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Update readme, add recipe to build Singularity img from docker

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Harro Verkouter 1 year ago
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6757a043a6
  1. 36
      containers/jive-casa-from-docker.recipe
  2. 39
      containers/jive-casa.recipe

36
containers/singularity-from-docker.recipe → containers/jive-casa-from-docker.recipe

@ -26,11 +26,37 @@ exec /usr/local/bin/tConvert "$@"
j2ms2 converts SFXC correlator output to CASA MeasurementSet
tConvert converts CASA MeasurementSet to FITS-IDI
In order to do so, the binaries inside this container must be able to read/write
the data file(s) on the host system. To that effect you should mount a host directory
with the the input data files inside the container.
Use the singularity "--bind outer-path:inner-path" option one or more times to expose
For j2ms2 to work the binary should be run from the experiment root directory;
i.e. the directory where the VEX file and the SFXC subjobs are located.
Your SFXC data area should look like this:
/path/to/data/EXPERIMENT/
EXPERIMENT.vix
<some name>.lis
jobnr1/*.cor
jobnr2/*.cor
.... /experiment2/
experiment2.vix
<some name>.lis
jobnrX/*.cor
jobnrY/*.cor
Note that the "*.vix" files must have the same name as the directory they are in.
Running j2ms2:
$> cd /path/to/data/EXPERIMENT
Using the "lis file":
$> singularity run --app j2ms2 /path/to/this/image -v <some name>.lis
Or creating a MS on-the-fly from a (subset) of SFXC output files:
$> singularity run --app j2ms2 /path/to/this/image -o <msname>.ms [other options] jobnr1/*.cor
tConvert is more flexible - it takes two arguments, "infile" and "outfile":
$> singularity run --app tConvert /path/to/this/image /path/to/<msname>.ms /path/to/some/OUTPUT.IDI
Alternatively use the singularity "--bind outer-path:inner-path" option one or more times to expose
directories from the host (outer) to a path inside the container (inner). After that
the inner-path(s) can be used in command line options to j2ms2/tConvert

39
containers/jive-casa.recipe

@ -42,16 +42,43 @@ exec /usr/local/bin/tConvert "$@"
j2ms2 converts SFXC correlator output to CASA MeasurementSet
tConvert converts CASA MeasurementSet to FITS-IDI
In order to do so, the binaries inside this container must be able to read/write
the data file(s) on the host system. To that effect you should mount a host directory
with the the input data files inside the container.
For j2ms2 to work the binary should be run from the experiment root directory;
i.e. the directory where the VEX file and the SFXC subjobs are located.
Your SFXC data area should look like this:
/path/to/data/EXPERIMENT/
EXPERIMENT.vix
<some name>.lis
jobnr1/*.cor
jobnr2/*.cor
.... /experiment2/
experiment2.vix
<some name>.lis
jobnrX/*.cor
jobnrY/*.cor
Note that the "*.vix" files must have the same name as the directory they are in.
Running j2ms2:
$> cd /path/to/data/EXPERIMENT
Using the "lis file":
$> singularity run --app j2ms2 /path/to/this/image -v <some name>.lis
Or creating a MS on-the-fly from a (subset) of SFXC output files:
$> singularity run --app j2ms2 /path/to/this/image -o <msname>.ms [other options] jobnr1/*.cor
tConvert is more flexible - it takes two arguments, "infile" and "outfile":
$> singularity run --app tConvert /path/to/this/image /path/to/<msname>.ms /path/to/some/OUTPUT.IDI
Use the singularity "--bind outer-path:inner-path" option one or more times to expose
Alternatively use the singularity "--bind outer-path:inner-path" option one or more times to expose
directories from the host (outer) to a path inside the container (inner). After that
the inner-path(s) can be used in command line options to j2ms2/tConvert
To run j2ms2 and tConvert all you need to do is run the following:
singularity run --bind outer-path:inner-path --app j2ms2 /path/to/jive-casa.simg [options for j2ms2]
singularity run --bind outer-path:inner-path --app tConvert /path/to/jive-casa.simg [options for tConvert]
singularity run --bind outer-path:inner-path --app j2ms2 /path/to/this/image [options for j2ms2]
singularity run --bind outer-path:inner-path --app tConvert /path/to/this/image [options for tConvert]

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