</font></font></div>
</div>
<div class="">
<div class="">Then one can run Gate. But what if I want to run Gate directly:</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="Courier, monospace"><font class="" style="font-size:8pt" size="1">docker run -it opengatecollaboration/gate:latest Gate</font></font></div>
</div>
<div class=""></div>
<div class=""><br class="">
</div>
<div class="">I am new to containers.. hopefully my question makes sense :)</div>
<div class=""><br class="">
</div>
<div class="">Thank you and kind regards,</div>
<div class="">Parisa<br class="">
</div>
<div class=""><font class="" size="2" face="Tahoma"><b class="">--------------------------------------------------------------<br class="">
</b></font></div>
<div class=""><font class="" size="2" face="Tahoma"><b class="">From:</b><span class="Apple-converted-space"> </span>Maxime Chauvin [<a href="mailto:maxime.chauvin@inserm.fr" class="" rel="noopener noreferrer" target="_blank">maxime.chauvin@inserm.fr</a>]</font></div>
<div id="divRplyFwdMsg" class=""><font class="" size="2" face="Tahoma"><b class="">Sent:</b><span class="Apple-converted-space"> </span>22 October 2018 17:46<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Parisa Khateri<br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Gate-users] GATE Docker container now available !<br class="">
</font><br class="">
</div>
<div class=""></div>
<div class="">Good news !
<div class=""><br class="">
</div>
<div class="">Youre welcome,</div>
<div class=""> Maxime<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 22 Oct 2018, at 16:54, Parisa Khateri <<a href="mailto:parisa.khateri@cern.ch" class="" rel="noopener noreferrer" target="_blank">parisa.khateri@cern.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; direction:ltr; font-family:Tahoma; font-size:10pt">
<div class="">Dear Maxime,</div>
<div class=""><br class="">
</div>
<div class="">The error was:</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="Courier New">Error R__unzip_header: error in header<br class="">
Info in <TFile::GetStreamerInfoList>: cannot find the StreamerInfo record in file /home/pkhateri/Desktop/rootfile1.root<br class="">
</font><br class="">
</div>
<div class="">Anyway, I found that the problem was due to the root version. I installed the new version of ROOT on my computer and it can successfully open the root file that was generated by the new version of Gate & ROOT.</div>
<div class=""><br class="">
</div>
<div class="">Thank you again and kind regards,</div>
<div class="">Parisa<br class="">
</div>
<div class="" style="font-family:"Times New Roman"; font-size:16px">
<hr tabindex="-1" class="">
<div id="divRpF380242" class="" style="direction:ltr"><font class="" size="2" face="Tahoma"><b class="">From:</b><span class="Apple-converted-space"> </span>Maxime Chauvin [<a href="mailto:maxime.chauvin@inserm.fr" class="" rel="noopener noreferrer" target="_blank">maxime.chauvin@inserm.fr</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>22 October 2018 15:53<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Parisa Khateri<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" class="" rel="noopener noreferrer" target="_blank">gate-users@lists.opengatecollaboration.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Gate-users] GATE Docker container now available !<br class="">
</font><br class="">
</div>
<div class=""></div>
<div class="">Dear Parisa,
<div class=""><br class="">
</div>
<div class="">which error do you get when trying to open it on your laptop ?<br class="">
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class=""> Maxime</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 22 Oct 2018, at 14:34, Parisa Khateri <<a href="mailto:parisa.khateri@cern.ch" class="" rel="noopener noreferrer" target="_blank">parisa.khateri@cern.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; direction:ltr; font-family:Tahoma; font-size:10pt">
<div class="">Dear Maxime,</div>
<div class=""><br class="">
</div>
<div class="">Thank you for your reply.</div>
<div class=""><br class="">
</div>
<div class="">Actually, I tried to open the file with Root v6-08-06 installed on my laptop. But it also failed there. I thought the reason was the difference in the versions. Because the Root version in the container is 6.1/02. Do you think this could be reason?</div>
<div class=""><br class="">
</div>
<div class="">I pulled the Gate container on an HPC. I cannot install those packages in there.</div>
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class="">Parisa</div>
<div class="" style="font-family:"Times New Roman"; font-size:16px">
<hr tabindex="-1" class="">
<div id="divRpF634189" class="" style="direction:ltr"><font class="" size="2" face="Tahoma"><b class="">From:</b><span class="Apple-converted-space"> </span>Maxime Chauvin [<a href="mailto:maxime.chauvin@inserm.fr" class="" rel="noopener noreferrer" target="_blank">maxime.chauvin@inserm.fr</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>19 October 2018 16:58<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Parisa Khateri<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Joćo Marcos;<span class="Apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" class="" rel="noopener noreferrer" target="_blank">gate-users@lists.opengatecollaboration.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Gate-users] GATE Docker container now available !<br class="">
</font><br class="">
</div>
<div class=""></div>
<div class="">Dear Parisa,
<div class=""><br class="">
</div>
<div class="">ROOT needs some packages to be installed on the system if you want to use more than its libraries.</div>
<div class="">You can install them using this command:</div>
<span class="">yum -y install libX11-devel libXpm-devel libXft-devel libXext-devel<br class="">
</span><span class=""><br class="">
</span>
<div class="">But keep in mind that the docker container is intended for computing, not for data analysis or visualisation.</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">Kind regards,</div>
<div class=""> Maxime Chauvin</div>
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 19 Oct 2018, at 15:47, Parisa Khateri <<a href="mailto:parisa.khateri@cern.ch" class="" rel="noopener noreferrer" target="_blank">parisa.khateri@cern.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" style="font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; direction:ltr; font-family:Tahoma; font-size:10pt">
<div class="">Dear Maxime, dear Joao,<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I tried to pull it on a HPC using shifter (instead of Docker). Then I ran a simple Gate simulation without an error but when I attempt to run root to open the simulation root file I get this error:</div>
<div class=""><br class="">
</div>
<div class=""><font class="" face="Courier New">root: error while loading shared libraries: libSM.so.6: cannot open shared object file: No such file or directory</font><br class="">
<br class="">
</div>
<div class="">I checked and found this library doesn't exist in the /cern/root-install/lib/ directory.<span class="Apple-converted-space"> </span><br class="">
</div>
<div class="">Could it be because of an inappropriate installation?</div>
<div class=""><br class="">
</div>
<div class="">Thank you and kind regards,</div>
<div class="">Parisa<br class="">
</div>
<div class=""><br class="">
</div>
<div class="" style="font-family:"Times New Roman"; font-size:16px">
<hr tabindex="-1" class="">
<div id="divRpF227275" class="" style="direction:ltr"><font class="" size="2" face="Tahoma"><b class="">From:</b><span class="Apple-converted-space"> </span>Gate-users [<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" class="" rel="noopener noreferrer" target="_blank">gate-users-bounces@lists.opengatecollaboration.org</a>]
on behalf of Joćo Marcos [<a href="mailto:joao.marcos@coimbra.lip.pt" class="" rel="noopener noreferrer" target="_blank">joao.marcos@coimbra.lip.pt</a>]<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>17 September 2018 12:50<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Maxime Chauvin<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:gate-users@lists.opengatecollaboration.org" class="" rel="noopener noreferrer" target="_blank">gate-users@lists.opengatecollaboration.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [Gate-users] GATE Docker container now available !<br class="">
</font><br class="">
</div>
<div class=""></div>
<div class="">
<pre class="">Dear Maxime,</pre>
<pre class=""><br class=""></pre>
<pre class="">I followed your instructions and I got my first Gate installation successfully.</pre>
<pre class="">This docker approach seems to be very useful.</pre>
<pre class=""><br class=""></pre>
<pre class="">Thank you very much.</pre>
<pre class="">Best regards,</pre>
<pre class="">Joćo Marcos</pre>
<pre class=""> </pre>
<pre class="">On Wed, 22 Aug 2018 15:24:03 +0200, Maxime Chauvin
wrote:
> Dear gate-users,
>
> GATE is now available as a Docker container:
> <a href="https://hub.docker.com/r/opengatecollaboration/gate/" class="" rel="noopener noreferrer" target="_blank">https://hub.docker.com/r/opengatecollaboration/gate/</a>
>
>
> A Docker container is a bit like a small virtual machine that is created
> for one job and then destroyed. It is fast to deploy, very robust and
> perfect for production on a cluster.
> More information on Docker containers here:
> <a href="https://www.docker.com/resources/what-container" class="" rel="noopener noreferrer" target="_blank">https://www.docker.com/resources/what-container</a>
>
>
> As a simple example, to launch GATE within a Docker container:
> install the Docker app <a href="https://www.docker.com/products/docker-desktop" class="" rel="noopener noreferrer" target="_blank">https://www.docker.com/products/docker-desktop</a>
>
> run in a terminal 'docker run -it opengatecollaboration/gate
> run Gate'
> Best regards,
> Maxime Chauvin</pre>
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