[Gate-users] GATE Docker container now available !

Wed Oct 24 17:34:31 CEST 2018

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> 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]
> 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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