Re: [AMBER] NetCDF error: Invalid argument

From: David Case <>
Date: Sat, 20 May 2017 22:45:58 -0600

On Sat, May 20, 2017, xu qingliang wrote:

> I am trying to use the method of molecular dynamics simulation to
> clarify the mechanism of our system. and I use the method of VPN to
> connect the national laboratory's computer. the first,I ran the script
> of order is "qsub"),normally,we
> could get the files of min.out and complex.min2.rst,and the later
> file is essential for the next step( but after the
> running,we only get the file of min.out and can't get the file of
> complex.min2.rst,I don't know what's wrong with it.

Does the error depend in any way on the specifics of the system you are
running? Do the test cases run correctly on the national laboratory computer?

Can you run your test case in serial mode? I note that you are using 240
threads for you calculation--this is both likley to be very inefficient,
and may trigger errors that we don't test for very much. So try a short
parallel simulation with a much smaller number of threads.

All the above will help to narrow down the source of the problem.

(Once things are working, try some test calculations to estimate the optimal
number of threads. It is likely to be smaller than what you are using.)

...good luck...dac

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Received on Sat May 20 2017 - 22:00:03 PDT
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