From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon May 16 2011 - 13:45:14 CDT
Well, the system is a symmetrical monolayer setup with some vacuum
space in +Z and -Z direction so I would the global density expect to
be significant lower then in a "general" solvated system.
The local density e.g. for water, after some equilibration steps,
should be around 1 g/cm^3.
Sure I can send you the input files.
Cheers,
Bjoern
On Mon, May 16, 2011 at 15:57, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> Hi again,
>
> Thanks. Is there a reason your system has half the typical density for a
> solvated periodic system? Can you point the input files so I can try to
> reproduce this myself?
>
> -Jim
>
> On Mon, 16 May 2011, Bjoern Olausson wrote:
>
>> 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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