My reason for looking into pbsa.mpi is to save time. I have to perform pbsa calculations on structures listed in a for loop; ideally, I'd like these for loop iterations to be divided over CPUs. I've tried rewriting my script to run over the iterations in parallel, but it is not successful (processes are killed randomly), even though my number of iterations is less than my number of available CPUs. I'm just trying to rule out all my options. Thank you.
Christina
----- Original Message -----
From: "David A Case" <david.case.rutgers.edu>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Wednesday, September 30, 2015 2:41:23 PM
Subject: Re: [AMBER] Updates for PBSA energy calculations
On Wed, Sep 30, 2015, Christina Berti wrote:
>
> Thank you for the fast reply. I am sadly having issues updating my
> amber14 bin directory to include pbsa.MPI. I am following tutorials and
> am not having luck, ever so sadly. I feel that this should be a quick
> update. Thank you again.
First, are you *sure* you need to run parallel pbsa calculations?
Amber users are *mostly* using pbsa in the context of MM/PBSA calculations.
There is not much point there in doing pbsa calculations in parallel; it is
far more straightforward to divide the snapshots among threads.
If you look at line 144 of $AMBERHOME/AmberTools/src/Makefile, you will
see that the installation of pbsa.MPI has been commented out:
# (cd pbsa && $(MAKE) clean && $(MAKE) install.parallel )
You could remove the "#" from column one, and re-run the parallel install, or
just run the indicated commands by hand. But it is likely that there is some
reason for not doing this by default, so you should not be surprised if
problems crop up. (Maybe the people at the UCI group know more about this.)
...hope this helps....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 30 2015 - 13:30:03 PDT
