[Gate-users] cluster run on GATE_v9
Xinjie Cao
xinjie.cao at stonybrook.edu
Sun Jul 12 18:51:51 CEST 2020
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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