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.
Many thanks,
Irfan Alibay
PhD Student
Pharmacy School
The University of Manchester
________________________________________
From: George Tzotzos [gtzotzos.me.com]
Sent: Tuesday, January 12, 2016 2:44 AM
To: AMBER Mailing List
Subject: Re: [AMBER] premed.MPI warning
Hi Ross,
Here’s the mdinfo:
NSTEP = 2500000 TIME(PS) = 7100.000 TEMP(K) = 299.78 PRESS = -274.3
Etot = -120290.1746 EKtot = 29540.3646 EPtot = -149830.5392
BOND = 762.6093 ANGLE = 2312.4788 DIHED = 2699.0110
1-4 NB = 931.5619 1-4 EEL = 14284.3805 VDWAALS = 18384.6313
EELEC = -189205.2120 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13273.6879 VIRIAL = 16148.6093 VOLUME = 485338.7691
Density = 1.0160
Ewald error estimate: 0.1922E-04
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 5000 steps:
| Elapsed(s) = 202.72 Per Step(ms) = 40.54
| ns/day = 4.26 seconds/ns = 20271.77
|
| Average timings for all steps:
| Elapsed(s) = 101933.57 Per Step(ms) = 40.77
| ns/day = 4.24 seconds/ns = 20386.71
| ——————————————————————————
and the final timings of the mdout.
A V E R A G E S O V E R 500 S T E P S
NSTEP = 2500000 TIME(PS) = 7100.000 TEMP(K) = 300.00 PRESS = 6.8
Etot = -120469.6075 EKtot = 29562.1963 EPtot = -150031.8038
BOND = 769.6383 ANGLE = 2302.7069 DIHED = 2696.7246
1-4 NB = 910.1209 1-4 EEL = 14230.5867 VDWAALS = 18833.7001
EELEC = -189775.2812 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 13331.5969 VIRIAL = 13260.2528 VOLUME = 485548.9629
Density = 1.0156
Ewald error estimate: 0.4656E-04
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 2500000 TIME(PS) = 7100.000 TEMP(K) = 1.38 PRESS = 115.2
Etot = 229.9611 EKtot = 135.6656 EPtot = 184.8159
BOND = 23.9947 ANGLE = 34.9852 DIHED = 20.3784
1-4 NB = 12.1171 1-4 EEL = 41.1527 VDWAALS = 177.6902
EELEC = 287.7258 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 92.9956 VIRIAL = 1202.0997 VOLUME = 473.8583
Density = 0.0010
Ewald error estimate: 0.3340E-04
------------------------------------------------------------------------------
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| NonSetup CPU Time in Major Routines, Average for All Tasks:
|
| Routine Sec %
| ------------------------------
| DataDistrib 14927.87 14.67
| Nonbond 80497.15 79.12
| Bond 17.38 0.02
| Angle 200.33 0.20
| Dihedral 661.87 0.65
| Shake 678.33 0.67
| RunMD 4750.86 4.67
| Other 2.86 0.00
| ------------------------------
| Total 101736.65
| PME Nonbond Pairlist CPU Time, Average for All Tasks:
|
| Routine Sec %
| ---------------------------------
| Set Up Cit 784.94 0.77
| Build List 6252.66 6.15
| ---------------------------------
| Total 7037.60 6.92
| PME Direct Force CPU Time, Average for All Tasks:
|
| Routine Sec %
| ---------------------------------
| NonBonded Calc 42024.53 41.31
| Exclude Masked 1197.16 1.18
| Other 6227.20 6.12
| ---------------------------------
| Total 49448.89 48.60
| PME Reciprocal Force CPU Time, Average for All Tasks:
|
| Routine Sec %
| ---------------------------------
| 1D bspline 2055.87 2.02
| Grid Charges 1722.17 1.69
| Scalar Sum 5638.56 5.54
| Gradient Sum 2748.39 2.70
| FFT 11830.51 11.63
| ---------------------------------
| Total 23995.50 23.59
| PME Load Balancing CPU Time, Average for All Tasks:
|
| Routine Sec %
| ------------------------------------
| Atom Reassign 6.32 0.01
| Image Reassign 3.40 0.00
| FFT Reassign 0.02 0.00
| ------------------------------------
| Total 9.74 0.01
| Final Performance Info:
| -----------------------------------------------------
| Average timings for last 0 steps:
| Elapsed(s) = 0.06 Per Step(ms) = Infinity
| ns/day = 0.00 seconds/ns = Infinity
|
| Average timings for all steps:
| Elapsed(s) = 101933.62 Per Step(ms) = 40.77
| ns/day = 4.24 seconds/ns = 20386.72
| -----------------------------------------------------
| Master Setup CPU time: 0.36 seconds
| Master NonSetup CPU time: 101780.81 seconds
| Master Total CPU time: 101781.17 seconds 28.27 hours
| Master Setup wall time: 1 seconds
| Master NonSetup wall time: 101934 seconds
| Master Total wall time: 101935 seconds 28.32 hours
Hope this helps
Cheers
George
> On 12 Jan 2016, at 03:35, Ross Walker <ross.rosswalker.co.uk> wrote:
>
> Ah yeah - that would make sense - or in the timings. George can you see what it reports for the final timings in mdinfo and mdout. Does it try to average over a window of zero steps?
>
>> On Jan 11, 2016, at 19:46, Jason Swails <jason.swails.gmail.com> wrote:
>>
>> On Mon, Jan 11, 2016 at 6:26 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> Hi Ross,
>>>
>>> For what’s worth, in this latest run, the warning was produced once at the
>>> end of the simulations.
>>>
>>
>> Oh, I'll bet it's in the final timings.... Number of steps left == 0.
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Tue Jan 12 2016 - 08:00:03 PST
