Hello,
This is my first post, so let me start off by saying thanks for a great
tool! I am using GNU parallel to manage some data-parallel tasks on a
cluster where the resources are managed by PBS.
Here are my two questions:
1) How do I transfer my environment variables to a remote machine using the
--slf option
2) How does parallel read in the config file. I can't seem to set `--slf
$PBS_NODEFILE' in the config file.
--
1)
My first issue is that my local environment variables are not getting
transfered to remote nodes
local> echo $PYTHONPATH /global/home/users/petigura/Kepler//keppycode//
local> seq 0 15 | parallel -j8 --slf $PBS_NODEFILE 'echo {}; echo
$PYTHON_PATH; echo $PWD'
/global/home/users/petigura
15
<snip>
/global/home/users/petigura
10
I can work around this by explicitly sourcing my bashrc file
local> seq 0 15 | parallel -j8 --slf $PBS_NODEFILE 'source ~/.bashrc;echo
{}; echo $PYTHONPATH; echo $PWD'
8
/global/home/users/petigura/Kepler//keppycode//
/global/home/users/petigura
4
/global/home/users/petigura/Kepler//keppycode//
/global/home/users/petigura
2)
I'd like to use a config file to simplify my commands, but I can't get it
to work.
local> cat ~/.parallel/nodes
#Config file. Options to parallel when running on multiple nodes
--slf $PBS_NODEFILE
source $HOME/.bashrc;
local > seq 0 15 | parallel -j8 -Jnodes --wd $PWD 'source ~/.bashrc;echo
{}; echo $PYTHONPATH; echo $PWD'
Cannot open $PBS_NODEFILE
--
Thanks for your help!
Erik
