<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Parisa,<div class=""><br class=""></div><div class="">I am sorry I don’t 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="">parisa.khateri@cern.ch</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="caret-color: rgb(0, 0, 0); font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; direction: ltr; font-family: Tahoma; font-size: 10pt;" class=""><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 style="font-family: "Times New Roman"; font-size: 16px;" class=""><hr tabindex="-1" class=""><div id="divRpF242585" style="direction: ltr;" class=""><font size="2" face="Tahoma" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Maxime Chauvin [<a href="mailto:maxime.chauvin@inserm.fr" class="">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="">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="" 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, 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="" size="1" style="font-size: 8pt;"><br class=""></font></font></div><div class=""><font class="" face="Courier, monospace"><font class="" size="1" style="font-size: 8pt;"><br class=""></font></font></div><div class=""><font class="" face="Courier, monospace"><font class="" size="1" style="font-size: 8pt;">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="" size="1" style="font-size: 8pt;">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="" size="1" style="font-size: 8pt;">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="" target="_blank" rel="noopener noreferrer">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="">You’re 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>João 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 João 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="">João 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></div></div></div></div></blockquote></div></div></div></div></div></div></blockquote></div></div></div></div></div></div></blockquote></div></div></div></div></div></blockquote></div></div></div></div></div></div></blockquote></div><br class=""></div></body></html>