From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Dec 08 2016 - 16:04:41 CST
Hello Amy, I don't think there would be a big difference between a local
run and Stampede, so it's a good idea to download a precompiled multicore
binary and check.
This sounds like a probable bug in the atom selection routines: many of the
atom groups involved in the alpha function, which are not being initialized
properly (see 0 atoms and/or the mass exactly 1 for some of them).
Please send a starting configuration (whether or not you attach the .state
file shouldn't matter) and the NAMD config file.
Giacomo
On Thu, Dec 8, 2016 at 4:23 PM, Amy Rice <arice3_at_hawk.iit.edu> wrote:
> Hi all,
> I am writing to report an issue with the alpha colvar in 2.12b1, or at
> least as it is installed on the Stampede supercomputer. I recently went
> back to extend some 2D REUS simulations that I had done previously on
> Stampede ~5 months ago, and when I tried to restart the colvar simulations
> they kept crashing with '-nan' for MISC, kinetic, total energy,
> temperature, etc. The log file shows that it is correctly reading in the
> colvar configuration and state file. From here, I attempted to restart only
> one replica instead of all 81 at once, but the simulation still crashed
> with 'nan'. However, when I turned collective variables off and used the
> same coor, vel, and xsc to restart, it ran without issue. From there, I
> tested using only the distance or only the alpha colvar, and distance ran
> fine but alpha gave 'nan' so the problem seems to be isolated to the alpha
> colvar. I was able to run the one replica locally without errors using NAMD
> 2.11 and these same input files. We have not yet installed 2.12b1 locally,
> so I am unsure if the problem is with 2.12b1 or only the build on Stampede.
> I have copied my colvars input file and some portions of the output below.
> Please let me know if there is any other information I can provide; I am
> more than happy to supply files for testing purposes.
>
>
> -------------------------------colvars.conf-----------------
> ---------------
> colvarsTrajFrequency 200
>
> colvar {
> name length
> width 5
>
> lowerboundary 0.0
> upperboundary 50.0
>
> distance {
> group1 {
> atomnumbers {1}
> }
> group2 {
> atomnumbers {233}
> }
> forceNoPBC on
>
> }
> }
>
> colvar {
> name alpha
> width 0.1
>
> lowerboundary 0.0
> upperboundary 1.0
>
> alpha {
> residueRange 2-11
> psfSegID P1
> }
> }
>
> harmonic {
> name lenpot
> colvars alpha length
> centers 0.5 15.0
> forceConstant 10
> }
>
> # 10/25 = 0.4 for length
> # 10/0.001 = 1000 for alpha
>
> --------------------------------------Selected
> Output-------------------------------------------
> harm++> cpuaffinity PE-core map : 0-15
> Charm++> Running on 1 unique compute nodes (16-way SMP).
> Charm++> cpu topology info is gathered in 0.014 seconds.
> Info: NAMD 2.12b1 for Linux-x86_64-verbs-Stampede
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: for updates, documentation, and support information.
> Info:
> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 60701 for verbs-linux-x86_64-iccstatic
> Info: Built Mon Nov 7 17:51:38 CST 2016 by tg455591 on
> login4.stampede.tacc.utexas.edu
> Info: 1 NAMD 2.12b1 Linux-x86_64-verbs-Stampede 16
> c461-702.stampede.tacc.utexas.edu tg824315
> [...]
> colvars: ------------------------------------------------------------
> ----------
> colvars: Initializing the collective variables module, version 2016-10-21.
> colvars: Please cite Fiorin et al, Mol Phys 2013:
> colvars: http://dx.doi.org/10.1080/00268976.2013.813594
> colvars: in any publication based on this calculation.
> colvars: Using NAMD interface, version 2016-10-20.
> colvars: ------------------------------------------------------------
> ----------
> colvars: Reading new configuration from file "colvars.conf":
> colvars: # indexFile = "" [default]
> colvars: # smp = on [default]
> colvars: # analysis = off [default]
> colvars: # colvarsTrajFrequency = 200
> colvars: # colvarsRestartFrequency = 0 [default]
> colvars: # colvarsTrajAppend = off [default]
> colvars: # scriptedColvarForces = off [default]
> colvars: # scriptingAfterBiases = on [default]
> colvars: ------------------------------------------------------------
> ----------
> colvars: Initializing a new collective variable.
> colvars: # name = "length"
> colvars: Initializing a new "distance" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: # scalable = on [default]
> colvars: Initializing atom group "group1".
> colvars: # indexGroup = "" [default]
> colvars: # psfSegID = [default]
> colvars: # atomsFile = "" [default]
> colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
> colvars: # enableForces = on [default]
> colvars: # centerReference = off [default]
> colvars: # rotateReference = off [default]
> colvars: # enableFitGradients = on [default]
> colvars: Enabling scalable calculation for group "group1".
> colvars: Atom group "group1" defined, 1 atoms initialized: total
> mass = 14.007, total charge = -0.3.
> colvars: Initializing atom group "group2".
> colvars: # indexGroup = "" [default]
> colvars: # psfSegID = [default]
> colvars: # atomsFile = "" [default]
> colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
> colvars: # enableForces = on [default]
> colvars: # centerReference = off [default]
> colvars: # rotateReference = off [default]
> colvars: # enableFitGradients = on [default]
> colvars: Enabling scalable calculation for group "group2".
> colvars: Atom group "group2" defined, 1 atoms initialized: total
> mass = 12.011, total charge = 0.34.
> colvars: # forceNoPBC = on
> colvars: Computing distance using absolute positions (not
> minimal-image)
> colvars: # oneSiteSystemForce = off [default]
> colvars: # oneSiteTotalForce = off [default]
> colvars: All components initialized.
> colvars: # width = 5
> colvars: # lowerBoundary = 0
> colvars: # lowerWallConstant = 0 [default]
> colvars: # upperBoundary = 50
> colvars: # upperWallConstant = 0 [default]
> colvars: # hardLowerBoundary = off [default]
> colvars: # hardUpperBoundary = off [default]
> colvars: # expandBoundaries = off [default]
> colvars: # timeStepFactor = 1 [default]
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputTotalForce = off [default]
> colvars: # outputAppliedForce = off [default]
> colvars: # subtractAppliedForce = off [default]
> colvars: ------------------------------------------------------------
> ----------
> colvars: Initializing a new collective variable.
> colvars: # name = "alpha"
> colvars: Initializing a new "alpha" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: # scalable = on [default]
> colvars: # psfSegID = "P1"
> colvars: # hBondCoeff = 0.5 [default]
> colvars: # angleRef = 88 [default]
> colvars: # angleTol = 15 [default]
> colvars: # hBondCutoff = 3.3 [default]
> colvars: # hBondExpNumer = 6 [default]
> colvars: # hBondExpDenom = 8 [default]
> colvars: All components initialized.
> colvars: # width = 0.1
> colvars: # lowerBoundary = 0
> colvars: # lowerWallConstant = 0 [default]
> colvars: # upperBoundary = 1
> colvars: # upperWallConstant = 0 [default]
> colvars: # hardLowerBoundary = off [default]
> colvars: # hardUpperBoundary = off [default]
> colvars: # expandBoundaries = off [default]
> colvars: # timeStepFactor = 1 [default]
> colvars: # extendedLagrangian = off [default]
> colvars: # outputValue = on [default]
> colvars: # outputVelocity = off [default]
> colvars: # outputTotalForce = off [default]
> colvars: # outputAppliedForce = off [default]
> colvars: # subtractAppliedForce = off [default]
> colvars: ------------------------------------------------------------
> ----------
> colvars: Collective variables initialized, 2 in total.
> colvars: ------------------------------------------------------------
> ----------
> colvars: Initializing a new "harmonic" instance.
> colvars: # name = "lenpot"
> colvars: # colvars = { alpha, length }
> colvars: # outputEnergy = off [default]
> colvars: # forceConstant = 10
> colvars: # centers = { 0.5, 15 }
> colvars: # targetCenters = { 0.5, 15 } [default]
> colvars: # targetForceConstant = 0 [default]
> colvars: # outputCenters = off [default]
> colvars: The force constant for colvar "alpha" will be rescaled to 1000
> according to the specified width.
> colvars: The force constant for colvar "length" will be rescaled to 0.4
> according to the specified width.
> colvars: ------------------------------------------------------------
> ----------
> colvars: Collective variables biases initialized, 1 in total.
> colvars: ------------------------------------------------------------
> ----------
> colvars: Collective variables module (re)initialized.
> colvars: ------------------------------------------------------------
> ----------
> colvars: Updating NAMD interface:
> colvars: updating atomic data (24 atoms).
> colvars: updating group data (2 scalable groups, 2 atoms in total).
> colvars: Updating NAMD interface:
> colvars: updating atomic data (24 atoms).
> colvars: updating group data (2 scalable groups, 2 atoms in total).
> colvars: Re-initialized atom group length:0/0. 1 atoms: total mass =
> 14.007.
> colvars: Re-initialized atom group length:0/1. 1 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/0. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/1. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/2. 0 atoms: total mass = 12.011.
> colvars: Re-initialized atom group alpha:0/3. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/4. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/5. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/6. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/7. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/8. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/9. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/10. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/11. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/12. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/13. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/14. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/15. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/16. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/17. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/18. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/19. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/20. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/21. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/22. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/23. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/24. 2 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/25. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/26. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/27. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/28. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/29. 2 atoms: total mass = 1.
> colvars: ------------------------------------------------------------
> ----------
> colvars: Restarting from file "output/33/stretch_K-KR12.
> job3.restart10000.33.colvars.state".
> colvars: Restarting collective variable "length" from value: 8.91863
> colvars: Restarting collective variable "alpha" from value: 0.562412
> colvars: Restarting restraint bias "lenpot".
> colvars: ------------------------------------------------------------
> ----------
> colvars: The final output state file will be "output/33/stretch_K-KR12.
> job4.33.colvars.state".
> colvars: Writing to colvar trajectory file "output/33/stretch_K-KR12.
> job4.33.colvars.traj".
> colvars: Initializing step number as firstTimestep.
> Info: Startup phase 10 took 0.127216 s, 418.281 MB of memory in use
> Info: useSync: 0 useProxySync: 0
> Info: Startup phase 11 took 0.000180006 s, 418.281 MB of memory in use
> Info: Startup phase 12 took 0.000692129 s, 418.281 MB of memory in use
> Info: Finished startup at 1.78317 s, 418.281 MB of memory in use
>
> colvars: # forceConstant = 10 [default]
> colvars: # centers = { 0.6, 10 }
> TCL: Running for 1000 steps
> colvars: Updating NAMD interface:
> colvars: updating atomic data (24 atoms).
> colvars: updating group data (2 scalable groups, 2 atoms in total).
> colvars: Re-initialized atom group length:0/0. 1 atoms: total mass =
> 14.007.
> colvars: Re-initialized atom group length:0/1. 1 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/0. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/1. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/2. 0 atoms: total mass = 12.011.
> colvars: Re-initialized atom group alpha:0/3. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/4. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/5. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/6. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/7. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/8. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/9. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/10. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/11. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/12. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/13. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/14. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/15. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/16. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/17. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/18. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/19. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/20. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/21. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/22. 0 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/23. 0 atoms: total mass =
> 12.011.
> colvars: Re-initialized atom group alpha:0/24. 2 atoms: total mass = 1.
> colvars: Re-initialized atom group alpha:0/25. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/26. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/27. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/28. 2 atoms: total mass =
> 30.006.
> colvars: Re-initialized atom group alpha:0/29. 2 atoms: total mass = 1.
> colvars: The final output state file will be "output/33/stretch_K-KR12.
> job4.33.colvars.state".
> ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE
> GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> *ENERGY: 10000000 45.6835 125.1564 117.2970
> 6.9290 -123167.7157 11659.4683 0.0000
> -nan -nan -nan -nan
> -nan nan -nan -nan -nan
> 319243.9616 -nan -nan*
>
> ------------------------------------------------------------
> ------------------------------------------------------------
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
>
-- Giacomo Fiorin Associate Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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