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mdtd_bound.pre_exec spans multiple lines #1

Closed antonst closed 10 years ago

antonst commented 10 years ago

I have defined pre_exec in namd.json as: "trestles.sdsc.xsede.org": { "pre_exec" : "module load namd/2.9", "executable" : "/opt/namd/bin/namd2", "uses_mpi" : "True" } and later in my "script" I did: . . . mdtd_bound = mdtd.bind(resource=resource) . . . cu.pre_exec = mdtd_bound.pre_exec . . . This results in "module load namd/2.9" being called as: m o d u l e

l o a d

n a m d / 2 . 9

I have tried to use square brackets and it doesn't help, so I simply hard-coded this: cu.pre_exec = ["module load namd/2.9"] and then it works. Not sure why this happens.

oleweidner commented 10 years ago

pre_exec has to be a list 

"pre_exec" : ["module load namd/2.9”]
marksantcroos commented 10 years ago

On 25 Jun 2014, at 8:38 , Ole Weidner notifications@github.com wrote:

pre_exec has to be a list

"pre_exec" : ["module load namd/2.9”]

Antons wrote: "I have tried to use square brackets and it doesn't help”, which reads like he tried to use a list.

Note that I didn’t test it myself.

oleweidner commented 10 years ago

Hm. I use the kernels in HT-BAC with "square brackets" for pre-exec and this works. There's a unit test for it which I just ran and it works.

@AntonsT, please attach a self-contained script that reproduces the error. Thanks.