From: Rulong Ma (rulong.ma.jlu_at_gmail.com)
Date: Fri Nov 11 2022 - 12:09:02 CST
Hi NAMD team.
I have used NAMD3 for more than one years. However, NAMD3 did not work when
the simulation was longer than 4.2μs. There are no errors in the output
file. This problem happened in more than four simulation systems. The
following is the job script and output information. Could you help to
solve this problem?
******* job script********************************************
#!/bin/bash
#SBATCH -J jobname # Name of the job
#SBATCH -N 1 # Number of nodes
#SBATCH -n 1 # number of processors(cores)
#SBATCH -t 7-00:00:00 # Runtime in HH:MM:SS
#SBATCH --mem=16GB # Memory requested in MB (see also
--mem-per-cpu)
#SBATCH -o comp_ca_%j.out # File to write STDOUT, %j=jobid
#SBATCH -e comp_ca_%j.err # File to wrote STDERR, %j=jobid
#SBATCH --mail-type=ALL # Send email when job starts, ends,
fails, etc
#SBATCH --mail-user=
#SBATCH --gres=gpu:1
#Load NAMD
module purge
module add NAMD/.3.0alpha-cuda
namd3 +setcpuaffinity +CmiSpinOnIdle +idlepoll step7_29production.inp
> step7_29production.out
***************************************************
********output file*******************************************
Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-CTO1-HAL1
PREVIOUS VALUES MULTIPLICITY: 1
k=0 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
k=0 n=2 delta=180
Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT
Info: SUMMARY OF PARAMETERS:
Info: 1955 BONDS
Info: 6609 ANGLES
Info: 19569 DIHEDRAL
Info: 425 IMPROPER
Info: 28 CROSSTERM
Info: 736 VDW
Info: 120 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Ignored 62273 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
Info: TIME FOR READING PSF FILE: 31.1866
Info: Reading pdb file step5_input.pdb
Info: TIME FOR READING PDB FILE: 0.321895
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 253847 ATOMS
Info: 190982 BONDS
Info: 187813 ANGLES
Info: 176049 DIHEDRALS
Info: 3308 IMPROPERS
Info: 992 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 225753 RIGID BONDS
Info: 535788 DEGREES OF FREEDOM
Info: 90367 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 90367 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 1.537e+06 amu
Info: TOTAL CHARGE = 3.14508e-05 e
Info: MASS DENSITY = 1.02128 g/cm^3
Info: ATOM DENSITY = 0.101575 atoms/A^3
Info: *****************************
Info: Reading from binary file step7_28production.restart.coor
Info:
Info: Entering startup at 62.5222 s, 0 MB of memory in use
Info: Startup phase 0 took 0.000432299 s, 0 MB of memory in use
Info: ADDED 554265 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.114848 s, 0 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.0130796 s, 0 MB of memory in use
Info: Startup phase 3 took 3.568e-05 s, 0 MB of memory in use
Info: Startup phase 4 took 0.000184432 s, 0 MB of memory in use
Info: Startup phase 5 took 2.4695e-05 s, 0 MB of memory in use
Info: PATCH GRID IS 4 (PERIODIC) BY 4 (PERIODIC) BY 6 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file step7_28production.restart.vel
Info: REMOVING COM VELOCITY 0.016666 -0.0256322 -0.0159315
Info: LARGEST PATCH (13) HAS 2846 ATOMS
Info: TORUS A SIZE 1 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.083115 s, 0 MB of memory in use
Info: Use 3D box decompostion in PME FFT.
Info: PME using 1 x 1 x 1 pencil grid for FFT and reciprocal sum.
Info: Startup phase 7 took 0.000105719 s, 0 MB of memory in use
Info: Updated CUDA force table with 4096 elements.
Info: Updated CUDA LJ table with 736 x 736 elements.
Info: Startup phase 8 took 0.00881762 s, 0 MB of memory in use
Info: Startup phase 9 took 5.543e-05 s, 0 MB of memory in use
Info: Startup phase 10 took 1.2858e-05 s, 0 MB of memory in use
Info: Startup phase 11 took 0.00160414 s, 0 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 12 took 0.000869604 s, 0 MB of memory in use
Info: CREATING 2024 COMPUTE OBJECTS
Info: Found 421 unique exclusion lists needing 1512 bytes
Info: Startup phase 13 took 0.0548679 s, 0 MB of memory in use
Info: Startup phase 14 took 3.4815e-05 s, 0 MB of memory in use
Info: Startup phase 15 took 0.000198313 s, 0 MB of memory in use
Info: Finished startup at 62.8005 s, 0 MB of memory in use
TCL: Running for 75000000 steps
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL TOTAL3
TEMPAVG PRESSURE GPRESSURE VOLUME
PRESSAVG GPRESSAVG
ENERGY: 2100000000 9000.2671 39907.6747 29885.8292
794.7429 -772113.2446 44539.8570 0.0000 0.0000
164962.7556 -483022.1179 309.8727 -647984.8735
-482186.8765 309.8727 -130.1821 -130.8904
2499116.2446 -130.1821 -130.8904
OPENING EXTENDED SYSTEM TRAJECTORY FILE
WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP -2119967296
CLOSING EXTENDED SYSTEM TRAJECTORY FILE
WRITING COORDINATES TO OUTPUT FILE AT STEP -2119967296
COORDINATE DCD FILE step7_29production.dcd WAS NOT CREATED
The last position output (seq=-2) takes 0.010 seconds, 0.000 MB of memory
in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP -2119967296
The last velocity output (seq=-2) takes 0.007 seconds, 0.000 MB of memory
in use
====================================================
WallClock: 63.171822 CPUTime: 62.054176 Memory: 0.000000 MB
[Partition 0][Node 0] End of program
********output file*******************************************
-- Best, Rulong Ma
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