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add MPICH recipe with current master #53

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add MPICH recipe with current master #53

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58dbb32
add MPICH recipe with current master
espenhgn Nov 4, 2020
5979b47
fixed typo
espenhgn Nov 4, 2020
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71 changes: 36 additions & 35 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,13 +7,14 @@ If you know how to use docker, you know how to use NEST.
Currently the following docker images are provided

- nestsim/nest:latest (~1,07GB)
- nestsim/nest:latest_mpich (~???GB)
- nestsim/nest:2.12.0 (~535MB)
- nestsim/nest:2.14.0 (~537MB)
- nestsim/nest:2.16.0 (~539MB)
- nestsim/nest:2.18.0 (~543MB)
- nestsim/nest:2.20.0 (~634MB)
- nestsim/nest:3.0 (~1,07GB) (until now equal with 'latest')

All are build with these environment variable:

- 'WITH_MPI=ON'
Expand All @@ -24,7 +25,7 @@ All are build with these environment variable:

You can change this on top of every 'dockerfile'.


## Usage

You can use the docker images direct out of docker hub like this:
Expand All @@ -35,47 +36,47 @@ You can use the docker images direct out of docker hub like this:
-v $(pwd):/opt/data \
-p 8080:8080 nestsim/nest:<version> <args>


[<args>] can be either 'notebook', 'nest-server', interactice' or '/bin/bash'
[<version>] kind of docker image (e.g. 'latest', '2.12.0', '2.14.0',
[<version>] kind of docker image (e.g. 'latest', '2.12.0', '2.14.0',
'2.16.0', '2.18.0', '3.0')

eg.
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app \
-v $(pwd):/opt/data \
-p 8080:8080 nestsim/nest:latest notebook

or for starting nest-server in background (only 'latest')
docker run -d --rm -e LOCAL_USER_ID=`id -u $USER` -p 5000:5000 nestsim/nest:latest nest-server

If you want to work with a container for a longer time, you should remove the '--rm':

docker run -it -e LOCAL_USER_ID=`id -u $USER` --name my_app \
-v $(pwd):/opt/data \
-p 8080:8080 nestsim/nest:<version> <args>

After you stop the container, it still exists ('docker ps -a'). To restart simply use:

docker start -i my_app

### On Windows

docker run -it --rm -v %cd%:/opt/data -p 8080:8080 nestsim/nest:<version> <args>
In Powershell, '%cd%' might not work for the current directory. Then

In Powershell, '%cd%' might not work for the current directory. Then
you should explicitly specify a folder with existing write permissions.

In any case, this will download the docker image with the pre-installed
NEST master form docker hub and start it. After booting an URL is presented.
Click on it or copy it to your browser. Voilá jupyter notebook starts from
Click on it or copy it to your browser. Voilá jupyter notebook starts from
the docker image.

You can update the image with:

docker pull nestsim/nest:<version>

## Usage of the local build system

You can clone this repository and use the shell script:

sh run.sh [--help] <command> [<args>] [<version>]
Expand Down Expand Up @@ -105,31 +106,31 @@ Two little steps to get started

### 1 - Provisioning

This step is only necessary if you want to build the images directly
This step is only necessary if you want to build the images directly
from the docker files.

sh run.sh provision VERSION
Be careful with the version 'all'. This really takes a long time.
After every build of a NEST docker image, there are two more images - the one
with the name of the NEST version (e.g. 'nestsim/nest:master') and

Be careful with the version 'all'. This really takes a long time.

After every build of a NEST docker image, there are two more images - the one
with the name of the NEST version (e.g. 'nestsim/nest:master') and
another without any name. The last one you can delete.
More information about this so called 'multi-stage build' here:
More information about this so called 'multi-stage build' here:
<https://docs.docker.com/develop/develop-images/multistage-build/>

### 2 - Run

- with Jupyter Notebook (recommended)

sh run.sh run notebook VERSION
or

or

docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app \
-v $(pwd):/opt/data \
-p 8080:8080 nestsim/nest:VERSION notebook

(For VERSION see above)

Open the displayed URL in your browser and have fun with Jupyter
Expand All @@ -138,13 +139,13 @@ More information about this so called 'multi-stage build' here:
- in interactive mode

sh run.sh run interactive VERSION
or

or

docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app \
-v $(pwd):/opt/data \
-p 8080:8080 nestsim/nest:VERSION interactive

(For VERSION see above)

After the prompt 'Your python script:' enter the filename of the script
Expand All @@ -154,13 +155,13 @@ More information about this so called 'multi-stage build' here:
- as virtual image

sh run.sh run virtual VERSION
or

or

docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app \
-v $(pwd):/opt/data \
-p 8080:8080 nestsim/nest:VERSION /bin/bash

(For VERSION see above)

You are logged in as user 'nest'. Enter 'python' and in the
Expand All @@ -180,7 +181,7 @@ In the folder with your music scripts run:
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` \
-v $(pwd):/opt/data \
nestsim/nest:3.0 /bin/bash

You are now on container's shell, but can use the programs on your local machine

mpirun -np 2 music /opt/data/minimalmusicsetup.music
Expand Down
17 changes: 9 additions & 8 deletions run.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -48,12 +48,12 @@ fi
case $command in
provision)
echo
echo "Provisioning needs an argument: 'latest' '2.12.0', '2.14.0',"
echo "'2.16.0', '2.18.0', '2.20.0', '3.0' or 'all'."
echo "Provisioning needs an argument: 'latest', 'latest_mpich', '2.12.0',"
echo "'2.14.0', '2.16.0', '2.18.0', '2.20.0', '3.0' or 'all'."
echo
while test $# -gt 0; do
case "$1" in
latest | 2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0 )
latest | latest_mpich | 2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0 )
echo "Build the NEST image for NEST $1"
echo
docker build -t nestsim/nest:"$1" ./src/"$1"
Expand All @@ -62,14 +62,15 @@ case $command in
;;
all)
echo "Build the NEST image for NEST 2.12.0, 2.14.0,"
echo "2.16.0, 2.18.0, 2.20.0, 3.0 and latest"
echo "2.16.0, 2.18.0, 2.20.0, 3.0 latest_mpich and latest"
echo
docker build -t nestsim/nest:2.12.0 ./src/2.12.0
docker build -t nestsim/nest:2.14.0 ./src/2.14.0
docker build -t nestsim/nest:2.16.0 ./src/2.16.0
docker build -t nestsim/nest:2.18.0 ./src/2.18.0
docker build -t nestsim/nest:2.20.0 ./src/2.20.0
docker build -t nestsim/nest:3.0 ./src/3.0
docker build -t nestsim/nest:latest_mpich ./src/latest_mpich
docker build -t nestsim/nest:latest ./src/latest
echo
echo "Finished!"
Expand All @@ -91,14 +92,14 @@ case $command in
echo " - 'virtual VERSION'"
echo
echo "VERSION is the version of NEST"
echo "(e.g. latest, 2.12.0, 2.14.0, 2.16.0, 2.18.0, 2.20.0, 3.0)"
echo "(e.g. latest, latest_mpich, 2.12.0, 2.14.0, 2.16.0, 2.18.0, 2.20.0, 3.0)"
echo
LOCALDIR="$(pwd)"
while test $# -gt 1; do
case "$1" in
notebook)
case "$2" in
latest | 2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0)
latest | latest_mpich | 2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0)
echo "Run NEST-$2 with Jupyter Notebook".
echo
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app \
Expand All @@ -114,7 +115,7 @@ case $command in
;;
interactive)
case "$2" in
latest | 2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0)
latest | latest_mpich |2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0)
echo "Run NEST-$2 in interactive mode."
echo
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app \
Expand All @@ -130,7 +131,7 @@ case $command in
;;
virtual)
case "$2" in
latest | 2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0)
latest | latest_mpich |2.12.0 | 2.14.0 | 2.16.0 | 2.18.0 | 2.20.0 | 3.0)
echo "Run NEST-$2 like a virtual machine."
echo
docker run -it --rm -e LOCAL_USER_ID=`id -u $USER` --name my_app \
Expand Down
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