sum_hills internal error disordered hills

[Enrico Gandini]

I am doing Well Tempered metadynamics of some organic compounds in water. In most of the cases the job ended regularly and I obtained an HILLS file that sum_hills was able to process.
In one case, I obtained a disordered HILLS file, and when I try to run sum_hills on it I obtain the following message:


PLUMED: PLUMED is starting
PLUMED: Version: 2.2.2 (git: Unknown) compiled on May 12 2016 at 12:31:46
PLUMED: Please cite this paper when using PLUMED [1]
PLUMED: For further information see the PLUMED web page at http://www.plumed-code.org
PLUMED: Molecular dynamics engine:
PLUMED: Precision of reals: 8
PLUMED: Running over 1 node
PLUMED: Number of threads: 1
PLUMED: Cache line size: 512
PLUMED: Number of atoms: 1
PLUMED: File suffix:
PLUMED: Timestep: 0.000000
PLUMED: KbT has not been set by the MD engine
PLUMED: It should be set by hand where needed
PLUMED: Relevant bibliography:
PLUMED:   [1] Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)
PLUMED: Please read and cite where appropriate!
PLUMED: Finished setup
PLUMED: Action FAKE
PLUMED:   with label torsion1
PLUMED: Action FAKE
PLUMED:   with label torsion2
PLUMED: Action FUNCSUMHILLS
PLUMED:   with label @2
PLUMED:   with arguments torsion1 torsion2
PLUMED:   Output format is %14.9f
PLUMED:   hillsfile  : HILLS
PLUMED:   
PLUMED:   No boundaries defined: need to do a prescreening of hills
PLUMED:   doing serialread
PLUMED:   opening file HILLS


********** STACK DUMP **********
plumed(_ZN4PLMD9Exception28abortIfExceptionsAreDisabledEv+0x3f) [0x692967]
plumed(_ZN4PLMD9ExceptionC2ERKSsS2_jS2_+0x28) [0x693118]
plumed(_ZN4PLMD5IFile12advanceFieldEv+0x7ff) [0x6a5b5f]
plumed(_ZN4PLMD5IFile9scanFieldERKSsRSs+0x18) [0x6a5e22]
plumed(_ZN4PLMD5IFile9scanFieldERKSsRd+0x23) [0x6a5e93]
plumed(_ZN4PLMD8function12FilesHandler11scanOneHillEPNS_18BiasRepresentationEPNS_5IFileE+0x39) [0x5b6ce7]
plumed(_ZN4PLMD8function12FilesHandler9readBunchEPNS_18BiasRepresentationEi+0x1f4) [0x5b7dae]
plumed(_ZN4PLMD8function12FilesHandler12getMinMaxBinESt6vectorIPNS_5ValueESaIS4_EERNS_12CommunicatorERS2_IdSaIdEESB_RS2_IjSaIjEE+0x10b) [0x5b828b]
plumed(_ZN4PLMD8function12FuncSumHillsC1ERKNS_13ActionOptionsE+0x14c1) [0x5be2f7]
plumed(_ZN4PLMD8function25FuncSumHillsRegisterMe2036createERKNS_13ActionOptionsE+0x21) [0x5c46f7]
plumed(_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE+0x523) [0x56adcf]
plumed(_ZN4PLMD10PlumedMain14readInputWordsERKSt6vectorISsSaISsEE+0x33b) [0x59722b]
plumed(_ZN4PLMD7cltools14CLToolSumHills4mainEP8_IO_FILES3_RNS_12CommunicatorE+0x41dd) [0x50875b]
plumed(_ZN4PLMD10CLToolMain3runEiPPcP8_IO_FILES4_RNS_12CommunicatorE+0x1676) [0x584336]
plumed(_ZN4PLMD10CLToolMain3cmdERKSsPv+0xa8b) [0x585d81]
plumed(_ZN4PLMD10PlumedMain3cmdERKSsPv+0x6abd) [0x5a129f]
plumed(plumedmain_cmd+0xed) [0x5a6be6]
plumed(plumed_cmd+0x23) [0x723504]
plumed(main+0xe2) [0x4797d2]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x2af355f6fb15]
plumed() [0x479629]
******** END STACK DUMP ********

+++ Internal PLUMED error
+++ file IFile.cpp, line 96
+++ message: mismatch between number of fields in file and expected number
Segmentation fault (core dumped)

The HILLS file is too big to be attached, i just report here some lines where I imagine there could be a problem:

      9.400000446476042     -1.124075084783231     -2.037373385423435                    0.1                    0.1     0.5204931645024495                      6
      9.600000455975533     -1.169640227041443     -1.523425186815702                    0.1                    0.1     0.5934258037423383                      6
      9.800000465475023    -0.5054811590604786     -1.777438410832406                    0.1                    0.1     0.5999808357600885                      6
      10.00000047497451    -0.8128360199754683     -1.8192      15220.20072292071    -0.8248449634782218     0.1290547994209454                    0.1                    0.1     0.1140821971536351                      6
      15220.40072293021    -0.6952970518148507     0.2876096875761398                    0.1                    0.1      0.109541453263125                      6
      15220.60072293971     -1.461456241490302     0.1348965081885281                    0.1                    0.1     0.1092371520961035                      6
      15220.80072294921     -1.330982017308814     0.1803878407082502                    0.1                    0.1     0.1032267505721389                      6

As you can see, there is a sudden "jump" in the line that starts with 10.00000047497451 .

I cannot explain why I obtained this corrupted HILLS file with this particular compound, which is very similar to other compounds I analyzed with the same technique without problems.
The plumed.dat file I used is the following:

torsion1: TORSION ATOMS=7,5,11,12
torsion2: TORSION ATOMS=18,16,15,13
betas: DISTANCE ATOMS=7,18

METAD ...
LABEL=metad
ARG=torsion1,torsion2
PACE=100
HEIGHT=0.5
SIGMA=0.1,0.1
FILE=HILLS
GRID_MIN=-pi,-pi
GRID_MAX=pi,pi
GRID_SPACING=0.1,0.1
BIASFACTOR=6.0
TEMP=300.0
... METAD

PRINT STRIDE=10 ARG=torsion1,torsion2,betas,metad.bias FILE=COLVAR


Thank you all for your attention, let me know if the same problem happened to any of you or if you have any guesses of a possible solution!
Enrico Gandini

[Francesco Oliva]

UP

The problem seems to randomly appear and it's very frustrating.

Francesco Oliva

[Giovanni Bussi]

Hi,

the only explanation is that a simulation did not complete properly. You can easily make a script that fixes the HILLS file. Something like

mv HILLS HILLS.copy

awk '{if($1=="#!" || NF==9) print}' HILLS.copy > HILLS

where 9 is the number of columns that you expect (should be adapted case by case).

Giovanni

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[Alejandro Gil Ley]

Hi,
It looks like your grid spacing is too large, equal to the Gaussian width, but I'm not sure whether plumed2.2 changes the value automatically to use 1/5 of the Gaussian width as grid spacing also when the value of GRID_SPACING is large or only when is omitted on the input. Giovanni will probably tell you.
Best
Alejandro

On Thu, Feb 2, 2017, 04:06 Giovanni Bussi <giovann...@gmail.com> wrote:

Hi,

the only explanation is that a simulation did not complete properly. You can easily make a script that fixes the HILLS file. Something like

mv HILLS HILLS.copy

awk '{if($1=="#!" || NF==9) print}' HILLS.copy > HILLS

where 9 is the number of columns that you expect (should be adapted case by case).

Giovanni

On Thu, Feb 2, 2017 at 10:03 AM, Francesco Oliva <frances...@gmail.com> wrote:

UP

The problem seems to randomly appear and it's very frustrating.

Francesco Oliva

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[Giovanni Bussi]

I think plumed does not enforce it, it just complains in the output (perhaps).

In any case Alejandro is right, grid spacing is too large

Giovanni

On Thu, Feb 2, 2017 at 2:10 PM, Alejandro Gil Ley <gil8...@gmail.com> wrote:

Hi,
It looks like your grid spacing is too large, equal to the Gaussian width, but I'm not sure whether plumed2.2 changes the value automatically to use 1/5 of the Gaussian width as grid spacing also when the value of GRID_SPACING is large or only when is omitted on the input. Giovanni will probably tell you.
Best
Alejandro

On Thu, Feb 2, 2017, 04:06 Giovanni Bussi <giovann...@gmail.com> wrote:

Hi,

the only explanation is that a simulation did not complete properly. You can easily make a script that fixes the HILLS file. Something like

mv HILLS HILLS.copy

awk '{if($1=="#!" || NF==9) print}' HILLS.copy > HILLS

where 9 is the number of columns that you expect (should be adapted case by case).

Giovanni

On Thu, Feb 2, 2017 at 10:03 AM, Francesco Oliva <frances...@gmail.com> wrote:

UP

The problem seems to randomly appear and it's very frustrating.

Francesco Oliva

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