[gmx-users] core dump error in grompp command

[(학생) 박세영 (에너지및화학공학부)]

Dear all,
I am trying to run large coarse-grained biomolecular system which includes about 800million beads in it. (about 500million among them are water beads). The .gro file of my system is about 35.62GB. The problem is, that although I’m trying to run grompp command to make input .tpr file, I continuously get this not enough memory error:
===========================================================================================
.
.
Excluding 1 bonded neighbours molecule type 'W'
Excluding 1 bonded neighbours molecule type 'WF'
Excluding 1 bonded neighbours molecule type 'W'
Excluding 1 bonded neighbours molecule type 'WF'
Removing all charge groups because cutoff-scheme=Verlet

-------------------------------------------------------
Program gmx_mpi, VERSION 5.0.6
Source code file: /scratch/x1671a04/gromacs/gromacs-5.0.6/src/gromacs/utility/smalloc.c, line: 224

Fatal error:
Not enough memory. Failed to realloc -6970315816 bytes for b->a, b->a=ceb96010
(called from file /scratch/x1671a04/gromacs/gromacs-5.0.6/src/gromacs/gmxlib/index.c, line 153)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
: Cannot allocate memory
Halting program gmx_mpi
===========================================================================================


or this segmentation fault error:
===========================================================================================
.
.
Excluding 1 bonded neighbours molecule type 'WF'
Excluding 1 bonded neighbours molecule type 'W'
Excluding 1 bonded neighbours molecule type 'NA'
Excluding 1 bonded neighbours molecule type 'WF'

NOTE 2 [file 11_billion.top, line 372]:
  System has non-zero total charge: 22320.000000
  Total charge should normally be an integer. See
  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
  for discussion on how close it should be to an integer.


Removing all charge groups because cutoff-scheme=Verlet
/var/spool/slurm/d/job06849/slurm_script: line 10: 36729 Segmentation fault      (core dumped) gmx_mpi grompp -f minimization.mdp -c 11_billion.gro -p 11_billion.top -o 11_billion.tpr
===========================================================================================


The gromacs version that I’m using is 5.0.6. I tried gromacs version of 5.0.6 and 2018.3, and grompp by double and single, but both did not work.
This is my command line : gmx_mpi grompp -f minimization.mdp -c waterbox_for100billion.gro -p 800_billions_only_water_box.top -o test.tpr
I’m running grompp command in CPU node which has 768GB of memory. I tried to find any method to generate .tpr file with parallel calculation, but I couldn’t, so I had to grompp the system in node with very large memory.
However, when I tracked my memory usage during grompp, the maximum memory usage was only about 20% of total available memory. Therefore, I guess it may not be the problem of memory shortage.

The .mdp file that I used in grompp is for minimization, and the contents are like this:

define              = -DPOSRES
integrator               = steep
dt                       = 0.01
nsteps                   = 25000
nstcomm                  = 100
comm-grps                         =

nstxout                  = 0
nstvout                  = 0
nstfout                  = 0
nstlog                   = 1000
nstenergy                = 1000
nstxout-compressed       = 0
compressed-x-precision   = 100
compressed-x-grps        =
nstpcouple              = 1
energygrps               = system ;Protein non-Protein ;Water_and_ions

nstlist                  = 20
ns_type                  = grid
pbc                      = xyz

rlist                                   = 1.4
coulombtype              = PME
pme-order              = 4
fourierspacing                      = 0.16
rcoulomb               = 1.2
epsilon_r               = 15

cutoff-scheme                      = Verlet
vdw_type                 = Cut-off
rvdw_switch              = 0.9
vdw-modifier             = Force-switch
rvdw                     = 1.2

constraints              = None
constraint_algorithm     = Lincs
lincs_iter              = 1         ; accuracy of LINCS
lincs-order              = 4


What could be the reason of this error? Also, I’m wondering that why gromacs does not fully use the available memory. Is there any option that restricts the memory usage of gromacs?

Any comment will be helpful.
Thank you for your time.
Sincerely,
Seyeong.