Peter -
ntr=1 should work (its in the stand pmemd test suite). There are various
aspects of pgi compilers + pmemd I am less certain about. I have pgi 5.2
basically working on cray opteron boxes, but have not tested everything yet,
and there are a lot of cray mods involved. I was actually trying to get 5.2
running today on a linux opteron cluster, and it was a total nightmare in
regard to being sure that pgi is getting the right libraries. Ultimately, I
had some i/o problems and cpu_time does not work, so I don't have a lot of
faith in this combination. I got pathscale working beautifully in about 10
minutes on the opteron, on the other hand. I would be interested in getting
more info on your exact setup, but it is entirely possible that pgi simply
cannot correctly compile pmemd at this point in time. I will be working on
this more, but in the meantime I might suggest trying a pathscale evaluation
copy (www.pathscale.com). It is known to produce faster code. I will have
a more complete opinion on the suitability of this compiler for opterons in
the near future.
Regards - Bob
----- Original Message -----
From: "Peter Varnai" <pv232.cam.ac.uk>
To: <amber.scripps.edu>
Sent: Thursday, February 24, 2005 5:25 PM
Subject: AMBER: pmemd + pgi 5.1 + ntr = 1
> Hi,
>
> I have compiled pmemd for opteron using pgi 5.1 and mpich-1.2.6.
> When I use ntr=0 all is fine, but I cannot get it to read ntr=1:
>
> title
> &cntrl
> imin=0, ntx=1, ntpr=2500, ntwr=2500, ntwx=2500, ntwe=2500,
> nscm=99001, ntf=2, ntc=2, ntb=1, ntp=0, ntt=1, tautp=0.5,
> cut=8.0, dt=0.002, tempi=300, nstlim=25000, irest=0, ntr=1, &end
> group title
> 25.0
> RES 1 160
> END
> END
>
> [...]
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> imin=0, ntx=1, ntpr=2500, ntwr=2500, ntwx=2500, ntwe=2500,
>
> GROUP 1 HAS HARMONIC CONSTRAINTS250006.00000
>
> rfree: Error decoding variable 7 2 from:
> cut=8.0, dt=0.002, tempi=300, nstlim=25000, irest=0, ntr=1, &end
>
> Is it a compilation problem or pmemd has a problem with this entry?
>
> Thanks,
> Peter
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Feb 24 2005 - 22:53:01 PST
