From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon May 16 2011 - 04:02:51 CDT
Here are the requested test result with NAMD 2.8b2
One is particular interesting. The setup with "twoAwayX yes", PME and 264
cores did not fail consistently. From 4 tries it stalled only two times.
The timestep NAMD stalls on is not consitent too.
Without PME there were no problems at all.
Please find all relevant data here:
http://daten-transport.de/?id=8kNGP4tykfLp
If you need more Information, don't hesitate to ask.
Cheers,
Bjoern
On Saturday 14 May 2011 20:56:26 Jim Phillips wrote:
> 2.8b2 would be best. -Jim
>
> On Sat, 14 May 2011, Bjoern Olausson wrote:
> > Should I run those tests with 2.8b2 or are you satisfied with 2.7?
> >
> > Cheers,
> > Bjoern
> >
> > On Fri, May 13, 2011 at 21:52, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> >> Thanks. It looks like the switch from PME slabs to pencils happens
> >> between 144 and 156, but there's no obvious change from 252 to 264.
> >> The 264-core runs for over 1000 steps so it's not a deterministic
> >> problem.
> >>
> >> Please try for the two failing cases first adding outputTiming 1 so that
> >> we'll know what timestep it actually hangs on and then turning off PME
> >> so that we can tell if there's a connection to PME or not.
> >>
> >> -Jim
> >>
> >> On Fri, 13 May 2011, Bjoern Olausson wrote:
> >>> Hi,
> >>>
> >>> while tuning the "twoAway" options, the simulation which stalled on
> >>> 156 cores now stalled on 264 cores.
> >>> with twoAwayX, twoAwayY, twoAwayZ all set to NO it stalls on 156 cores
> >>> with twoAwayX set to YES and twoAwayY, twoAwayZ set to NO it stalles
> >>> on 264 cores.
> >>>
> >>> (This was tested with NAMD 2.7, but I guess 2.8 will behave the same
> >>> way) Please find the according logs under the following Link:
> >>> http://daten-transport.de/?id=7qK3HdCVnM7W (namd-logs.tar.bz2 584,5
> >>> Kilobytes)
> >>>
> >>> Cheers and many thanks,
> >>> Bjoern
> >>>
> >>> On Fri, May 13, 2011 at 15:20, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> >>>> Hi,
> >>>>
> >>>> Please send me the complete log file for the largest working and
> >>>> smallest hanging runs (I guess that's 144 and 156 cores).
> >>>>
> >>>> -Jim
> >>>>
> >>>> On Fri, 13 May 2011, Bjoern Olausson wrote:
> >>>>> Hi,
> >>>>>
> >>>>> with one of my Simulation I ran into the following problem.
> >>>>> Running the simulation "B" on less then 156 Cores works fine (Each
> >>>>> try incremented by 12 Cores).
> >>>>> But with 156 Cores the simulations hangs after minimization. Another
> >>>>> bigger simulation "A" runs fine with 156 Cores but stalls with 252.
> >>>>>
> >>>>> I am using
> >>>>> NAMD_2.8b2_Linux-x86_64-ibverbs-net-linux-x86_64-ibverbs-icc
> >>>>> currently, but the same happens with NAMD 2.7:
> >>>>>
> >>>>> Simulation A is a monolayer (Vacuum | Monolayer with attached Protein
> >>>>>
> >>>>> | Water | Monolayer with attached Protein | Vacuum)
> >>>>>
> >>>>> Simulation B is the same but I removed the two proteins and some
> >>>>> water between the two monolayers.
> >>>>>
> >>>>> A has 163214 Atoms
> >>>>> B has 79687 Atoms
> >>>>>
> >>>>> I can't find a reason why it happens at a certain Core number.
> >>>>>
> >>>>> LINE MINIMIZER BRACKET: DX 2.26297e-05 6.07123e-05 DU -0.112343
> >>>>> 0.803579 DUDX -9856.98 -88.7072 26529.9
> >>>>> LINE MINIMIZER REDUCING GRADIENT FROM 488884 TO 488.884
> >>>>> PRESSURE: 998 -3096.26 0.240235 -2.11389 0.240235 -3036.98 30.6163
> >>>>> -2.11389 30.6163 -2719.13
> >>>>> GPRESSURE: 998 -3053.97 0.0322738 -2.31931 1.70752 -2997.23 32.1548
> >>>>> 1.12647 30.6867 -2682.59
> >>>>> ENERGY: 998 5798.1099 9606.5134 11613.1689
> >>>>> 14.3917 -220491.3201 259.2408 0.0000
> >>>>> 0.0000 0.0000 -193199.8954 0.0000
> >>>>> -193199.8954 -193199.8954 0.0000 -2950.7895
> >>>>> -2911.2626
> >>>>>
> >>>>> PRESSURE: 999 -3101.92 0.427017 -1.88108 0.427017 -3029.82 30.4947
> >>>>> -1.88108 30.4947 -2731.63
> >>>>> GPRESSURE: 999 -3056.02 0.387877 -3.93892 3.00918 -2994.69 32.1866
> >>>>> 0.17135 30.0678 -2692.69
> >>>>> ENERGY: 999 5831.4354 9616.9842 11604.8301
> >>>>> 13.8257 -220677.3820 308.1108 0.0000
> >>>>> 0.0000 0.0000 -193302.1958 0.0000
> >>>>> -193302.1958 -193302.1958 0.0000 -2954.4553
> >>>>> -2914.4624
> >>>>>
> >>>>> PRESSURE: 1000 -3101.92 0.427017 -1.88108 0.427017 -3029.82 30.4947
> >>>>> -1.88108 30.4947 -2731.63
> >>>>> GPRESSURE: 1000 -3056.02 0.387877 -3.93892 3.00918 -2994.69 32.1866
> >>>>> 0.171348 30.0678 -2692.69
> >>>>> TIMING: 1000 CPU: 24.3443, 0.0242553/step Wall: 24.388,
> >>>>> 0.0242993/step, 0 hours remaining, 238.144531 MB of memory in use.
> >>>>> ETITLE: TS BOND ANGLE DIHED
> >>>>> IMPRP ELECT VDW BOUNDARY
> >>>>> MISC KINETIC TOTAL TEMP POTENTIAL
> >>>>> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> >>>>> ENERGY: 1000 5831.4354 9616.9842 11604.8301
> >>>>> 13.8257 -220677.3820 308.1108 0.0000
> >>>>> 0.0000 0.0000 -193302.1958 0.0000
> >>>>> -193302.1958 -193302.1958 0.0000 -2954.4553
> >>>>> -2914.4624
> >>>>>
> >>>>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
> >>>>> WRITING COORDINATES TO DCD FILE AT STEP 1000
> >>>>> WRITING COORDINATES TO RESTART FILE AT STEP 1000
> >>>>> FINISHED WRITING RESTART COORDINATES
> >>>>> The last position output (seq=1000) takes 0.026 seconds, 238.145 MB
> >>>>> of memory in use
> >>>>> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
> >>>>> FINISHED WRITING RESTART VELOCITIES
> >>>>> The last velocity output (seq=1000) takes 0.019 seconds, 238.145 MB
> >>>>> of memory in use
> >>>>> REINITIALIZING VELOCITIES AT STEP 1000 TO 303 KELVIN.
> >>>>> TCL: Running for 9000 steps
> >>>>> PRESSURE: 1000 -1607.18 5.85548 -10.9122 5.85548 -1546.56 26.3568
> >>>>> -10.9122 26.3568 -886.287
> >>>>> GPRESSURE: 1000 -1469.55 7.5989 -10.7156 10.9579 -1410.74 22.6426
> >>>>> -10.5674 20.7688 -1127
> >>>>> ETITLE: TS BOND ANGLE DIHED
> >>>>> IMPRP ELECT VDW BOUNDARY
> >>>>> MISC KINETIC TOTAL TEMP POTENTIAL
> >>>>> TOTAL3 TEMPAVG PRESSURE GPRESSURE
> >>>>> ENERGY: 1000 607.1667 6226.7038 11604.6460
> >>>>> 13.8497 -203337.4899 27.6364 0.0000
> >>>>> 0.0000 52831.6131 -132025.8742 303.3486
> >>>>> -184857.4873 -132057.5192 303.3486 -1346.6784
> >>>>> -1335.7638
> >>>>>
> >>>>>
> >>>>>
> >>>>> it takes some hours until this message is printed:
> >>>>> [0] processControlPoints() haveControlPointChangeCallback=0
> >>>>> frameworkShouldAdvancePhase=0
> >>>>>
> >>>>> Any clue where I could search?
> >>>>> If you need more information, don't hesitate to ask.
> >>>>>
> >>>>> Cheers,
> >>>>> Bjoern
-- Bjoern Olausson Martin-Luther-Universität Halle-Wittenberg Fachbereich Biochemie/Biotechnologie Kurt-Mothes-Str. 3 06120 Halle/Saale Phone: +49-345-55-24942
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