Re: namd2.5 on myrinet cluster

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Sat Apr 03 2004 - 20:40:12 CST

Hi Florian,

 I have checked in a minor changes to charm-5.8 into cvs. Could you please
try it out (check out 5.8 again and build it from *scratch*)?

Gengbin

On Sun, 4 Apr 2004, Florian Barth wrote:

> Hello,
>
> I tried to install charm++ (5.8 from cvs) and namd2.5 from source code
> to run it on a athlon cluster with myrinet interconnect (gm version
> 1.6.4). Therefore, I compiled a mpi-linux-gm version of charm++ (queens
> test is ok) and then built namd2.5 using this charm++ version plus fftw,
> tcl and plugins. When trying to run a test job, namd starts to write a
> regular output file, but stops prior to the md stuff (output below). I
> don't get any error message and the same job runs fine using namd2.5b1
> over mpich-gm on the cluster. Other jobs using 'native' namd inputs
> (pdb,psf) instead of amber fail as well. It always stops after 'finished
> startup'. Does anyone have any idea how to get namd running using
> myrinet mpich-gm?
>
> Thanks
>
> Florian Barth
>
>
>
>
> Info: NAMD 2.5 for Linux-i686
> 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 Kale et al., J. Comp. Phys. 151:283-312 (1999)
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 0143160 for mpi-linux-gm
> Info: Built Fri Apr 2 05:30:45 CEST 2004 by flb on cortex1.biowulf.itb
> Info: Sending usage information to NAMD developers via UDP. Sent data is:
> Info: 1 NAMD 2.5 Linux-i686 4 neuron070.biowulf.itb flb
> Info: Running on 4 processors.
> Info: 22130 kB of memory in use.
> Measuring processor speeds... Done.
> Info: Configuration file is a2y_namd.in
> TCL: Suspending until startup complete.
> Warning: The parameter fullElectFrequency now defaults to nonbondedFreq
> (1) rather than stepsPerCycle.
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 1
> Info: NUMBER OF STEPS 2000
> Info: STEPS PER CYCLE 5
> Info: PERIODIC CELL BASIS 1 70 0 0
> Info: PERIODIC CELL BASIS 2 0 60.5 0
> Info: PERIODIC CELL BASIS 3 0 0 54.5
> Info: PERIODIC CELL CENTER 0 0 0
> Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
> Info: LOAD BALANCE STRATEGY Other
> Info: LDB PERIOD 1000 steps
> Info: FIRST LDB TIMESTEP 25
> 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: INITIAL TEMPERATURE 300
> Info: CENTER OF MASS MOVING? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 SCALE FACTOR 0.83333
> Info: DCD FILENAME /home/flb/test/a2y_namd.dcd
> Info: DCD FREQUENCY 20
> Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
> Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
> Info: NO VELOCITY DCD OUTPUT
> Info: OUTPUT FILENAME /home/flb/test/a2y_namd
> Info: RESTART FILENAME /home/flb/test/a2y_namd.restart
> Info: RESTART FREQUENCY 1000
> Info: BINARY RESTART FILES WILL BE USED
> Info: CUTOFF 8
> Info: PAIRLIST DISTANCE 8
> 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 0.315
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 10.815
> Info: ENERGY OUTPUT STEPS 20
> Info: TIMING OUTPUT STEPS 20
> Info: LANGEVIN DYNAMICS ACTIVE
> Info: LANGEVIN TEMPERATURE 300
> Info: LANGEVIN DAMPING COEFFICIENT IS 10 INVERSE PS
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
> Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
> Info: TARGET PRESSURE IS 1 BAR
> Info: OSCILLATION PERIOD IS 100 FS
> Info: DECAY TIME IS 100 FS
> Info: PISTON TEMPERATURE IS 300 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 0 0 0
> Info: CELL FLUCTUATION IS ISOTROPIC
> Info: PARTICLE MESH EWALD (PME) ACTIVE
> Info: PME TOLERANCE 1e-06
> Info: PME EWALD COEFFICIENT 0.39467
> Info: PME INTERPOLATION ORDER 4
> Info: PME GRID DIMENSIONS 72 64 54
> Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
> Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
> Info: Writing FFTW data to FFTW_NAMD_2.5_Linux-i686.txt
> Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1
> 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 1234
> Info: USE HYDROGEN BONDS? NO
> Info: Using AMBER format force field!
> Info: AMBER PARM FILE prmtop
> Info: AMBER COORDINATE FILE md12.x
> Info: Exclusions will be read from PARM file!
> Info: SCNB (VDW SCALING) 2
> Reading parm file (prmtop) ...
> Warning: Encounter 10-12 H-bond term
> Warning: Found 6810 H-H bonds.
> Info: SUMMARY OF PARAMETERS:
> Info: 45 BONDS
> Info: 91 ANGLES
> Info: 33 DIHEDRAL
> Info: 0 IMPROPER
> Info: 0 VDW
> Info: 153 VDW_PAIRS
> Info: ****************************
> Info: STRUCTURE SUMMARY:
> Info: 22930 ATOMS
> Info: 22953 BONDS
> Info: 4561 ANGLES
> Info: 8166 DIHEDRALS
> Info: 0 IMPROPERS
> Info: 34070 EXCLUSIONS
> Info: 21651 RIGID BONDS
> Info: 47139 DEGREES OF FREEDOM
> Info: 8089 HYDROGEN GROUPS
> Info: TOTAL MASS = 140931 amu
> Info: TOTAL CHARGE = -4.99701e-06 e
> Info: *****************************
> Info: Entering startup phase 0 with 27081 kB of memory in use.
> Info: Entering startup phase 1 with 27081 kB of memory in use.
> Info: Entering startup phase 2 with 28382 kB of memory in use.
> Info: Entering startup phase 3 with 28561 kB of memory in use.
> Info: PATCH GRID IS 6 (PERIODIC) BY 5 (PERIODIC) BY 5 (PERIODIC)
> Info: REMOVING COM VELOCITY 0.0272437 -0.0936849 -0.0288729
> Info: LARGEST PATCH (121) HAS 181 ATOMS
> Info: Entering startup phase 4 with 31773 kB of memory in use.
> Info: PME using 4 and 4 processors for FFT and reciprocal sum.
> Creating Strategy 4
> Creating Strategy 4
> Info: PME GRID LOCATIONS: 0 1 2 3
> Info: PME TRANS LOCATIONS: 0 1 2 3
> Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
> Info: Entering startup phase 5 with 32285 kB of memory in use.
> Info: Entering startup phase 6 with 30291 kB of memory in use.
> Info: Entering startup phase 7 with 30338 kB of memory in use.
> Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
> Info: COULOMB TABLE SIZE: 641 POINTS
> Info: NONZERO IMPRECISION IN COULOMB TABLE: 0 (0) 6.88214e-22 (639)
> Info: Entering startup phase 8 with 31666 kB of memory in use.
> Info: Finished startup with 37559 kB of memory in use.
>

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