namd 2.7b2 or later - amberff/prmtop causes segfault during startup phase

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Sun Feb 21 2010 - 18:01:43 CST

Hi Everybody,

has anyone tried to run namd 2.7b2 or later with amber force field (in
amber prmtop format) lately?

For a large variety of systems (solvated/unsolvated,
periodic/non-periodic) and machines I keep getting a segementation fault
during the startup phase. See bellow.

Versions 2.6 or 2.7b1 do not cause this problem.

Thanks in advance for any tip,

George

-------------------------------------------------
output from 2.7b2:
-------------------------------------------------

Charm++: standalone mode (not using charmrun)
Charm++> cpu topology info is being gathered.
Charm++> Running on 1 unique compute nodes (2-way SMP).
Info: NAMD CVS for Linux-x86_64
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 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 60103 for net-linux-x86_64-iccstatic
Info: Built Sat Feb 20 02:12:33 CST 2010 by jim on lisboa.ks.uiuc.edu
Info: 1 NAMD CVS Linux-x86_64
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0106549 s
Info: 1.49818 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is namd_0.inp
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 200
Info: STEPS PER CYCLE 10
Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
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: MAX SELF PARTITIONS 20
Info: MAX PAIR PARTITIONS 8
Info: SELF PARTITION ATOMS 154
Info: SELF2 PARTITION ATOMS 154
Info: PAIR PARTITION ATOMS 318
Info: PAIR2 PARTITION ATOMS 637
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 0.833333
Info: DCD FILENAME fep.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME fep
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME fep.restart
Info: RESTART FREQUENCY 5000
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF 99
Info: PAIRLIST DISTANCE 99
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 101.5
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 50
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 200
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
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 : ALL
Info: ERROR TOLERANCE : 0.0005
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1266795610
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE test.parm7
Info: AMBER COORDINATE FILE test.crd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (test.parm7) ...
PARM file in AMBER 7 format
Info: SUMMARY OF PARAMETERS:
Info: 20 BONDS
Info: 36 ANGLES
Info: 28 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 55 VDW_PAIRS
Info: TIME FOR READING PDB FILE: 1.09673e-05
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 32 ATOMS
Info: 34 BONDS
Info: 58 ANGLES
Info: 120 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 168 EXCLUSIONS
Info: 13 RIGID BONDS
Info: 83 DEGREES OF FREEDOM
Info: 19 HYDROGEN GROUPS
Info: 3 ATOMS IN LARGEST HYDROGEN GROUP
Info: 19 MIGRATION GROUPS
Info: 3 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 267.254 amu
Info: TOTAL CHARGE = 7.45058e-08 e
Info: *****************************
Info:
Info: Entering startup at 0.0290091 s, 1.63704 MB of memory in use
Info: Startup phase 0 took 0.000170946 s, 1.63713 MB of memory in use
Segmentation fault

-------------------------------------------------
output from 2.7b1:
-------------------------------------------------

Charm++: standalone mode (not using charmrun)
Charm++> cpu topology info is being gathered!
Charm++> 1 unique compute nodes detected!
Info: NAMD 2.7b1 for Linux-x86_64
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 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 60100 for net-linux-x86_64-iccstatic
Info: Built Mon Mar 23 02:40:42 CDT 2009 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.7b1 Linux-x86_64 1
Info: Running on 1 processors.
Info: Charm++/Converse parallel runtime startup completed at 0.00889206 s
Info: 1.50023 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is namd_0.inp
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 200
Info: STEPS PER CYCLE 10
Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
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: MAX SELF PARTITIONS 20
Info: MAX PAIR PARTITIONS 8
Info: SELF PARTITION ATOMS 154
Info: SELF2 PARTITION ATOMS 154
Info: PAIR PARTITION ATOMS 318
Info: PAIR2 PARTITION ATOMS 637
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 0
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 0.833333
Info: DCD FILENAME fep.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME fep
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME fep.restart
Info: RESTART FREQUENCY 5000
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF 99
Info: PAIRLIST DISTANCE 99
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 101.5
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 50
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 200
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
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 : ALL
Info: ERROR TOLERANCE : 0.0005
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1266796666
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE test.parm7
Info: AMBER COORDINATE FILE test.crd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (test.parm7) ...
PARM file in AMBER 7 format
Info: SUMMARY OF PARAMETERS:
Info: 20 BONDS
Info: 36 ANGLES
Info: 28 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 55 VDW_PAIRS
Info: TIME FOR READING PDB FILE: 9.05991e-06
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 32 ATOMS
Info: 34 BONDS
Info: 58 ANGLES
Info: 120 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 168 EXCLUSIONS
Info: 13 RIGID BONDS
Info: 83 DEGREES OF FREEDOM
Info: 19 HYDROGEN GROUPS
Info: TOTAL MASS = 267.254 amu
Info: TOTAL CHARGE = 7.45058e-08 e
Info: *****************************
Info:
Info: Entering startup at 0.0206242 s, 1.6342 MB of memory in use
Info: Startup phase 0 took 9.29832e-05 s, 1.63429 MB of memory in use
Info: Startup phase 1 took 0.000417948 s, 1.64842 MB of memory in use
Info: Startup phase 2 took 9.29832e-05 s, 1.65178 MB of memory in use
Info: PATCH GRID IS 1 BY 1 BY 1
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0 0 0
Info: LARGEST PATCH (0) HAS 32 ATOMS
Info: CREATING 11 COMPUTE OBJECTS
Info: Startup phase 3 took 0.00030899 s, 1.68639 MB of memory in use
Info: Startup phase 4 took 5.50747e-05 s, 1.68626 MB of memory in use
Info: Startup phase 5 took 5.88894e-05 s, 1.68614 MB of memory in use
LDB: Measuring processor speeds ... Done.
Info: Startup phase 6 took 0.00012207 s, 1.68755 MB of memory in use
Info: CREATING 11 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 1153 POINTS
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.83671e-40 AT 98.6303
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.70398e-42 AT 98.6303
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 4.68386e-30 AT 98.6303
Info: Startup phase 7 took 0.00640392 s, 2.28033 MB of memory in use
Info: Startup phase 8 took 0.000113964 s, 2.53265 MB of memory in use
Info: Finished startup at 0.028291 s, 2.53265 MB of memory in use

ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP POTENTIAL
   TOTAL3 TEMPAVG

ENERGY: 0 2.1010 34.4807 19.7000
0.0000 -52.5241 21.0530 0.0000
0.0000 0.0000 24.8106 0.0000
24.8106
  24.9936 0.0000

ENERGY: 1 1.9859 33.5135 19.6919
0.0000 -52.5778 20.0761 0.0000
0.0000 2.1910 24.8805 26.5673
22.6896
  25.1843 26.5673
.......

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