[Gate-users] GATE Docker container now available !

Mon Oct 29 15:51:16 CET 2018

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/
>
>
> 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
>
>
> As a simple example, to launch GATE within a Docker container:
> install the Docker app 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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