[Gate-users] GATE Cluster Running with HTCondor

[Zhengzhi Liu]

Hi Xinjie,

DON'T modify condor.script except adding "getenv=True" to its very first
line.
If you set up the environment correctly in .bashrc by strictly following
the instructions in the user manual, all shall be good to go.

Following is my entire GATE related env setting:

### ROOT ENV ###
source /home/zliu/Products/root/bin/thisroot.sh
alias root='root -l'

### GEANT4 ENV ###
source /home/zliu/Products/Geant4/geant4.10.05.p01-install/bin/geant4.sh

### GATE PATH ###
export PATH=/home/zliu/Products/Gate/Gate-8.2-install/bin:$PATH

### ClusterGATE ENV ###
export GC_DOT_GATE_DIR=/home/zliu/Products/Gate/output/
export GC_GATE_EXE_DIR=/home/zliu/Products/Gate/Gate-8.2-install/bin/


Please note that .Gate is a hidden directory under
/home/zliu/Products/Gate/output/ in my case. Hopefully these would help a
little bit.

Good luck and have fun with Condor.

Zhengzhi



On Mon, Mar 30, 2020 at 11:40 AM Xinjie Cao <xinjie.cao at stonybrook.edu>
wrote:

> Hi Zhengzhi,
>
> Thanks for your immediate response, I really appreciate that. I have a
> question about the following condor script, could you help answering it?
> ```
> Executable     = $GC_EXEC
>
> universe       = vanilla
> getenv=True
>
> #Requirements   = Memory >= 512 && Arch =="INTEL"
> #Rank       = Memory >= 512
> #Image_Size     = 28 Meg
>
> #GJS PART => DO NOT REMOVE OR CHANGE ANYTHING FROM THIS POINT ON
> #INCLUDING THESE COMMENT LINES!!
>
> Arguments      = $GC_MACRO
> Input   = $GC_EXEC.in1
> Output  = $GC_EXEC.out1
>
> Error   = $GC_EXEC.err1
> Log     = $GC_EXEC.log1
> Queue
> ```
> For $GC_EXEC, we just replace it with Gate executable directory? Or we
> need to write a .sh with Gate bash command? Thank you!
>
> Best,
>
> On Mon, Mar 30, 2020 at 2:31 PM Zhengzhi Liu <zliu36 at stanford.edu> wrote:
>
>> Hi Xinjie,
>>
>> Has it thrown any error message? I also followed the instruction (the
>> second link in your email) step by step. Although I also had some minor
>> issues at the very beginning, I got it to work very well. To me,  the only
>> thing I need to add to condor.script to make it work is adding
>> "getenv=true" to the script.
>>
>> Here are my suggestions to debug:
>>
>>
>>    - First, make sure that your GATE code runs correctly in non-Server
>>    mode and check the output;
>>    - Second, make sure that Condor runs normally.
>>    - Third, try to run your GATE code with condor.
>>
>>
>> If you have further questions, please let me know.
>>
>> Good luck,
>>
>> Zhengzhi
>>
>> On Mon, Mar 30, 2020 at 7:09 AM Xinjie Cao <xinjie.cao at stonybrook.edu>
>> wrote:
>>
>>> Dear all,
>>>
>>> I am using HTCondor platform for GATE cluster running with the following
>>> guides:
>>> 1.
>>> http://www.opengatecollaboration.org/Materials2015/PracticalExercises2015/RunningGATECluster
>>> 2.
>>> https://opengate.readthedocs.io/en/latest/how_to_use_gate_on_a_cluster.html
>>>
>>> I can run every step but just always get wrong output with 0 byte .out
>>> file. I am a rookie to GATE cluster running, any reply will be highly
>>> appreciated. Thank you!
>>>
>>> Best,
>>>
>>> --
>>> *....................................................*
>>> *Xinjie Cao*
>>> *M.E. / Ph.D. student*
>>> *Research Project Assistant*
>>> *Department of Electrical and Computer Engineering & Radiology *
>>> *Novel Medical Imaging Technologies Lab*
>>> *Health Science Center Level 8*
>>> *Stony Brook, NY 11794-8460 *
>>> *Tel: +1 (631)202-9445*
>>> you.stonybrook.edu/goldan/people/
>>> *email: **xinjie.cao at stonybroo*k.edu <xinjie.cao at stonybrook.edu>
>>>
>>>
>>> *....................................................*
>>> It is prohibited to distribute or publish the files attached to any
>>> other people unless you get permission from the writer himself. All rights
>>> reserved.
>>> _______________________________________________
>>> Gate-users mailing list
>>> Gate-users at lists.opengatecollaboration.org
>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>
>>
>
> --
> *....................................................*
> *Xinjie Cao*
> *M.E. / Ph.D. student*
> *Research Project Assistant*
> *Department of Electrical and Computer Engineering & Radiology *
> *Novel Medical Imaging Technologies Lab*
> *Health Science Center Level 8*
> *Stony Brook, NY 11794-8460 *
> *Tel: +1 (631)202-9445*
> you.stonybrook.edu/goldan/people/
> *email: **xinjie.cao at stonybroo*k.edu <xinjie.cao at stonybrook.edu>
>
>
> *....................................................*
> It is prohibited to distribute or publish the files attached to any other
> people unless you get permission from the writer himself. All rights
> reserved.
>
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