Re: [AMBER] Problem with running Python script in AMBER environment.

From: David A Case <>
Date: Thu, 9 Jul 2020 20:32:24 -0400

>On Thu, Jul 9, 2020 at 2:52 AM Vishal Singh <>
>> How to run a python script (which import numpy module) in AMBER environment
>> using pbs script file ? A simple python script (which did not import numpy
>> module) is running fine using qsub of the pbs script file. I am giving
>> python path like:

Being able to import numpy doesn't really have anything to do with whether or
not Amber's site-packages directory is in your PYTHONPATH. You need to check
which python is being executed in your pbs script. Your system python may not
have numpy installed; if you installed the miniconda version of python via
Amber's setup scripts, *that* version of python will have numpy and lots
of other needed packages.

So: try to run python outside of pbs, to make sure that you can import numpy.
Then, double check your script to see that the correct version of python is
being executed. If you followed the default installation, this will be
in $AMBERHOME/miniconda/bin. If you chose some other location, then use that
other location.

...hope this helps...dac

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Received on Thu Jul 09 2020 - 18:00:03 PDT
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