[gmx-users] gmx mdrun std::bad_alloc whilst using PLUMED
Mark Abraham
mark.j.abraham at gmail.com
Tue Nov 17 23:24:52 CET 2015
Hi,
GROMACS is apparently the first to notice that memory is a problem, but you
should also be directing questions about memory use with different kinds of
CVs to the PLUMED people. mdrun knows nothing at all about the PLUMED CVs.
The most likely explanation is that they have some data structure that
works OK on small scale problems, but which doesn't do well as the number
of atoms, CVs, CV complexity, and/or ranks increases.
Mark
On Tue, Nov 17, 2015 at 11:05 PM Nash, Anthony <a.nash at ucl.ac.uk> wrote:
> Hi all,
>
> I am using PLUMED 2.2 and gromacs 5.0.4. For a while I had been testing
> the viability of three collective variables for plumed, two dihedral
> angles and one centre of mass distance. After observing my dimer rotate
> about each other I decided it needed an intrahelical distance between two
> of the dihedral atoms (A,B,C,D), per helix, to sample the CV space whilst
> maintaining the Œregular¹ alpha-helical structure (the dihedral sampling
> was coming from the protein uncoiling rather than rotating). Note: it is
> likely that I will change these distances to the built-in alpha helical
> CV.
>
> The moment I increased the number of CVs from three to five, gromacs
> throws out a memory error. When I remove the 5th CV it still crashes. When
> I remove the 4th it stops crashing.
>
> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
> CLUSTER OUTPUT FILE
> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>
>
> starting mdrun 'NEU_MUT in POPC in water'
> 50000000 steps, 100000.0 ps.
>
> -------------------------------------------------------
> Program: gmx mdrun, VERSION 5.0.4
>
> Memory allocation failed:
> std::bad_alloc
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> Halting parallel program mdrun_mpi_d on CPU 0 out of 12
>
>
>
>
> It halts all 12 processes and the job dies. I increased the memory so I am
> using 43.2 GB of RAM distributed over 12 processes. The job still fails
> (but then, allocation of memory is very different to not having any memory
> at all).
>
> The contents of the gromacs.log file only reports the initialisation of
> gromacs followed by the initialisation of plumed. After this I would have
> expected the regular MD stepping output. I¹ve included the plumed
> initialisation below. I would appreciate any help. I suspect the problem
> lies with the 4th and 5th CV although systematically removing them and
> playing around with the parameters hasn¹t yielded anything yet. Please
> ignore what parameter values I have set. Besides the atom number
> everything else is a result of me trying to work out where certain ranges
> of values is causing PLUMED to exit and gromacs to crash. PLUMED input
> file below:
>
>
> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
> PLUMED INPUTFILE
> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>
> phi: TORSION ATOMS=214,230,938,922
> psi: TORSION ATOMS=785,801,367,351
>
> c1: COM ATOMS=1-571
> c2: COM ATOMS=572-1142
> COMdist: DISTANCE ATOMS=c1,c2
>
> d1: DISTANCE ATOMS=214,367
> d2: DISTANCE ATOMS=938,785
>
> UPPER_WALLS ARG=COMdist AT=2.5 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
> LABEL=COMuwall
> LOWER_WALLS ARG=COMdist AT=1.38 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
> LABEL=COMlwall
>
> UPPER_WALLS ARG=d1 AT=1.260 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
> LABEL=d1uwall
> LOWER_WALLS ARG=d1 AT=1.228 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
> LABEL=d1lwall
>
> UPPER_WALLS ARG=d2 AT=1.228 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
> LABEL=d2uwall
> LOWER_WALLS ARG=d2 AT=1.196 KAPPA=1000 EXP=2.0 EPS=1.0 OFFSET=0
> LABEL=d2lwall
>
> METAD ...
> LABEL=metad
> ARG=phi,psi,COMdist,d1,d2
> PACE=1
> HEIGHT=0.2
> SIGMA=0.06,0.06,0.06,0.06,0.06
> FILE=HILLS_neu_mut_meta_A
> BIASFACTOR=10.0
> TEMP=310.0
> GRID_MIN=-pi,-pi,0,0,0
> GRID_MAX=pi,pi,2.5,2.5,2.5
> GRID_SPACING=0.01,0.01,0.01,0.01,0.01
> ... METAD
>
>
> PRINT STRIDE=100
> ARG=phi,psi,COMdist,COMlwall.bias,COMuwall.bias,d1,d1lwall.bias,d1uwall.bia
> s,d2,d2lwall.bias,d2uwall.bias,metad.bias FILE=COLVAR_neu_mut_meta_A
>
>
>
> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
> GROMACS LOGFILE
> ‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹‹
>
> Center of mass motion removal mode is Linear
> We have the following groups for center of mass motion removal:
> 0: rest
> There are: 53575 Atoms
> Charge group distribution at step 0: 4444 4474 4439 4268 4913 4471 4298
> 4519 4395 4584 4474 4296
> Initial temperature: 311.436 K
>
>
> PLUMED: PLUMED is starting
> PLUMED: Version: 2.2.0 (git: Unknown) compiled on Nov 6 2015 at 11:15:41
> 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: gromacs
> PLUMED: Precision of reals: 8
> PLUMED: Running over 12 nodes
> PLUMED: Number of threads: 1
> PLUMED: Cache line size: 512
> PLUMED: Number of atoms: 53575
> PLUMED: File suffix:
> PLUMED: FILE: neu_mut_meta_A.dat
> PLUMED: Action TORSION
> PLUMED: with label phi
> PLUMED: between atoms 214 230 938 922
> PLUMED: using periodic boundary conditions
> PLUMED: Action TORSION
> PLUMED: with label psi
> PLUMED: between atoms 785 801 367 351
> PLUMED: using periodic boundary conditions
> PLUMED: Action COM
> PLUMED: with label c1
> PLUMED: serial associated to this virtual atom is 53576
>
> <ATOMS FROM A RANGE - I have removed for clarity>
>
> PLUMED: PBC will be ignored
> PLUMED: Action COM
> PLUMED: with label c2
> PLUMED: serial associated to this virtual atom is 53577
>
> <ATOMS FROM A RANGE - I have removed for clarity>
> PLUMED: PBC will be ignored
> PLUMED: Action DISTANCE
> PLUMED: with label COMdist
> PLUMED: between atoms 53576 53577
> PLUMED: using periodic boundary conditions
> PLUMED: Action DISTANCE
> PLUMED: with label d1
> PLUMED: between atoms 214 367
> PLUMED: using periodic boundary conditions
> PLUMED: Action DISTANCE
> PLUMED: with label d2
> PLUMED: between atoms 938 785
> PLUMED: using periodic boundary conditions
>
> PLUMED: Action UPPER_WALLS
> PLUMED: with label COMuwall
> PLUMED: with stride 1
> PLUMED: with arguments COMdist
> PLUMED: at 2.500000
> PLUMED: with an offset 0.000000
> PLUMED: with force constant 1000.000000
> PLUMED: and exponent 2.000000
> PLUMED: rescaled 1.000000
> PLUMED: added component to this action: COMuwall.bias
> PLUMED: added component to this action: COMuwall.force2
> PLUMED: Action LOWER_WALLS
> PLUMED: with label COMlwall
> PLUMED: with stride 1
> PLUMED: with arguments COMdist
> PLUMED: at 1.380000
> PLUMED: with an offset 0.000000
> PLUMED: with force constant 1000.000000
> PLUMED: and exponent 2.000000
> PLUMED: rescaled 1.000000
> PLUMED: added component to this action: COMlwall.bias
> PLUMED: added component to this action: COMlwall.force2
> PLUMED: Action UPPER_WALLS
> PLUMED: with label d1uwall
> PLUMED: with stride 1
> PLUMED: with arguments d1
> PLUMED: at 1.260000
> PLUMED: with an offset 0.000000
> PLUMED: with force constant 1000.000000
> PLUMED: and exponent 2.000000
> PLUMED: rescaled 1.000000
> PLUMED: added component to this action: d1uwall.bias
> PLUMED: added component to this action: d1uwall.force2
> PLUMED: Action LOWER_WALLS
> PLUMED: with label d1lwall
> PLUMED: with stride 1
> PLUMED: with arguments d1
> PLUMED: at 1.228000
> PLUMED: with an offset 0.000000
> PLUMED: with force constant 1000.000000
> PLUMED: and exponent 2.000000
> PLUMED: rescaled 1.000000
> PLUMED: added component to this action: d1lwall.bias
> PLUMED: added component to this action: d1lwall.force2
>
> PLUMED: Action UPPER_WALLS
> PLUMED: with label d2uwall
> PLUMED: with stride 1
> PLUMED: with arguments d2
> PLUMED: at 1.228000
> PLUMED: with an offset 0.000000
> PLUMED: with force constant 1000.000000
> PLUMED: and exponent 2.000000
> PLUMED: rescaled 1.000000
> PLUMED: added component to this action: d2uwall.bias
> PLUMED: added component to this action: d2uwall.force2
> PLUMED: Action LOWER_WALLS
> PLUMED: with label d2lwall
> PLUMED: with stride 1
> PLUMED: with arguments d2
> PLUMED: at 1.196000
> PLUMED: with an offset 0.000000
> PLUMED: with force constant 1000.000000
> PLUMED: and exponent 2.000000
> PLUMED: rescaled 1.000000
> PLUMED: added component to this action: d2lwall.bias
> PLUMED: added component to this action: d2lwall.force2
> PLUMED: Action METAD
> PLUMED: with label metad
> PLUMED: with stride 1
> PLUMED: with arguments phi psi COMdist d1 d2
> PLUMED: The number of bins will be estimated from GRID_SPACING
> PLUMED: Gaussian width 0.060000 0.060000 0.060000 0.060000 0.060000
> Gaussian height 0.200000
> PLUMED: Gaussian deposition pace 1
> PLUMED: Gaussian file HILLS_neu_mut_meta_A
> PLUMED: Well-Tempered Bias Factor 10.000000
> PLUMED: Hills relaxation time (tau) 0.231973
> PLUMED: KbT 2.577483
> PLUMED: Grid min -pi -pi 0 0 0
> PLUMED: Grid max pi pi 2.5 2.5 2.5
> PLUMED: Grid bin 629 629 251 251 251
> PLUMED: Grid uses spline interpolation
> PLUMED: added component to this action: metad.bias
> PLUMED: added component to this action: metad.work
>
>
>
>
>
> Many thanks
> Anthony
>
> Dr Anthony Nash
> Department of Chemistry
> University College London
>
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