From: Cheri M Turman (Cheri.M.Turman_at_uth.tmc.edu)
Date: Mon Oct 18 2004 - 16:23:42 CDT
Hi,
I am having some issues running SA on a gigabit beowulf cluster. I got
this error and bug report. My minimization for 8000 steps ran fine but
during the heating process, the problems started. I have found some
people have written questions here about the ERROR: Margin is too small
for 1 atoms during timestep 52258. ERROR: Incorrect nonbonded forces
and energies may be calculated! However, I could not find any answers
to these questions about this error. Did any ever figure this out?
My next error was:
WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 54000
WRITING COORDINATES TO DCD FILE AT STEP 54000
WRITING COORDINATES TO RESTART FILE AT STEP 54000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 54000
FINISHED WRITING RESTART VELOCITIES
LDB: LOAD: AVG 8.70782 MAX 10.2825 MSGS: TOTAL 387 MAXC 41 MAXP 5 None
LDB: LOAD: AVG 8.70782 MAX 8.88166 MSGS: TOTAL 387 MAXC 41 MAXP 5 Refine
ERROR: Stray PME grid charges detected: 7 sending to 8 for planes 56
ERROR: Stray PME grid charges detected: 7 sending to 8 for planes 56
BUG ALERT: Stray PME grid charges detected!
BUG ALERT: NAMD has detected a bug. Please notify namd_at_ks.uiuc.edu.
Stack Traceback:
[0] _ZN10Controller16compareChecksumsEii+0x685 [0x81a649d]
[1] _ZN10Controller21printDynamicsEnergiesEi+0x89 [0x81af4a5]
[2] _ZN10Controller9integrateEv+0x10c [0x81a916c]
[3] _ZN10Controller9algorithmEv+0x718 [0x81a4680]
[4] _ZN10Controller9threadRunEPS_+0xc [0x81b0d64]
[5] /apps/namd/./namd2 [0x82758a4]
[6] Charm++ Runtime: Converse thread (qt_args+0x66 [0x82c40aa])
Any ideas about this one? Do they both point to problems with running
on multiple computers/passing off jobs? I olny think this because I
have been having problems with these issues and have been playing with
my PBS batch scripts. Please let me know if you have any clue about
this. Following is the beginning of my logfile to let you know the
parameters used.
/tmp/pbs.6281.Trinity/6281.Trinity.nodelist
12 nodes
Info: NAMD 2.5 for Linux-i686
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 050612 for net-linux-icc
Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: 1 NAMD 2.5 Linux-i686 12 Morpheus10 cmturman
Info: Running on 12 processors.
Info: 1477 kB of memory in use.
Measuring processor speeds... Done.
Info: Changed directory to /home/cmturman/NAMD
Info: Configuration file is Simulated_annealing_2DV1_92704
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 78.94 0 0
Info: PERIODIC CELL BASIS 2 0 78.393 0
Info: PERIODIC CELL BASIS 3 0 0 75.347
Info: PERIODIC CELL CENTER 5.54633 32.9508 19.3833
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: INITIAL TEMPERATURE 310
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME
/home/cmturman/NAMD/2DV1_supcom/2DV1_annealing_92704.dcd
Info: DCD FREQUENCY 1000
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: XST FILENAME
/home/cmturman/NAMD/2DV1_supcom/2DV1_annealing_92704.xst
Info: XST FREQUENCY 1000
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME
/home/cmturman/NAMD/2DV1_supcom/2DV1_annealing_92704
Info: RESTART FILENAME
/home/cmturman/NAMD/2DV1_supcom/2DV1_92704_restart
Info: RESTART FREQUENCY 2000
Info: RESTART FILES WILL NOT BE OVERWRITTEN
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8.5
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 10
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
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 12.5
Info: ENERGY OUTPUT STEPS 1000
Info: VELOCITY REASSIGNMENT FREQ 500
Info: VELOCITY REASSIGNMENT TEMP 300
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.312341
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 82 80 80
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.5_Linux-i686.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
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: RANDOM NUMBER SEED 1098114157
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB /home/cmturman/NAMD/output/2DV1_wb.pdb
Info: STRUCTURE FILE /home/cmturman/NAMD/output/2DV1_wb.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS /home/cmturman/NAMD/par_all22_prot_2.inp
Info: SUMMARY OF PARAMETERS:
Info: 139 BONDS
Info: 343 ANGLES
Info: 443 DIHEDRAL
Info: 43 IMPROPER
Info: 60 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 42793 ATOMS
Info: 31257 BONDS
Info: 26076 ANGLES
Info: 21240 DIHEDRALS
Info: 1347 IMPROPERS
Info: 0 EXCLUSIONS
Info: 34935 RIGID BONDS
Info: 93441 DEGREES OF FREEDOM
Info: 15570 HYDROGEN GROUPS
Info: TOTAL MASS = 265405 amu
Info: TOTAL CHARGE = 4.00001 e
Info: *****************************
Info: Entering startup phase 0 with 9282 kB of memory in use.
Info: Entering startup phase 1 with 9282 kB of memory in use.
Info: Entering startup phase 2 with 13578 kB of memory in use.
Info: Entering startup phase 3 with 13914 kB of memory in use.
Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 6 (PERIODIC)
Info: REMOVING COM VELOCITY 0.0360994 -0.0131584 0.0112262
Info: LARGEST PATCH (58) HAS 269 ATOMS
Info: Entering startup phase 4 with 20028 kB of memory in use.
Info: PME using 12 and 12 processors for FFT and reciprocal sum.
Creating Strategy 4
Creating Strategy 4
Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ...
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Entering startup phase 5 with 20408 kB of memory in use.
Info: Entering startup phase 6 with 15335 kB of memory in use.
Info: Entering startup phase 7 with 15335 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 705 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 4.23516e-22 (675)
8.47033e-22 (675)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 5.04871e-29 (699)
1.26218e-28 (699)
Info: NONZERO IMPRECISION IN COULOMB TABLE: 1.05879e-22 (698)
2.64698e-22 (698)
Info: Entering startup phase 8 with 16015 kB of memory in use.
Info: Finished startup with 18523 kB of memory in use.
TCL: Minimizing for 8000 steps
Thanks,
Cheri
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cheri M. Turman
Graduate Student
University of Texas-Houston Medical School
6431 Fannin
Houston, TX 77030 USA
e-mail: cheri.m.turman_at_uth.tmc.edu
Ph.: 713-500-6126
Fax: 713-500-0652
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