Re: [AMBER] copy charges using Python API

From: Thomas Evangelidis <>
Date: Sun, 7 Aug 2016 15:50:23 +0200

​Thanks Jason! 'xargs' looks very practical to run multiple jobs
concurrently on a PC or laptop. However, I would rather use 'scoop' from
Python to run the jobs on a multi-node cluster since the database may
contain several thousands or millions of compounds. Just wanted to know if
something similar has been made before for antechamber in order not to
re-invent the wheel :)


> Another question: is anyone aware of any effort made to parallelize
> > antechamber computations? I want to screen a database using bcc charges.
> >
> ​Not parallelize within antechamber. But there are ways of doing this at
> the shell level. If you are doing some kind of database for this, "xargs"
> is actually a great way to parallelize. You can tell it how many
> processors to use, and it will run through a list of arguments and dispatch
> it to the target program. Once one job finishes, it will pull the next one
> from the queue and dispatch it to the program (making sure never to have
> more than the requested number of jobs active at a time).​
> The man page and googling for examples will show you how to use it. I've
> personally used it in AF-NMR to process each snapshot in a multi-model PDB
> file in parallel. You can see this here:
> (look for '').
> You will probably also have to wrap antechamber in a shell script to make
> sure that each antechamber run runs in a separate directory to avoid
> collisions of intermediate files.
> There is another way to do it through the shell, but it's not as
> efficient. You can do something like this:
> cd dir1
> antechamber <args> &
> cd ../dir2
> antechamber <args> &
> cd ../dir3
> antechamber <args> &
> cd ../dir4
> antechamber <args> &
> cd ..
> wait
> cd dir5
> antechamber <args> &
> ...
> This has the effect that 4 jobs will run at a time, but the next group of 4
> will only proceed when each of the previous group finishes (rather than
> xargs, where it uses a queue-like approach to make sure processors are
> rarely idle).
> HTH,
> Jason
> --
> Jason M. Swails
> _______________________________________________
> AMBER mailing list

Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic

AMBER mailing list
Received on Sun Aug 07 2016 - 07:00:03 PDT
Custom Search