Tutorial-l Mailing List

From: Anna Dejardin (anna.dejardin_at_ucl.ac.uk)
Date: Mon Jun 15 2009 - 06:55:07 CDT

Hi Chris,

I'm not sure if this is what you're asking me, but attempting to run
produced a log file (see below).
I'm not familiar with the debug flags, how do you use debug? I'm very
new to Namd and was just trying to run the tutorial simulations, so was
using the configuration files provided by Namd.
Let me know if I've misunderstood you.

Anna

Log File:

Info: NAMD 2.6 for Linux-amd64-MPI
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 50900 for mpi-linux-amd64
Info: Built Wed May 27 12:38:12 BST 2009 by atg on reinette.lcn.ucl.ac.uk
Info: 1 NAMD 2.6 Linux-amd64-MPI 1 reinette.lcn.ucl.ac.uk acd
Info: Running on 1 processors.
Info: 8096 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Changed directory to /homes/acd/NAMD2.6/namd-tutorial-files/1-2-sphere
Info: Configuration file is ubq_ws_eq.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
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: 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: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME ubq_ws_eq.dcd
Info: DCD FREQUENCY 250
Info: DCD FIRST STEP 250
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME ubq_ws_eq
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME ubq_ws_eq.restart
Info: RESTART FREQUENCY 500
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
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE
Info: RADIUS #1 26
Info: FORCE CONSTANT #1 10
Info: EXPONENT #1 2
Info: SPHERE BOUNDARY CENTER(30.3082, 28.805, 15.354)
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
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 : 1e-08
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1245054415
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ../common/ubq_ws.pdb
Info: STRUCTURE FILE ../common/ubq_ws.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ../common/par_all27_prot_lipid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 180 BONDS
Info: 447 ANGLES
Info: 566 DIHEDRAL
Info: 46 IMPROPER
Info: 6 CROSSTERM
Info: 119 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 6682 ATOMS
Info: 4871 BONDS
Info: 4074 ANGLES
Info: 3293 DIHEDRALS
Info: 204 IMPROPERS
Info: 74 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 6080 RIGID BONDS
Info: 13966 DEGREES OF FREEDOM
Info: 2419 HYDROGEN GROUPS
Info: TOTAL MASS = 41298.8 amu
Info: TOTAL CHARGE = 1.00955e-06 e
Info: *****************************
Info: Entering startup phase 0 with 8096 kB of memory in use.
Info: Entering startup phase 1 with 8096 kB of memory in use.
Info: Entering startup phase 2 with 8096 kB of memory in use.
Info: Entering startup phase 3 with 8096 kB of memory in use.
Info: PATCH GRID IS 3 BY 3 BY 3
Info: REMOVING COM VELOCITY 0.0863496 -0.00480725 -0.0432049
Info: LARGEST PATCH (13) HAS 449 ATOMS
Info: CREATING 443 COMPUTE OBJECTS
Info: Entering startup phase 4 with 8096 kB of memory in use.
Info: Entering startup phase 5 with 8096 kB of memory in use.
Info: Entering startup phase 6 with 8096 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 8096 kB of memory in use.
Info: CREATING 443 COMPUTE OBJECTS
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 11.8295
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 5.45773e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 8.47033e-22 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.6856e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-32 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-14 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-32 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-25 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-26 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-16 AT 11.9138
Info: Entering startup phase 8 with 8712 kB of memory in use.

Chris Harrison wrote:
> Anna,
>
> Did this produce a coredump file and did you configure with
> "--with-debug" or using whatever debug flags are appropriate for the
> pg compiler?
>
>
> Chris
>
>
> --
> Chris Harrison, Ph.D.
> Theoretical and Computational Biophysics Group
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> char_at_ks.uiuc.edu <mailto:char_at_ks.uiuc.edu>
> Voice: 217-244-1733
> http://www.ks.uiuc.edu/~char <http://www.ks.uiuc.edu/%7Echar>
> Fax: 217-244-6078
>
>
>
> On Mon, Jun 15, 2009 at 3:49 AM, Anna Dejardin
> <anna.dejardin_at_ucl.ac.uk <mailto:anna.dejardin_at_ucl.ac.uk>> wrote:
>
> Hi Peter,
>
> Thanks for your advice. I'm still having problems unfortunately.
> We've tried recompiling with TCL 8.4 support. My compiler is
> Portland Group 7.2-5 and my operating system is Redhat Enterprise
> Linux 5. I'm still getting error messages when I try to run the
> tutorial programs. Example:
>
> Error: in routine alloca() there is a
> stack overflow: thread 0, max 10228KB, used 4KB, request -18888208B
>
> We are a bit stumped. Any ideas?
>
> Thanks so much
>
> Anna
>
>
> Peter Freddolino wrote:
>
> Hi Anna,
> it looks like your namd binary wasn't built with tcl support.
> While you
> can get namd to work this way, many features will be disabled,
> and the
> syntax in the tutorials assumes a fully functional build. I'd
> recommend
> either rebuilding with tcl support or using one of the precompiled
> binaries available on the namd website.
> Best,
> Peter
>
> Anna Dejardin wrote:
>
>
> Hi Peter,
>
> Here is the logfile:
>
> Charm++> Running on MPI version: 1.2 multi-thread support: 1/0
> Charm warning> Randomization of stack pointer is turned on
> in Kernel,
> run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root
> to disable
> it. Thread migration may not work!
> Info: NAMD 2.6 for Linux-amd64-MPI
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
> <mailto: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 60000 for
> mpi-linux-amd64-pgf90-mpicxx
> Info: Built Tue May 5 12:36:23 BST 2009 by atg on
> reinette.lcn.ucl.ac.uk <http://reinette.lcn.ucl.ac.uk>
> Info: 1 NAMD 2.6 Linux-amd64-MPI 1
> reinette.lcn.ucl.ac.uk <http://reinette.lcn.ucl.ac.uk> acd
> Info: Running on 1 processors.
> Info: 1592 kB of memory in use.
> Info: Memory usage based on mallinfo
> Info: Changed directory to
> /homes/acd/NAMD2.6/namd-tutorial-files/1-2-sphere
> Info: Configuration file is ubq_ws_eq.conf
> ERROR: Expecting value and optional units for option
> 'temperature'
> ERROR: Expecting value and optional units for option
> 'langevinTemp'
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: run
> ERROR: reinitvels
> ERROR: minimize
> ERROR: set
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> p0_14453: p4_error: : 1
>
> Thanks
>
> Anna
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