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I have a use-case where I'd like to be able to create and submit jobs from the head node of a cluster that does not itself have the packages being used by the compute nodes. In this case, it's because the dependencies are a PITA to set up, and so I have built a singularity container for running them. Per futureverse/future.batchtools#44, I've put the singularity command in my template file and can submit jobs to be run in the container with batchMap and submitJobs.
However, I run into a problem when defining jobs with batchMap using functions not installed on the head node.
Assume pita_package contains pita_function and can't be installed on the head node. Then a call to batchMap results in
> batchMap(pita_package::pita_function, 1:10)
Error in loadNamespace(x) : there is no package called ‘pita_package’
I've been able to work around this by creating a wrapper function for pita_function. E.g.
I'm adding this issue in part to help anyone runs into this question in the future, and in part to see if it makes sense to implement some sort of lazy evaluation into batchMap and its cousins to avoid the workaround.
The text was updated successfully, but these errors were encountered:
I have a use-case where I'd like to be able to create and submit jobs from the head node of a cluster that does not itself have the packages being used by the compute nodes. In this case, it's because the dependencies are a PITA to set up, and so I have built a singularity container for running them. Per futureverse/future.batchtools#44, I've put the singularity command in my template file and can submit jobs to be run in the container with
batchMap
andsubmitJobs
.However, I run into a problem when defining jobs with
batchMap
using functions not installed on the head node.Assume
pita_package
containspita_function
and can't be installed on the head node. Then a call tobatchMap
results inI've been able to work around this by creating a wrapper function for
pita_function
. E.g.I'm adding this issue in part to help anyone runs into this question in the future, and in part to see if it makes sense to implement some sort of lazy evaluation into
batchMap
and its cousins to avoid the workaround.The text was updated successfully, but these errors were encountered: