From: Amy Rice (arice3_at_hawk.iit.edu)
Date: Thu Dec 08 2016 - 15:23:16 CST
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
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