[Gate-users] GATE Cluster Running with HTCondor

Mon Mar 30 22:48:38 CEST 2020

You code failed at the very first step I mentioned below:

   - 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.

Good luck.

Zhengzhi

On Mon, Mar 30, 2020 at 1:27 PM Zhengzhi Liu <zliu36 at stanford.edu> wrote:

> 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.
>>
>
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