From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Jun 15 2009 - 07:12:15 CDT

Hi Anna,
is there any particular reason that you're not using one of the
precompiled binaries? You may need to build your own to get optimal
performance on a cluster eventually, but for the purposes of the
tutorial you may wish to first become familiar with namd using a
known-good version.

As far as the problem that you're encountering, have you run the tests
that come with charm++ to make sure that you're charm build is working?
You may also want to try building with gcc or icc; we haven't generally
had great experience with the portland group compilers for building NAMD.

Best,
Peter

Anna Dejardin wrote:
> 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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