[Gate-users] GATE Docker container now available !

Mon Oct 29 15:59:11 CET 2018

Dear Parisa,

I am sorry I don’t know about that.

Kind regards,
  Maxime

> On 29 Oct 2018, at 15:51, Parisa Khateri <parisa.khateri at cern.ch> wrote:
> 
> Dear Maxime,
> 
> 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?
> 
> Kind regards,
> Parisa
> From: Maxime Chauvin [maxime.chauvin at inserm.fr]
> Sent: 24 October 2018 17:34
> To: Parisa Khateri
> Cc: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] GATE Docker container now available !
> 
> Dear Parisa,
> 
> you can run the GATE Docker container non-interactively like this (-d for daemon):
> docker run -id opengatecollaboration/gate:latest
> 
> then you can copy data to it:
> docker cp /data $container_id:/data
> 
> then execute a script inside the container:
> docker exec $container_id bash /data/gate.sh
> with gate.sh a script of your own that will set the environment variables and run Gate main.mac
> 
> Cheers,
>   Maxime Chauvin
> 
>> On 24 Oct 2018, at 15:49, Parisa Khateri <parisa.khateri at cern.ch <mailto:parisa.khateri at cern.ch>> wrote:
>> 
>> Dear Maxime, dear gate-users,
>> 
>> 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:
>> 
>> docker run -it opengatecollaboration/gate:latest bash
>> 
>> Then environmental variables:
>> source /root/.bashrc
>> Then one can run Gate. But what if I want to run Gate directly:
>> 
>> docker run -it opengatecollaboration/gate:latest Gate
>> 
>> I am new to containers.. hopefully my question makes sense :)
>> 
>> Thank you and kind regards,
>> Parisa
>> --------------------------------------------------------------
>> From: Maxime Chauvin [maxime.chauvin at inserm.fr <mailto:maxime.chauvin at inserm.fr>]
>> Sent: 22 October 2018 17:46
>> To: Parisa Khateri
>> Subject: Re: [Gate-users] GATE Docker container now available !
>> 
>> Good news !
>> 
>> You’re welcome,
>>   Maxime
>> 
>>> On 22 Oct 2018, at 16:54, Parisa Khateri <parisa.khateri at cern.ch <mailto:parisa.khateri at cern.ch>> wrote:
>>> 
>>> Dear Maxime,
>>> 
>>> The error was:
>>> 
>>> Error R__unzip_header: error in header
>>> Info in <TFile::GetStreamerInfoList>: cannot find the StreamerInfo record in file /home/pkhateri/Desktop/rootfile1.root
>>> 
>>> 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.
>>> 
>>> Thank you again and kind regards,
>>> Parisa
>>> From: Maxime Chauvin [maxime.chauvin at inserm.fr <mailto:maxime.chauvin at inserm.fr>]
>>> Sent: 22 October 2018 15:53
>>> To: Parisa Khateri
>>> Cc: gate-users at lists.opengatecollaboration.org <mailto:gate-users at lists.opengatecollaboration.org>
>>> Subject: Re: [Gate-users] GATE Docker container now available !
>>> 
>>> Dear Parisa,
>>> 
>>> which error do you get when trying to open it on your laptop ?
>>> 
>>> Kind regards,
>>>   Maxime
>>> 
>>>> On 22 Oct 2018, at 14:34, Parisa Khateri <parisa.khateri at cern.ch <mailto:parisa.khateri at cern.ch>> wrote:
>>>> 
>>>> Dear Maxime,
>>>> 
>>>> Thank you for your reply.
>>>> 
>>>> 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?
>>>> 
>>>> I pulled the Gate container on an HPC. I cannot install those packages in there.
>>>> 
>>>> Kind regards,
>>>> Parisa
>>>> From: Maxime Chauvin [maxime.chauvin at inserm.fr <mailto:maxime.chauvin at inserm.fr>]
>>>> Sent: 19 October 2018 16:58
>>>> To: Parisa Khateri
>>>> Cc: João Marcos; gate-users at lists.opengatecollaboration.org <mailto:gate-users at lists.opengatecollaboration.org>
>>>> Subject: Re: [Gate-users] GATE Docker container now available !
>>>> 
>>>> Dear Parisa,
>>>> 
>>>> ROOT needs some packages to be installed on the system if you want to use more than its libraries.
>>>> You can install them using this command:
>>>> yum -y install libX11-devel libXpm-devel libXft-devel libXext-devel
>>>> 
>>>> But keep in mind that the docker container is intended for computing, not for data analysis or visualisation.
>>>> 
>>>> Kind regards,
>>>>   Maxime Chauvin
>>>> 
>>>>> On 19 Oct 2018, at 15:47, Parisa Khateri <parisa.khateri at cern.ch <mailto:parisa.khateri at cern.ch>> wrote:
>>>>> 
>>>>> Dear Maxime, dear Joao,
>>>>> 
>>>>> 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:
>>>>> 
>>>>> root: error while loading shared libraries: libSM.so.6: cannot open shared object file: No such file or directory
>>>>> 
>>>>> I checked and found this library doesn't exist in the /cern/root-install/lib/ directory. 
>>>>> Could it be because of an inappropriate installation?
>>>>> 
>>>>> Thank you and kind regards,
>>>>> Parisa
>>>>> 
>>>>> From: Gate-users [gate-users-bounces at lists.opengatecollaboration.org <mailto:gate-users-bounces at lists.opengatecollaboration.org>] on behalf of João Marcos [joao.marcos at coimbra.lip.pt <mailto:joao.marcos at coimbra.lip.pt>]
>>>>> Sent: 17 September 2018 12:50
>>>>> To: Maxime Chauvin
>>>>> Cc: gate-users at lists.opengatecollaboration.org <mailto:gate-users at lists.opengatecollaboration.org>
>>>>> Subject: Re: [Gate-users] GATE Docker container now available !
>>>>> 
>>>>> Dear Maxime,
>>>>> 
>>>>> I followed your instructions and I got my first Gate installation successfully.
>>>>> This docker approach seems to be very useful.
>>>>> 
>>>>> Thank you very much.
>>>>> Best regards,
>>>>> João Marcos
>>>>>  
>>>>> On Wed, 22 Aug 2018 15:24:03 +0200, Maxime Chauvin
>>>>>  wrote:
>>>>> > Dear gate-users,
>>>>> > 
>>>>> > GATE is now available as a Docker container:
>>>>> > https://hub.docker.com/r/opengatecollaboration/gate/ <https://hub.docker.com/r/opengatecollaboration/gate/>
>>>>> > 
>>>>> > 
>>>>> > 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:
>>>>> > https://www.docker.com/resources/what-container <https://www.docker.com/resources/what-container>
>>>>> > 
>>>>> > 
>>>>> > As a simple example, to launch GATE within a Docker container:
>>>>> > install the Docker app https://www.docker.com/products/docker-desktop <https://www.docker.com/products/docker-desktop>
>>>>> > 
>>>>> > run in a terminal 'docker run -it opengatecollaboration/gate’
>>>>> > run ‘Gate'
>>>>> > Best regards,
>>>>> >   Maxime Chauvin

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