Appion

If I choose nproc=1, nproc is not passed into the python script because php script removes it. When there is no option specified, the default self.params['nproc'] becomes None, and therefore it will attempt to set to all processers available. This will create a conflict if submit job is used because nodes and ppn would have been set to 1.

runMaxlikeAlignment.php probably does the same.

Maybe these python files should have a different nproc default? Or if the user pick nproc as 1 in the web interface, it should not allow it since this can not be run on single processor, right?

There is an example on how to set a different default in the options without copying nproc option everywhere again in r16468 for imagicMultiReferenceAlignment.py