Hi there,
I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_music... https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_music.html in the docker environment of NEST (https://github.com/nest/nest-docker https://github.com/nest/nest-docker) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker.
The output was:
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. ------------------------------------------------------- Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted. ------------------------------------------------------- MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README. -------------------------------------------------------------------------- mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[46746,1],0] Exit code: 1
Can anyone help?
Thanks in advance, Benjamin
-- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com
Hi Benjamin
I have updated the docker image with NEST 2.18.0 ( the 'latest' image will follow in the next days). Please download/update with:
docker pull nestsim/nest:2.18.0
Go to the folder with your MUSIC scripts and start the container:
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data nestsim/nest:2.18.0 /bin/bash You are now in the shell of the container. Here you can execute the example program
mpirun -np 2 music /opt/data/minimalmusicsetup.music
So far I have only tested this simple example (minimalmusicsetup.music) on a Mac. It would be nice to know if this is a usable workflow for you and and if other, more realistic applications are possible.
In order to achieve the greatest flexibility in dealing with NEST and MUSIC, a standard installation from source code is recommended.
A small note: The example in the documentation is not up to date. Please use 'nest.ll_api.sli_run' and 'nest.ll_api.spp' instead of 'nest.sli_run' and 'nest.spp'. I will adjust this soon in the docs.
Best
Steffen
Am 08.10.19 um 09:56 schrieb Benjamin Staude:
Hi there,
I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_music... the docker environment of NEST (https://github.com/nest/nest-docker) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker.
The output was:
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[46746,1],0] Exit code: 1
Can anyone help?
Thanks in advance, Benjamin
-- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com mailto:benjamin.staude@gmail.com
NEST Users mailing list -- users@nest-simulator.org To unsubscribe send an email to users-leave@nest-simulator.org
Hi Stefan,
That worked perfectly, thanks a lot!
Two small comments concerning the documentation: 1) The python example misses the crucial `#!/usr/bin/python` in the first lines of minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py 2) nest 2.18.0 seem not to support `nest.sli_run` anymore, so I had to remove the checks in both files. Is there a new implementation of that functionality?
Best, Benjamin
On 15. Oct 2019, at 14:09, Steffen Graber s.graber@fz-juelich.de wrote:
Hi Benjamin
I have updated the docker image with NEST 2.18.0 ( the 'latest' image will follow in the next days). Please download/update with:
docker pull nestsim/nest:2.18.0
Go to the folder with your MUSIC scripts and start the container:
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data nestsim/nest:2.18.0 /bin/bashYou are now in the shell of the container. Here you can execute the example program
mpirun -np 2 music /opt/data/minimalmusicsetup.musicSo far I have only tested this simple example (minimalmusicsetup.music) on a Mac. It would be nice to know if this is a usable workflow for you and and if other, more realistic applications are possible.
In order to achieve the greatest flexibility in dealing with NEST and MUSIC, a standard installation from source code is recommended.
A small note: The example in the documentation is not up to date. Please use 'nest.ll_api.sli_run' and 'nest.ll_api.spp' instead of 'nest.sli_run' and 'nest.spp'. I will adjust this soon in the docs.
Best
Steffen
Am 08.10.19 um 09:56 schrieb Benjamin Staude:
Hi there,
I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_music... in the docker environment of NEST (https://github.com/nest/nest-docker) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker.
The output was:
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[46746,1],0] Exit code: 1
Can anyone help?
Thanks in advance, Benjamin
Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org
-- Steffen Graber
SimLab Neuroscience Division HPC in Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Jülich GmbH E-mail: s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de
Phone: +49 2461 61 85457
http://www.fz-juelich.de/ias/jsc
Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH
-- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com
Hi Benjamin,
Thank you for your feedback.
Your question 2): Use 'nest.ll_api.sli_run' and 'nest.ll_api.spp' instead of 'nest.sli_run' and 'nest.spp'.
Best
Steffen
Am 17.10.19 um 12:15 schrieb Benjamin Staude:
Hi Stefan,
That worked perfectly, thanks a lot!
Two small comments concerning the documentation:
- The python example misses the crucial `#!/usr/bin/python` in the first lines of minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py
- nest 2.18.0 seem not to support `nest.sli_run` anymore, so I had to remove the checks in both files. Is there a new implementation of that functionality?
Best, Benjamin
On 15. Oct 2019, at 14:09, Steffen Graber s.graber@fz-juelich.de wrote:
Hi Benjamin
I have updated the docker image with NEST 2.18.0 ( the 'latest' image will follow in the next days). Please download/update with:
docker pull nestsim/nest:2.18.0
Go to the folder with your MUSIC scripts and start the container:
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data nestsim/nest:2.18.0 /bin/bashYou are now in the shell of the container. Here you can execute the example program
mpirun -np 2 music /opt/data/minimalmusicsetup.musicSo far I have only tested this simple example (minimalmusicsetup.music) on a Mac. It would be nice to know if this is a usable workflow for you and and if other, more realistic applications are possible.
In order to achieve the greatest flexibility in dealing with NEST and MUSIC, a standard installation from source code is recommended.
A small note: The example in the documentation is not up to date. Please use 'nest.ll_api.sli_run' and 'nest.ll_api.spp' instead of 'nest.sli_run' and 'nest.spp'. I will adjust this soon in the docs.
Best
Steffen
Am 08.10.19 um 09:56 schrieb Benjamin Staude:
Hi there,
I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_music... in the docker environment of NEST (https://github.com/nest/nest-docker) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker.
The output was:
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[46746,1],0] Exit code: 1
Can anyone help?
Thanks in advance, Benjamin
Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com
NEST Users mailing list -- users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org
-- Steffen Graber
SimLab Neuroscience Division HPC in Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Jülich GmbH E-mail: s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de
Phone: +49 2461 61 85457
http://www.fz-juelich.de/ias/jsc
Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH
Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com
That’s it! Thanks, and apologies for my impatience in reading your previous mail ;)
On 17. Oct 2019, at 12:19, Steffen Graber s.graber@fz-juelich.de wrote:
Hi Benjamin,
Thank you for your feedback.
Your question 2): Use 'nest.ll_api.sli_run' and 'nest.ll_api.spp' instead of 'nest.sli_run' and 'nest.spp'.
Best
Steffen
Am 17.10.19 um 12:15 schrieb Benjamin Staude:
Hi Stefan,
That worked perfectly, thanks a lot!
Two small comments concerning the documentation:
- The python example misses the crucial `#!/usr/bin/python` in the first lines of minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py
- nest 2.18.0 seem not to support `nest.sli_run` anymore, so I had to remove the checks in both files. Is there a new implementation of that functionality?
Best, Benjamin
On 15. Oct 2019, at 14:09, Steffen Graber s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de wrote:
Hi Benjamin
I have updated the docker image with NEST 2.18.0 ( the 'latest' image will follow in the next days). Please download/update with:
docker pull nestsim/nest:2.18.0
Go to the folder with your MUSIC scripts and start the container:
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` -v $(pwd):/opt/data nestsim/nest:2.18.0 /bin/bashYou are now in the shell of the container. Here you can execute the example program
mpirun -np 2 music /opt/data/minimalmusicsetup.musicSo far I have only tested this simple example (minimalmusicsetup.music) on a Mac. It would be nice to know if this is a usable workflow for you and and if other, more realistic applications are possible.
In order to achieve the greatest flexibility in dealing with NEST and MUSIC, a standard installation from source code is recommended.
A small note: The example in the documentation is not up to date. Please use 'nest.ll_api.sli_run' and 'nest.ll_api.spp' instead of 'nest.sli_run' and 'nest.spp'. I will adjust this soon in the docs.
Best
Steffen
Am 08.10.19 um 09:56 schrieb Benjamin Staude:
Hi there,
I tried to run the basic example from https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_music... https://nest-simulator.readthedocs.io/en/latest/guides/using_nest_with_music.html in the docker environment of NEST (https://github.com/nest/nest-docker https://github.com/nest/nest-docker) on my OSX host. To be precise, I create the files minimalmusicsetup.music, minimalmusicsetup_sendnest.py and minimalmusicsetup_receivenest.py in the root directory (~/nest-docker) of the host system, and then called mpirun -np 2 music minimalmusicsetup.music from within docker.
The output was:
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
MUSIC: Unable to determine process rank. MUSIC: Did you launch music using mpirun? MUSIC: If so, check the comments about porting in README.
mpirun detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[46746,1],0] Exit code: 1
Can anyone help?
Thanks in advance, Benjamin
Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com mailto:benjamin.staude@gmail.com
NEST Users mailing list -- users@nest-simulator.org mailto:users@nest-simulator.org
To unsubscribe send an email to users-leave@nest-simulator.org mailto:users-leave@nest-simulator.org
-- Steffen Graber
SimLab Neuroscience Division HPC in Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Jülich GmbH E-mail: s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de
Phone: +49 2461 61 85457
http://www.fz-juelich.de/ias/jsc http://www.fz-juelich.de/ias/jsc
Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH
Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com mailto:benjamin.staude@gmail.com
-- Steffen Graber
SimLab Neuroscience Division HPC in Neuroscience Jülich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Jülich GmbH E-mail: s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de mailto:s.graber@fz-juelich.de Phone: +49 2461 61 85457 http://www.fz-juelich.de/ias/jsc http://www.fz-juelich.de/ias/jsc
Institute of Neuroscience and Medicine (INM-6) Computational and Systems Neuroscience & Institute for Advanced Simulation (IAS-6) Theoretical Neuroscience & JARA Institute Brain Structure-Function Relationships (INM-10) Forschungszentrum Jülich GmbH http://www.csn.fz-juelich.de http://www.csn.fz-juelich.de/
-- -- -- Dr. Benjamin Staude | Paul-Lincke-Ufer 7 | 10999 Berlin | benjamin.staude@gmail.com
-
Benjamin Staude -
Steffen Graber