Hey Eric,
This is great !
Is the code in the amber11 tree ?
a.
Eric Absgarten wrote:
> Hi,
>
> It was nice to meet many of you down at the developers meeting this weekend.
>
> After talking with Tom and Ross and others down at Sanibel, I have tried to
> improve the speed of ptraj, especially on large datasets.
> By default the experimental code isn't turned on. Two flags turn it on
> -DEXPFRAME and -DEXPHO
>
> You have to add -DEXPFRAME and -DEXPHO to turn it on
> for example you can change the Makefile in src/ptraj/Makefile like:
> .c.o:
> $(CC) -DEXPHO -DEXPFRAME -c $(CFLAGS) $(CPPFLAGS) -o $. $<
>
>
> Unfortunately I don't have any really large datasets to test it out on with.
> Please test it out, side by side with the flags unset (original ptraj) and
> let me know if it works and if its faster by how much.
>
> Appreciate any feedback.
> Thanks,
> Eric
>
>
> **** test runs follow ****
>
> Test Speed runs on 50k frame trajectory with 304 atoms:
>
> Original amber11/ptraj
> r1
> real 0m43.068s
> user 0m40.319s
> sys 0m2.124s
>
> r2
> real 0m42.861s
> user 0m40.155s
> sys 0m2.152s
>
> ********************************************
> New Ptraj w/ -DEXPFRAME and -DEXPHO
>
> r1
> real 0m26.306s
> user 0m24.550s
> sys 0m1.712s
>
> r2
> real 0m26.455s
> user 0m24.798s
> sys 0m1.616s
>
> ***********************************************
> New Ptraj w/ -DEXPFRAME only
> r1
> real 0m27.171s
> user 0m24.614s
> sys 0m2.092s
>
> r2
> real 0m27.042s
> user 0m24.810s
> sys 0m1.916s
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Fri Mar 06 2009 - 01:17:01 PST
