[Neurodebian-users] Condor and ANTs

[Arman Eshaghi]

Dear all,

This might be a bit off topic but I thought it is a good place to ask. I’m having trouble running ANTs with condor after I have migrated from SGE. Most of the codes that work with SGE will also work with Condor_qsub, given a trick that Chris suggested on Neurodebian website. For example this makes FSL work perfectly with condor. 

Specifically my problem is with buildtemplateparallel in ANTs that benefits from a couple of grid engines including SGE, Apple XGrid, PBS but not condor. For some reason the above trick (qsub symbolic link to condor_qsub) does not work here, and I receive “condor_qsub ‘-n’ option not recognized’. From the error message it clearly appears something is passed to condor_qsub that it can not handle, even when imitating SGE qsub. 

Here is what I have done:

1. Checking buildtemplateparallel.sh script to figure out the problem. So far no success, it sounds non-trivial (to me). 
2. Asking from ANTs mailing list, they suggested I make the script to work with condor on myself (see no. 1). 
3. Getting back to SGE: not an option, I bragged about  condor a few weeks ago to IT admin, I’ll lose credibility. 


Does anyone have a better recommendation for this, so that I can use buildtemplateparallel and condor?

All the best,
Arman