From: Uday Midya (umidya.iitkgp_at_gmail.com)
Date: Sun Aug 11 2013 - 02:19:47 CDT
Hi,
I have prepared the initial pdb and psf files from psfgen module of NAMD2.8
and NAMD2.9 for the same TIP4P water simulation in the two versions. The
order of the atoms in individual water was maintained as oxygen, hydrogen,
hydrogen, lone pair. 'waterModel tip4' was set in the configuration file.
The simulation run fine in NMAD2.8. But in case of NAMD2.9 following
'ERROR' lines equals to #waters appear in the log file followed by normal
outputs. After printing 'ERROR' simulation does not stop, and run ~4 times
faster than NAMD2.8. Same problem was reported in the mailing list earlier
(Jan 15, 2013) but I cant find the solution.
Following is the portion of a log file.
Charmrun> IBVERBS version of charmrun
Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21
Charm++> scheduler running in netpoll mode.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 2 unique compute nodes (32-way SMP).
Charm++> cpu topology info is gathered in 0.128 seconds.
Info: NAMD 2.9 for Linux-x86_64-ibverbs
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60400 for net-linux-x86_64-ibverbs-iccstatic
Info: Built Mon Apr 30 14:03:10 CDT 2012 by jim on dakar.ks.uiuc.edu
Info: 1 NAMD 2.9 Linux-x86_64-ibverbs 60 compute-0-0.local uday
Info: Running on 60 processors, 60 nodes, 2 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.146034 s
Info: 110.676 MB of memory in use based on /proc/self/stat
Info: Configuration file is tip4water_NVT300K05.conf
Info: Working in the current directory /home/uday/WATER_TIP4P/300K
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE tip4water_NVT300K04.restart.xsc
Info: Using TIP4P water model.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 3000000
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 65.4934 0 0
Info: PERIODIC CELL BASIS 2 0 65.4934 0
Info: PERIODIC CELL BASIS 3 0 0 65.4934
Info: PERIODIC CELL CENTER 0 0 0
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH 40
Info: INITIAL TEMPERATURE 300
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME tip4water_NVT300K05.dcd
Info: DCD FREQUENCY 500
Info: DCD FIRST STEP 3000500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME tip4water_NVT300K05.xst
Info: XST FREQUENCY 1000
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME tip4water_NVT300K05
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME tip4water_NVT300K05.restart
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0.48
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.48
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 10000
Info: PRESSURE OUTPUT STEPS 1000
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 68 68 68
Info: PME MAXIMUM GRID SPACING 1.5
Info: Attempting to read FFTW data from
FFTW_NAMD_2.9_Linux-x86_64-ibverbs.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.9_Linux-x86_64-ibverbs.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : WATER
Info: ERROR TOLERANCE : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED 1344668447
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB tip4water.pdb
Info: STRUCTURE FILE tip4water.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS tip4p.par
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES tip4water_NVT300K04.restart.coor
Info: FIRST TIMESTEP 3000000
Info: SUMMARY OF PARAMETERS:
Info: 3 BONDS
Info: 2 ANGLES
Info: 0 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 3 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: CORRECTION OF ZERO MASS ATOMS TURNED OFF BECAUSE LONE PAIRS ARE
USED
ERROR
ERROR
ERROR
ERROR
ERROR
ERROR
ERROR
ERROR
*********(such lines = #waters)
ERROR
ERROR
ERROR
Info: TIME FOR READING PSF FILE: 0.250154
Info: TIME FOR READING PDB FILE: 0.110621
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 37044 ATOMS
Info: 27783 BONDS
Info: 27783 ANGLES
Info: 0 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 37044 RIGID BONDS
Info: 9261 LONE PAIRS
Info: 55566 DEGREES OF FREEDOM
Info: 9261 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 9261 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 166841 amu
Info: TOTAL CHARGE = 0 e
Info: MASS DENSITY = 0.986208 g/cm^3
Info: ATOM DENSITY = 0.131864 atoms/A^3
Info: *****************************
Info: Reading from binary file tip4water_NVT300K04.restart.coor
Info:
Info: Entering startup at 3.51024 s, 216.117 MB of memory in use
Info: Startup phase 0 took 0.000556946 s, 216.117 MB of memory in use
Info: Startup phase 1 took 1.62672 s, 222.383 MB of memory in use
Info: Startup phase 2 took 0.0329819 s, 222.383 MB of memory in use
Info: Startup phase 3 took 0.0331202 s, 222.383 MB of memory in use
Info: PATCH GRID IS 3 (PERIODIC) BY 3 (PERIODIC) BY 3 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.0127847 0.0265591 0.0352821
Info: LARGEST PATCH (26) HAS 1416 ATOMS
Info: Startup phase 4 took 0.0720389 s, 229.797 MB of memory in use
Info: PME using 34 and 34 processors for FFT and reciprocal sum.
Info: PME USING 34 GRID NODES AND 34 TRANS NODES
Info: PME GRID LOCATIONS: 1 3 5 7 9 11 13 14 15 17 ...
Info: PME TRANS LOCATIONS: 1 2 4 6 8 9 10 12 14 16 ...
Info: Startup phase 5 took 2.92284 s, 229.797 MB of memory in use
Info: Startup phase 6 took 0.0430071 s, 229.797 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 0.04299 s, 229.797 MB of memory in use
Info: CREATING 675 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: Startup phase 8 took 0.0330031 s, 229.797 MB of memory in use
Info: useSync: 1 useProxySync: 0
Info: Startup phase 9 took 0.0329669 s, 229.797 MB of memory in use
Info: Startup phase 10 took 5.91278e-05 s, 229.797 MB of memory in use
Info: Finished startup at 8.35052 s, 229.797 MB of memory in use
TCL: Running for 300000 steps
PRESSURE: 3000000 -29420.7 -101.777 365.702 -101.777 -28469.6 48.4779
365.702 48.4779 -29221.1
GPRESSURE: 3000000 -295.332 -20.4379 210.808 72.6646 -103.459 42.3474
235.92 -79.9118 -355.028
GPRESSURE: 3000000 -295.332 -20.4379 210.808 72.6646 -103.459 42.3474
235.92 -79.9118 -355.028
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
POTENTIAL TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 3000000 0.0000 0.0000 0.0000
0.0000 -106994.3422 16084.4163 0.0000 0.0000
16622.6175 -74287.3083 301.0791 -90909.9258
-74251.2494 301.0791 -29037.1214 -251.2730
280926.4366 -29037.1214 -251.2730
OPENING EXTENDED SYSTEM TRAJECTORY FILE
LDB: ============= START OF LOAD BALANCING ============== 8.77631
LDB: ============== END OF LOAD BALANCING =============== 8.79251
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 8.82547
LDB: ============= START OF LOAD BALANCING ============== 9.94909
LDB: Largest compute 53 load 0.374655 is 89.4% of average load 0.418977
LDB: Average compute 0.040239 is 9.6% of average load 0.418977
LDB: Partitioning computes with target load 0.080479
LDB: Partitioning compute 223 with load 0.116683 by 2
LDB: Partitioning compute 225 with load 0.118591 by 2
LDB: Partitioning compute 231 with load 0.126217 by 2
LDB: Partitioning compute 47 with load 0.322070 by 5
LDB: Partitioning compute 40 with load 0.289760 by 4
LDB: Partitioning compute 43 with load 0.304382 by 4
LDB: Partitioning compute 379 with load 0.115287 by 2
LDB: Partitioning compute 381 with load 0.133004 by 2
LDB: Partitioning compute 387 with load 0.117490 by 2
LDB: Partitioning compute 340 with load 0.121420 by 2
LDB: Partitioning compute 342 with load 0.108825 by 2
LDB: Partitioning compute 348 with load 0.129462 by 2
*******************************(continue upto run finished)
Can anyone help me?
Thanks
Uday Sankar Midya
Department of Chemistry
IIT Kharagpur
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:33 CST