From: Florian Barth (bio_hazard_at_gmx.de)
Date: Sat Apr 03 2004 - 17:59:39 CST
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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