[Gate-users] GATE Cluster Running with HTCondor

Mon Mar 30 22:27:56 CEST 2020

Hi Xinjie,

There is no difference at all between the GATE code running on a single
core and the one running on a cluster with tens of cores. There are exactly
the same.
I am using Gate 8.2, there might be some difference. But as far as I know,
you don't need to modify condor.script except adding the single line
"getenv=true" to the script.
As the error message, it says you didn't put  'GateMaterials.db' at the
right location. Please go your macros to locate where GateMaterials.db is
called. It may refer to a location outside your current folder, thus no
matter where you put it in your folder running this code, it still can't
find it. Also, please do a thorough check before running any code. For
Gate, you want to do a visualization check as well and look at all error in
the console.

Zhengzhi

On Mon, Mar 30, 2020 at 12:59 PM Xinjie Cao <xinjie.cao at stonybrook.edu>
wrote:

> 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.
>>>>> _______________________________________________
>>>>> 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.
>>>
>>
>
> --
> *....................................................*
> *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.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200330/316fb960/attachment-0001.html>