[Gate-users] GATE Cluster Running with HTCondor

[Xinjie Cao]

Hi Zhengzhi,

Thanks for your immediate response again. I have done almost the same
before as you did on environmental variables except the difference on
/Path/to/Gate , what I am still confused with cluster running are as
follows:
1. Don't we need to replace the GC_EXEC and GC_MACRO as mentioned in the
script comment? Or just adding "getenv=True"?
2. There were no error show when I run every step following the guide, but
an error in the output .err file like the following:
*** G4Exception : GateMDBFile
      issued by : GateMDBFile::GateMDBFile
Could not find material database file 'GateMaterials.db'
*** Fatal Exception *** core dump ***
[G4-cerr]  **** Track information is not available at this moment
[G4-cerr]  **** Step information is not available at this moment
[G4-cerr]

In case that GATE cannot find the material database 'GateMaterials.db', I
copied it to any folder related to the cluster running, but it still showed
during running. Do I have to configure that database in some special way?
Thank you again!

Best,

On Mon, Mar 30, 2020 at 3:37 PM Zhengzhi Liu <zliu36 at stanford.edu> wrote:

> 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.
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>>>
>>>
>>
>> --
>> *....................................................*
>> *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.
>>
>

-- 
*....................................................*
*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
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