I'm using Charmm c34b1 on CentOS Linux 5.1 X86_64. My intel ifort version is 10.1 20080112.
Charmm was compiled by ifort with mpich-127/mpich2/openmpi/lammpi
I also compile a charmm with ifort and without any mpi.
Modify c34b1/test/cbenchtest/mbcodyn.inp
from
dyna cpt start nstep 1000 timestep 0.001 nbscale @s imscale @t -
to
dyna cpt start nstep 10000000 timestep 0.001 nbscale @s imscale @t -
With mpirun, all Charmmm program parallel on 8core within a node.
All of these program stop on step 2425 charmm output
Code:
SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2400
UPDECI: Image update at step 2425
SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000
UPDECI: Nonbond update at step 2425
TOTAL ENERGY CHANGE EXCEEDED
20. KCAL AND 10% OF THE TOTAL KINETIC ENERGY IN THE LAST STEP
PREVIOUS E = -0.3384E+05 CURRENT E = 0.2290E+07 KINETIC = 0.3909E+07
Writing RESTART FILE with previous and current coordinates,
which may be read by: READ COOR DYNR .... (see io.doc).
NOTE!! THIS FILE C A N N O T BE USED TO RESTART A RUN!!!
***** LEVEL -2 WARNING FROM <DYNAMC> *****
***** ENERGY CHANGE TOLERANCE EXCEEDED
******************************************
BOMLEV ( -3) IS NOT REACHED. WRNLEV IS 5
Parallel load balance (sec.):
Node Eext Eint Wait Comm List Integ Total
0 149.9 30.3 1.1 13.3 37.4 4.5 236.5
1 148.9 32.2 0.2 14.1 36.9 4.4 236.7
2 147.6 33.5 0.2 14.1 36.9 4.4 236.6
3 147.9 33.0 0.3 13.5 37.1 4.4 236.2
4 148.5 31.6 1.2 13.3 37.6 4.4 236.6
5 149.6 30.9 0.8 14.1 36.8 4.4 236.6
6 150.4 30.1 0.8 14.1 36.9 4.4 236.7
7 150.8 30.0 0.5 13.5 37.1 4.4 236.2
PARALLEL> Average timing for all nodes:
8 149.2 31.5 0.6 13.7 37.1 4.4 236.5
VCLOSE: Closing unit 1 with status "KEEP"
$$$$$$ New timer profile Local node$$$$$
First List 0.45 Other: 0.00
Comm coords 5.31 Other: 0.00
dynamc 0.15 Other: 0.00
Dynamics total 10.08 Other: 4.62
Image Update 3.86 Other: 0.00
List time 37.79 Other: 33.94
Direct Ewald time 100.21 Other: 0.00
Fill charge grid 14.66 Other: 0.00
Scalar sum 5.40 Other: 0.00
Grad sum 10.47 Other: 0.00
FFTcomm 10.48 Other: 0.00
FFT 16.59 Other: 6.11
Recip Ewald time 47.85 Other: 0.72
Ewald time 148.08 Other: 0.02
Nonbond force 149.87 Other: 1.79
Bond energy 1.98 Other: 0.00
Angle energy 1.38 Other: 0.00
Dihedral energy 1.30 Other: 0.00
Restraints energy 0.01 Other: 0.00
INTRNL energy 24.52 Other: 19.85
Comm force 8.37 Other: 0.00
Energy time 190.01 Other: 7.25
Total time 238.89 Other: 0.56
$$$$$$ Average profile $$$$$
First List 0.45 Other: 0.00
Comm coords 5.51 Other: 0.00
dynamc 0.14 Other: 0.00
Dynamics total 10.26 Other: 4.81
Image Update 3.86 Other: 0.00
List time 37.31 Other: 33.46
Direct Ewald time 99.09 Other: 0.00
Fill charge grid 14.02 Other: 0.00
Scalar sum 5.48 Other: 0.00
Grad sum 9.50 Other: 0.00
FFTcomm 11.13 Other: 0.00
FFT 17.15 Other: 6.68
Recip Ewald time 48.36 Other: 1.23
Ewald time 148.06 Other: 0.00
Nonbond force 149.19 Other: 1.11
Bond energy 1.86 Other: 0.00
Angle energy 1.19 Other: 0.00
Dihedral energy 1.26 Other: 0.00
Restraints energy 0.01 Other: 0.00
INTRNL energy 24.46 Other: 19.79
Comm force 8.40 Other: 0.00
Energy time 190.30 Other: 7.54
Total time 238.89 Other: 0.56
NORMAL TERMINATION BY END OF FILE
MAXIMUM STACK SPACE USED IS 772278
STACK CURRENTLY IN USE IS 0
MOST SEVERE WARNING WAS AT LEVEL -2
HEAP PRINTOUT- HEAP SIZE 10240000
SPACE CURRENTLY IN USE IS 0
MAXIMUM SPACE USED IS 3483268
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0
$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 3.98 MINUTES
CPU TIME: 0.02 SECONDS
