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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
