[Gate-users] cluster run on GATE_v9

Thu Jul 9 17:44:12 CEST 2020

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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200709/ec45362d/attachment-0001.html>