Re: Differences between 32bit and 64bit version of NAMD?

From: Carsten Olbrich (ocarsten_at_googlemail.com)
Date: Mon Jun 18 2007 - 13:34:45 CDT

Thanks,

I will check this...

There is just one "problem" with the TCP version: For my system (about
80000 atoms) the TCP version is a quarter day/ns slower than the UDP
version and is as fast as the 32bit version of NAMD.

With "built on top of a different compilation of charm++" do you mean
a mpi-compilation or something else?

Carsten

On 6/18/07, Victor Ovchinnikov <ovchinnv_at_mit.edu> wrote:
> Hi,
>
> I've had problems using TCL forces on an 8-node 64-bit Opteron cluster
> using the non-TCP binary; when I switched to the TCP binary, the
> calculations ran fine. Maybe another binary (i.e. built on top of a
> different compilation of charm++) would work for you?
>
> Victor
>
> On Mon, 2007-06-18 at 18:04 +0200, Carsten Olbrich wrote:
> > Dear users,
> >
> > I use the binaries from NAMD download side and apply tclfoces to my molecule.
> > When I'm using the 32bit binary on our cluster (quad core Intel Xeon
> > processors) the job runs fine.
> > But if I'm using the 64bit binary after some while (200000-1000000
> > steps) I get an error.
> > One time the error are "Atoms moving too fast", another time "Stray
> > PME grid charges detected!" or "Bad global exclusion count"....
> > The same things happen if I compile the binary myself.
> > Is there a way to work around or any idea for a reason?
> >
> > Thanks for your help...
> > Carsten
> >
> > A sample output:
> > Info: NAMD 2.6 for Linux-amd64
> > 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 net-linux-amd64-iccstatic
> > Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu
> > Info: 1 NAMD 2.6 Linux-amd64 24 node23 colbrich
> > Info: Running on 24 processors.
> > Info: 7612 kB of memory in use.
> > Info: Memory usage based on mallinfo
> > Info: Configuration file is Conf_pull_dna.conf
> > TCL: Suspending until startup complete.
> > Info: EXTENDED SYSTEM FILE out_eq_xy_dna.restart.xsc
> > Info: SIMULATION PARAMETERS:
> > Info: TIMESTEP 1
> > Info: NUMBER OF STEPS 0
> > Info: STEPS PER CYCLE 20
> > Info: PERIODIC CELL BASIS 1 68.2539 0 0
> > Info: PERIODIC CELL BASIS 2 0 165.76 0
> > Info: PERIODIC CELL BASIS 3 0 0 48.7528
> > Info: PERIODIC CELL CENTER 0 0 10
> > Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
> > Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
> > Info: LOAD BALANCE STRATEGY Other
> > Info: LDB PERIOD 4000 steps
> > Info: FIRST LDB TIMESTEP 100
> > Info: LDB BACKGROUND SCALING 1
> > Info: HOM BACKGROUND SCALING 1
> > Info: PME 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: VELOCITY FILE out_eq_xy_dna.restart.vel
> > Info: CENTER OF MASS MOVING INITIALLY? NO
> > Info: DIELECTRIC 1
> > Info: EXCLUDE SCALED ONE-FOUR
> > Info: 1-4 SCALE FACTOR 1
> > Info: DCD FILENAME out_pull_dna.dcd
> > Info: DCD FREQUENCY 5000
> > Info: DCD FIRST STEP 5000
> > Info: DCD FILE WILL CONTAIN UNIT CELL DATA
> > Info: XST FILENAME out_pull_dna.xst
> > Info: XST FREQUENCY 10000
> > Info: NO VELOCITY DCD OUTPUT
> > Info: OUTPUT FILENAME out_pull_dna
> > Info: BINARY OUTPUT FILES WILL BE USED
> > Info: RESTART FILENAME out_pull_dna.restart
> > Info: RESTART FREQUENCY 10000
> > 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 5
> > Info: HYDROGEN GROUP CUTOFF 2.5
> > Info: PATCH DIMENSION 21
> > Info: ENERGY OUTPUT STEPS 5000
> > Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> > Info: TIMING OUTPUT STEPS 10000
> > Info: PRESSURE OUTPUT STEPS 5000
> > Info: TCL GLOBAL FORCES ACTIVE
> > Info: TCL GLOBAL FORCES SCRIPT Force_pull_dna.tcl
> > Info: LANGEVIN DYNAMICS ACTIVE
> > Info: LANGEVIN TEMPERATURE 310
> > Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
> > Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> > Info: PARTICLE MESH EWALD (PME) ACTIVE
> > Info: PME TOLERANCE 1e-06
> > Info: PME EWALD COEFFICIENT 0.257952
> > Info: PME INTERPOLATION ORDER 4
> > Info: PME GRID DIMENSIONS 81 180 64
> > Info: PME MAXIMUM GRID SPACING 1.5
> > Info: Attempting to read FFTW data from FFTW_NAMD_2.6_Linux-amd64.txt
> > Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
> > Info: Writing FFTW data to FFTW_NAMD_2.6_Linux-amd64.txt
> > Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4
> > Info: USING VERLET I (r-RESPA) MTS SCHEME.
> > Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
> > Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
> > Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
> > Info: RANDOM NUMBER SEED 1182151013
> > Info: USE HYDROGEN BONDS? NO
> > Info: COORDINATE PDB dna_xy.pdb
> > Info: STRUCTURE FILE dna_xy.psf
> > Info: PARAMETER file: CHARMM format!
> > Info: PARAMETERS par_all27_prot_lipid_na.inp
> > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> > Info: BINARY COORDINATES out_eq_xy_dna.restart.coor
> >
> > Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
> > PREVIOUS VALUES k=130 theta0=107.5 k_ub=0 r_ub=0
> > USING VALUES k=130 theta0=107 k_ub=0 r_ub=0
> > Info: SUMMARY OF PARAMETERS:
> > Info: 299 BONDS
> > Info: 729 ANGLES
> > Info: 1145 DIHEDRAL
> > Info: 84 IMPROPER
> > Info: 0 CROSSTERM
> > Info: 161 VDW
> > Info: 0 VDW_PAIRS
> > Info: ****************************
> > Info: STRUCTURE SUMMARY:
> > Info: 55933 ATOMS
> > Info: 37689 BONDS
> > Info: 18164 ANGLES
> > Info: 0 DIHEDRALS
> > Info: 0 IMPROPERS
> > Info: 0 CROSSTERMS
> > Info: 0 EXCLUSIONS
> > Info: 167799 DEGREES OF FREEDOM
> > Info: 19143 HYDROGEN GROUPS
> > Info: TOTAL MASS = 344144 amu
> > Info: TOTAL CHARGE = 2.8424e-06 e
> > Info: *****************************
> > Info: Entering startup phase 0 with 21864 kB of memory in use.
> > Info: Entering startup phase 1 with 21864 kB of memory in use.
> > Info: Entering startup phase 2 with 30292 kB of memory in use.
> > Info: Entering startup phase 3 with 30292 kB of memory in use.
> > Info: PATCH GRID IS 3 (PERIODIC) BY 7 (PERIODIC) BY 2 (PERIODIC)
> > Info: REMOVING COM VELOCITY -0.0263814 0.0100015 0.00261442
> > Info: LARGEST PATCH (31) HAS 1460 ATOMS
> > Info: CREATING 9644 COMPUTE OBJECTS
> > Info: Entering startup phase 4 with 38448 kB of memory in use.
> > Info: PME using 21 and 23 processors for FFT and reciprocal sum.
> > Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
> > Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
> > Info: Entering startup phase 5 with 38448 kB of memory in use.
> > Info: Entering startup phase 6 with 38448 kB of memory in use.
> > Measuring processor speeds... Done.
> > Info: Entering startup phase 7 with 38448 kB of memory in use.
> > Info: CREATING 9644 COMPUTE OBJECTS
> > Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
> > Info: NONBONDED TABLE SIZE: 769 POINTS
> > Info: Entering startup phase 8 with 40012 kB of memory in use.
> > Info: Finished startup with 40012 kB of memory in use.
> > TCL: Running for 10000000 steps
>
>

-- 
With best regards / Mit freundlichen Grüßen
                               Carsten Olbrich
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Carsten Olbrich
Jacobs University Bremen *
Phone:  (+49) 421 200 3222
Fax:       (+49) 421 200 3229
Campus Ring 1  (Room III.49b)
28759 Bremen
Germany
 *  formerly International University Bremen
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