Hi,
Similarly to the results posted by George earlier, the "Final Performance Info" was printed in the mdinfo (see below) and the mdout's (see below) version of the "Final Performance Info" attempts to do an average over 0 steps (which I assume is because last_step_count gets set to current_step when it is called in runfiles before the final call?).
To see what would happen I added a test to prevent an mdinfo flush when there is equality between nstep & total_nstlim at the same time as the mdinfo_flush_interval check in runfiles and that appears to fix things.
Many thanks,
Irfan Alibay
PhD Student
Pharmacy School
The University of Manchester
mdinfo contents:
NSTEP = 500 TIME(PS) = 20501.000 TEMP(K) = 292.47 PRESS = 339.7
Etot = -13299.1721 EKtot = 3035.0159 EPtot = -16334.1880
BOND = 11.1472 ANGLE = 33.8218 DIHED = 44.1738
1-4 NB = 13.0001 1-4 EEL = 327.4698 VDWAALS = 2442.2472
EELEC = -19206.0478 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 1526.3358 VIRIAL = 1143.0184 VOLUME = 52257.6272
Density = 0.9954
Ewald error estimate: 0.1046E-03
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 10 steps:
| Elapsed(s) = 0.18 Per Step(ms) = 18.22
| ns/day = 9.48 seconds/ns = 9110.35
|
| Average timings for all steps:
| Elapsed(s) = 9.01 Per Step(ms) = 18.03
| ns/day = 9.58 seconds/ns = 9014.59
| -----------------------------------------------------
mdout final performance:
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 0 steps:
| Elapsed(s) = 0.00 Per Step(ms) = Infinity
| ns/day = 0.00 seconds/ns = Infinity
|
| Average timings for all steps:
| Elapsed(s) = 9.02 Per Step(ms) = 18.03
| ns/day = 9.58 seconds/ns = 9015.26
| -----------------------------------------------------
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Tuesday, January 12, 2016 4:05 PM
To: AMBER Mailing List
Subject: Re: [AMBER] premed.MPI warning
On Tue, Jan 12, 2016 at 10:44 AM, Irfan Alibay <
irfan.alibay.manchester.ac.uk> wrote:
> Hi all,
>
> Out of curiosity, is this just a case of an unlucky mdinfo flush on the
> last step?
>
> I tried to replicate the issue by setting mdinfo_flush_interval to a low
> value and got a similar outcome.
>
​What is the content of the mdinfo file?
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 12 2016 - 09:00:03 PST
