[Gate-users] cluster run on GATE_v9
Hadi Rezaei
hrezaei.m.ph at gmail.com
Sun Jul 12 09:38:12 CEST 2020
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.
>>>
>>
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