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
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Received on Fri Mar 06 2009 - 01:16:26 PST
