[HagenC]

Hi everyone,
I have a question concerning the Allrun script in background mode. Running Allrun redirects the output to log files, but still the command window is blocked for new commands. I tried running the script in background by

./Allrun &

But still the command window is blocked.

Thank you for your help.

[guin]

simplest way: edit the script Allrun, so that it uses foamJob utility.
Replace the line where the solver call appears （i.e. runApplication $yourSolverName）by:
foamJob $yourSolverName

in case of working in parallel you shall rather use
foamJob -parallel $yourSolverName
（no need to specify the number of processes, that is read automatically from system/decomposeParDict）

other （less recommended） possibilities:
a. stop process and send it to background manually
./Allrun ＆
Ctrl＋Z
bg

b. use nohup utility:
nohup ./Allrun ＆

[HagenC]

Thank you very much for your reply.
foamJob works, but then I get another problem when using several commands that should be executed one after another, like in the following example:

foamJob snappyHexMesh
foamJob simpleFoam

The execution of simpleFoam does not wait until snappyHexMesh is finished.
I tried

foamJob snappyHexMesh
wait
foamJob simpleFoam

But without success.
Has someone an idea on that?
Thank you very much.

[guin]

Originally Posted by HagenC

Thank you very much for your reply.
foamJob works, but then I get another problem when using several commands that should be executed one after another, like in the following example:

foamJob snappyHexMesh
foamJob simpleFoam

The execution of simpleFoam does not wait until snappyHexMesh is finished.
I tried

foamJob snappyHexMesh
wait
foamJob simpleFoam

But without success.
Has someone an idea on that?
Thank you very much.

Hi,
that is because foamJob executes the process in the background, so the next command does not have yo wait for it to finish before being executed. Try out to call snappyHexMesh using "runApplication" instead of "foamJob" .

[floquation]

What exactly does your script look like?

If I have a prepareCase script like:

##### Prepare Case #####
echo "> Preparing case."
if [ ! -d "./logs" ]; then
    mkdir "./logs"
fi
[ -d 0 ] && 'rm' -rf 0
cp -r 0.org 0
# Mesh
echo "----> blockMesh"
blockMesh > ./logs/blockMesh.log || exit 1
# setFields
echo "----> setFields"
mv "0/alpha.water.org" "0/alpha.water"
setFields > ./logs/setFields.log || exit 1

I can run it in the background by:

./prepareCase.sh &

Or silently:

./prepareCase.sh > log &

All commands inside the prepareCase.sh script are executed sequentially - as they should.
If this is not the case for you, I presume that you have inserted some background "&"s inside the script?

[HagenC]

Thank you again for your very quick answers!
My original ./Allrun file was:

#!/bin/sh
cd ${0%/*} || exit 1

# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions

runApplication blockMesh
runApplication surfaceFeatureExtract
runApplication snappyHexMesh -overwrite
runApplication simpleFoam
runApplication foamToVTK

And had the problem of blocked command window as described in the first post. So I changed the ./Allrun file to:

#!/bin/sh
cd ${0%/*} || exit 1

# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions

foamJob blockMesh
foamJob surfaceFeatureExtract
foamJob snappyHexMesh -overwrite
foamJob simpleFoam
foamJob foamToVTK

And had the problem of waiting for the previous job to be finished as described in the second post. By changing it to:

#!/bin/sh
cd ${0%/*} || exit 1

# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions

runApplication blockMesh
runApplication surfaceFeatureExtract
runApplication snappyHexMesh -overwrite
foamJob simpleFoam
runApplication foamToVTK

Then the problem is the foamToVTK not being executed after the solution process. Further I would like to have the snappyHexMesh also running in the background.
Cheers.

[guin]

Hi,

You original Allrun file was OK. You can just call it by using one of my previously called "less-recommended" options "a" or "b" (post #2):

Personally, I would use option "a" because I don't like the logfile written by nohup.

Your second version of the Allrun file is definitetly not a good idea. Short (and surely oversimplified) hint: use foamJob only for calling the solver and ensure that it is the last action in your Allrun file.

There would be more possibilities of having it done, but I think there is no point on getting more into deep on this in this forum, provided the given options shall just work and have the additional advantage of being simple...

[HagenC]

Yes, thanks guin.
Version a is exactly what I needed.

[arsimons]

Originally Posted by floquation

What exactly does your script look like?

If I have a prepareCase script like:

##### Prepare Case #####
echo "> Preparing case."
if [ ! -d "./logs" ]; then
    mkdir "./logs"
fi
[ -d 0 ] && 'rm' -rf 0
cp -r 0.org 0
# Mesh
echo "----> blockMesh"
blockMesh > ./logs/blockMesh.log || exit 1
# setFields
echo "----> setFields"
mv "0/alpha.water.org" "0/alpha.water"
setFields > ./logs/setFields.log || exit 1

I can run it in the background by:

./prepareCase.sh &

Or silently:

./prepareCase.sh > log &

All commands inside the prepareCase.sh script are executed sequentially - as they should.
If this is not the case for you, I presume that you have inserted some background "&"s inside the script?

Hello Foamers!


I am currently trying to work on a local cluster via ssh. I was just wondering about the advantage of using the standard 'Allrun' script which has a header and uses 'runApplication', as compared to the script I quote from floquation?



Thanks in advance.


Best regards
Arne Simons