[Gate-users] cluster run on GATE_v9

Hadi Rezaei hrezaei.m.ph at gmail.com
Wed Jul 15 10:39:26 CEST 2020 

Hi Xinjie
Thank you for responding
I installed gate 8.2 and test it and I saw this error :
"Error : Failed to detect the Gate executable directory
Please check your environment variables!
Generated submit file may be invalid...
Made clean exit !"
Also the .Gate is generated but it is empty.
Thank you so much.
Best regards



On Sun, Jul 12, 2020 at 9:22 PM Xinjie Cao <xinjie.cao at stonybrook.edu>
wrote:

> Hi Hadi,
>
> From my experience, there is a bug in the gjs tool of the GATE v9.0
> package for that error. Please download an older edition of the GATE
> package, like v8.2 which I have confirmed executable, and try to use the
> cluster tools of it.
>
> Best,
>
> On Sun, Jul 12, 2020 at 3:38 AM Hadi Rezaei <hrezaei.m.ph at gmail.com>
> wrote:
>
>> Hi Xinjie and all gate users
>> Thank you for your reply
>> My absoulute command that I used in the terminal is:" ./gjs
>> -numberofsplits 5 -clusterplatform openmosix -a NECR12kbq175.root ROOT_FILE
>> TBNECR175.mac"
>> and I found: " Summary of all outputs:
>>   ROOT       output is enabled
>>   ASCII      output is disabled
>>   ARF        output is disabled
>>   PROJECTION output is disabled
>>   ECAT7      output is disabled
>>   SINOGRAM   output is disabled
>>   SINOACCEL  output is disabled
>>   LMF        output is disabled
>>   CT         output is disabled
>>   GPUSPECT   output is disabled
>> Summary of all actors:
>>   ~~~
>> Number of enabled output: 1
>> Number of enabled actors: 0
>> Could not use the following aliases from the command line:
>>  ROOT_FILE
>> Floating point exception (core dumped)"
>>
>> The .Gate folder contains two files (TBNECR1751.mac and TBNECR175.split).
>> It is noticeable that the time that I input to original mac file has been
>> divided into 5 (because of -numberofsplits 5).
>>
>> some parts of my original mac file are bellow:
>>
>> /gate/cluster/setTimeSplitHalflife 6586.2 s
>>
>>
>> #=====================================================
>> #  D A T A   O U T P U T
>> #=====================================================
>> /gate/output/root/enable
>> /gate/output/root/setFileName             NECR12kbq175
>> /gate/output/root/setRootHitFlag          0
>> #/gate/output/root/setRootSinglesFlag      1
>> /gate/output/root/setRootCoincidencesFlag 1
>> /gate/output/root/setRootdelayFlag        1
>>
>> #====================================================
>> #  R A N D O M   E N G I N E  A N D  S E E D
>> #====================================================
>> # JamesRandom Ranlux64 MersenneTwister
>> /gate/random/setEngineName JamesRandom
>> #/gate/random/setEngineSeed default
>> #/gate/random/setEngineSeed auto
>> #/gate/random/setEngineSeed 123456789
>> /gate/random/setEngineSeed default
>> #/gate/random/resetEngineFrom fileName
>> /gate/random/verbose 1
>>
>> #=====================================================
>> #   M E A S U R E M E N T   S E T T I N G S
>> #=====================================================
>>
>> /gate/application/setTimeSlice   1 s
>> /gate/application/setTimeStart   0   s
>> /gate/application/setTimeStop    1 s
>>
>> /gate/application/startDAQ
>>
>> Thank you.
>> Best regards.
>>
>> On Fri, Jul 10, 2020 at 2:17 AM Xinjie Cao <xinjie.cao at stonybrook.edu>
>> wrote:
>>
>>> Hi Hadi,
>>>
>>> Is that command line absolutely the same as the command you input in
>>> your terminal? Or you use ROOT_FILE to replace your real .root file? If you
>>> input the real .root output file name from GATE and get that error, maybe
>>> you could describe it much more specifically.
>>>
>>> I think the second error is due to your clean of ROOT_FILE alias and
>>> that makes the command chaos. Once you input the right .root file it will
>>> not be an issue so do not worry about that.
>>>
>>> Also, if all files that gjs command needs and gjs exe file are in the
>>> same directory, you do not need to input those long paths in your command
>>> and that makes your command look better clear.
>>>
>>> PS: You'd better reply to us two and the gate-mailing list at the same
>>> time so other guys who met the same problem could take advantage of it.
>>>
>>> Best,
>>> Xinjie
>>>
>>> On Thu, Jul 9, 2020 at 5:27 PM Hadi Rezaei <hrezaei.m.ph at gmail.com>
>>> wrote:
>>>
>>>> Hi Xinjie and Ville-Veikko
>>>> many thanks to you for your reply
>>>> After I copied gjs execute file and type ./gjs I saw some help commands
>>>> and I think the first problem is resolved. When I enter my parameters the
>>>> .Gate folder is generated that only contains one macro file with number (1)
>>>> and one .split file.
>>>> ./gjs -numberofsplits 5 -clusterplatform openmosix -a
>>>> /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/nTBNECR175
>>>> ROOT_FILE
>>>>  /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/TBNECR175.mac
>>>> Summary of all outputs:
>>>>   ROOT       output is enabled
>>>>   ASCII      output is disabled
>>>>   ARF        output is disabled
>>>>   PROJECTION output is disabled
>>>>   ECAT7      output is disabled
>>>>   SINOGRAM   output is disabled
>>>>   SINOACCEL  output is disabled
>>>>   LMF        output is disabled
>>>>   CT         output is disabled
>>>>   GPUSPECT   output is disabled
>>>> Summary of all actors:
>>>>   ~~~
>>>> Number of enabled output: 1
>>>> Number of enabled actors: 0
>>>> Could not use the following aliases from the command line:
>>>>  ROOT_FILE
>>>> Floating point exception (core dumped)
>>>>
>>>> Also when I clean ROOT_FILE I saw this error "**** Your macro file
>>>> given in parameter does not have any extension. Please give it the .mac
>>>> extension."
>>>>
>>>> Best,
>>>>
>>>>
>>>>
>>>>
>>>> On Thu, Jul 9, 2020 at 8:14 PM Xinjie Cao <xinjie.cao at stonybrook.edu>
>>>> wrote:
>>>>
>>>>> Hi Hadi,
>>>>>
>>>>> I think Ville-Veikko's way is the most basic way to solve this
>>>>> problem, if you do not know how to export the path or source your exe file.
>>>>> Also, copy the exe file into your current folder could help you get rid of
>>>>> that long path typing, but either one should work. Thanks for
>>>>> Ville-Veikko's remind!
>>>>>
>>>>> Best,
>>>>>
>>>>> On Thu, Jul 9, 2020 at 11:37 AM Ville-Veikko Wettenhovi <
>>>>> ville-veikko.wettenhovi at uef.fi> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Have you tried running
>>>>>> /media/rezaei/Data/GATE_v9/gate/Gate/cluster_tools/jobsplitter/gjs
>>>>>> -numberofsplits 5 -clusterplatform openmosix -a
>>>>>> /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/example1.root
>>>>>> ROOT_FILE example.mac ?
>>>>>>
>>>>>> Regards,
>>>>>> Ville-Veikko Wettenhovi
>>>>>> ------------------------------
>>>>>> *From:* Gate-users <
>>>>>> gate-users-bounces at lists.opengatecollaboration.org> on behalf of
>>>>>> Xinjie Cao <xinjie.cao at stonybrook.edu>
>>>>>> *Sent:* Thursday, July 9, 2020 18:17
>>>>>> *To:* Hadi Rezaei <hrezaei.m.ph at gmail.com>;
>>>>>> gate-users at lists.opengatecollaboration.org <
>>>>>> gate-users at lists.opengatecollaboration.org>
>>>>>> *Subject:* Re: [Gate-users] cluster run on GATE_v9
>>>>>>
>>>>>> Hi Hadi,
>>>>>>
>>>>>> Did you copy the gjs or gjm executable icon into your current folder?
>>>>>> I think after the installation of the gjs or gjm in your GATE folder, where
>>>>>> the path should be /PATH/TO/cluster_tools/jobsplitter, you could see an
>>>>>> executable icon in purple named gjs. Wherever you want to use the gjs
>>>>>> command, you need to copy one into the folder you want to run it, or you
>>>>>> have to export the path to its original location in your .bashrc file. Let
>>>>>> me know whether it works for you, good luck!
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> On Thu, Jul 9, 2020 at 11:08 AM Hadi Rezaei <hrezaei.m.ph at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Hi Xinjie
>>>>>> Thank you for your reply.
>>>>>> I have ubuntu 20.04
>>>>>> After type ./gjs I found "bash: ./gjs: No such file or directory"
>>>>>> indeed it can not find gjs. But I installed it.
>>>>>> Best,
>>>>>>
>>>>>> On Wed, Jul 8, 2020 at 10:57 PM Xinjie Cao <xinjie.cao at stonybrook.edu>
>>>>>> wrote:
>>>>>>
>>>>>> Sorry, "./gjs".
>>>>>>
>>>>>> On Wed, Jul 8, 2020 at 2:26 PM Xinjie Cao <xinjie.cao at stonybrook.edu>
>>>>>> wrote:
>>>>>>
>>>>>> You should type ./jgs for some linux system. The "gjs>" is another
>>>>>> system default command.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> On Wed, Jul 8, 2020 at 1:52 PM Hadi Rezaei <hrezaei.m.ph at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Hi,
>>>>>> Thank you for responding.
>>>>>> after type gjs in terminal I get "gjs>".
>>>>>> Also, I installed gjs and gjm as follow:
>>>>>>
>>>>>> cd jobsplittermake
>>>>>>
>>>>>>
>>>>>> cd filemergermake
>>>>>>
>>>>>> Thank you.
>>>>>> Best,
>>>>>>
>>>>>> On Wed, Jul 8, 2020 at 7:17 PM Ville-Veikko Wettenhovi <
>>>>>> ville-veikko.wettenhovi at uef.fi> wrote:
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> If you simply type gjs in terminal, what do you get? You may have the
>>>>>> gjs-package installed (https://packages.ubuntu.com/focal/gjs
>>>>>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpackages.ubuntu.com%2Ffocal%2Fgjs&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012590849&sdata=X7EdJbGSOR6ldnkb%2FDI3bs3FZFKou0R2hD5qBezCXfc%3D&reserved=0>)
>>>>>> that probably takes precedence over the GATE gjs in which case you need to
>>>>>> call the GATE gjs with the full path.
>>>>>>
>>>>>> Regards,
>>>>>> Ville-Veikko Wettenhovi
>>>>>> ------------------------------
>>>>>> *From:* Gate-users <
>>>>>> gate-users-bounces at lists.opengatecollaboration.org> on behalf of
>>>>>> Hadi Rezaei <hrezaei.m.ph at gmail.com>
>>>>>> *Sent:* Wednesday, July 8, 2020 14:48
>>>>>> *To:* gate-users at lists.opengatecollaboration.org <
>>>>>> gate-users at lists.opengatecollaboration.org>
>>>>>> *Subject:* [Gate-users] cluster run on GATE_v9
>>>>>>
>>>>>> Dear all
>>>>>> I am trying to run cluster GATE_v9 but after type "gjs
>>>>>> -numberofsplits 5 -clusterplatform openmosix -a
>>>>>> /media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI/example1.root
>>>>>> ROOT_FILE example.mac"   I found "*Unknown option -numberofsplits*"
>>>>>>
>>>>>> I enter in .bashrc:
>>>>>> export
>>>>>> GC_DOT_GATE_DIR=/media/rezaei/Data/GATE_v9/gate/Gate/benchmarks/benchPET/HADI
>>>>>> export
>>>>>> GC_GATE_EXE_DIR=/media/rezaei/Data/GATE_v9/gate/Gate/cluster_tools/jobsplitter/gjs
>>>>>> and also in mac file I added the command :
>>>>>> /gate/cluster/setTimeSplitHalflife 6586.2 s
>>>>>> I used this link guidance step by step:
>>>>>>
>>>>>> https://opengate.readthedocs.io/en/latest/how_to_use_gate_on_a_cluster.html <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fhow_to_use_gate_on_a_cluster.html&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012590849&sdata=9AzECfVha8MnvLpOFb3M%2F4uiWJmas1Eaz5Tx4gGR3C4%3D&reserved=0>
>>>>>>
>>>>>> How can I fix this problem?
>>>>>> any help will be highly appreciated. Thank you
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Gate-users mailing list
>>>>>> Gate-users at lists.opengatecollaboration.org
>>>>>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>>>>>> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fmailman%2Flistinfo%2Fgate-users&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012600837&sdata=xYDLfnILeImWiRMS37mpEdRRQwsLRdtcrm2GYBtt81M%3D&reserved=0>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> *....................................................*
>>>>>> *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/
>>>>>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyou.stonybrook.edu%2Fgoldan%2Fpeople%2F&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012610838&sdata=2j7xH4RMgjHnklirrp2dMktD%2FbPS%2BP2d9H9dHRUlics%3D&reserved=0>
>>>>>> *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/
>>>>>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyou.stonybrook.edu%2Fgoldan%2Fpeople%2F&data=02%7C01%7C%7C8449f0440d644344c90308d8241d681e%7C87879f2e73044bf2baf263e7f83f3c34%7C0%7C0%7C637299056012610838&sdata=2j7xH4RMgjHnklirrp2dMktD%2FbPS%2BP2d9H9dHRUlics%3D&reserved=0>
>>>>>> *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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