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

From: Vlad Cojocaru (Vlad.Cojocaru_at_h-its.org)
Date: Mon Feb 22 2010 - 10:30:25 CST

HI George,

I assume that you correctly specified the scaling parameters to be used
with the amber ff.

If you did that, I really cannot explain your error. Did you try the
newest CVS code of NAMD ?

Vlad

George Madalin Giambasu wrote:
> Hi Vlad,
>
>
> Yes, I see the error coming when using amber prmtop files. For the
> sake of comparison, I run the "jac1000" benchmark (it comes with namd
> 2.6) both using the xplor psf and the amber prmtop with namd2.7b2 and
> the latest cvs version.
>
> The xplor version runs OK, whereas the amber prmtop gives the segfault
> in both cases.
>
> Apart from that, I have few DNA and RNA systems (solvated and
> unsolvated) that cause the same error.
>
>
> G
>
>
> Vlad Cojocaru wrote:
>> Hi George,
>>
>> I am running namd2.7b2 (the CVS code from September 2009) with the
>> amber force field and I don't see any problem.
>>
>> What makes you think its the amber force field the cause of the
>> problem ? Does the same simulation run with another force field ?
>>
>> Vlad
>>
>> George Madalin Giambasu wrote:
>>> 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
>>> .......
>>>
>>>
>>>
>>>
>>>
>>>
>>
>

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
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