[Gate-users] cluster run on GATE_v9

Thu Jul 9 17:37:41 CEST 2020

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<mailto: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<mailto:xinjie.cao at stonybrook.edu>> wrote:
Sorry, "./gjs".

On Wed, Jul 8, 2020 at 2:26 PM Xinjie Cao <xinjie.cao at stonybrook.edu<mailto: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<mailto: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 jobsplitter
make

cd filemerger
make

Thank you.
Best,

On Wed, Jul 8, 2020 at 7:17 PM Ville-Veikko Wettenhovi <ville-veikko.wettenhovi at uef.fi<mailto: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<mailto:gate-users-bounces at lists.opengatecollaboration.org>> on behalf of Hadi Rezaei <hrezaei.m.ph at gmail.com<mailto:hrezaei.m.ph at gmail.com>>
Sent: Wednesday, July 8, 2020 14:48
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto: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

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--
....................................................
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 stonybrook.edu<mailto:xinjie.cao at stonybrook.edu>

 [https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ]    [https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download]
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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 stonybrook.edu<mailto:xinjie.cao at stonybrook.edu>

 [https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ]    [https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download]
....................................................
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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