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

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Mon Feb 22 2010 - 10:26:46 CST

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
>> .......
>>
>>
>>
>>
>>
>>
>

-- 
________________________________________________________________________
George Madalin Giambasu                        PhD Student
University of Minnesota                        Phone : (612) 625-6317
Department of Chemistry                        Fax   : (612) 626-7541
207 Pleasant St. SE                            e-mail:
Minneapolis, MN USA 55455-0431                 GeorgeMGiambasu_at_umn.edu
York Research Group                            giambasu_at_gmail.com
http://theory.chem.umn.edu/~giambasu
________________________________________________________________________

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