From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Wed Jul 11 2007 - 11:28:31 CDT
I'm trying to get NAMD to run in parallel on a dual processor machine in
SMP mode. In many cases, everything is fine, but for certain systems I
get the following error:
FATAL ERROR: Tried to find atom type on node other than node 0
I found one instance of this on the NAMD mailing list, but no solution
was given. Does anyone know what this really means and how to fix it?
I am running NAMD via: charmrun /usr/local/NAMD/x64/namd2 ++verbose
++local +p2 fep.conf > test.log &
Output from the logfile follows:
Charmrun> adding client 0: "127.0.0.1", IP:127.0.0.1
Charmrun> adding client 1: "127.0.0.1", IP:127.0.0.1
Charmrun> Charmrun = 127.0.0.1, port = 33134
Charmrun> start 0 node program on localhost.
Charmrun> start 1 node program on localhost.
Charmrun> Waiting for 0-th client to connect.
Charmrun> client 0 connected (IP=127.0.0.1 data_port=54590)
Charmrun> Waiting for 1-th client to connect.
Charmrun> client 1 connected (IP=127.0.0.1 data_port=54591)
Charmrun> All clients connected.
Charmrun> IP tables sent.
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 2 potoff1.eng.wayne.edu jpotoff
Info: Running on 2 processors.
Info: 7604 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is fep.conf
TCL: Running FEP window 1: Lambda1 0 Lambda2 0.001 [dLambda 0.001 ]
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE emo_equil.restart.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 65.3174 0 0
Info: PERIODIC CELL BASIS 2 0 65.3174 0
Info: PERIODIC CELL BASIS 3 0 0 65.3174
Info: PERIODIC CELL CENTER 31.5 31.5 31.5
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
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: 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 emo_equil.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 emo_fep.dcd
Info: DCD FREQUENCY 2500
Info: DCD FIRST STEP 2500
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME emo_fep.xst
Info: XST FREQUENCY 2500
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME emo_fep
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME emo_fep.restart
Info: RESTART FREQUENCY 5000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 12
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 2.5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 17
Info: ENERGY OUTPUT STEPS 1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 10000
Info: PRESSURE OUTPUT STEPS 1000
Info: ALCHEMICAL FEP ON
Info: CURRENT LAMBDA VALUE 0
Info: COMPARISON LAMBDA VALUE 0.001
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS -9.97537e-05 -9.97537e-05 -9.97537e-05
Info: CELL FLUCTUATION IS ISOTROPIC
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.312341
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 64 64 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 2
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 1184171048
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB setup.pdb
Info: STRUCTURE FILE emofep.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_potoff.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES emo_equil.restart.coor
Info: SUMMARY OF PARAMETERS:
Info: 10 BONDS
Info: 8 ANGLES
Info: 8 DIHEDRAL
Info: 1 IMPROPER
Info: 0 CROSSTERM
Info: 8 VDW
Info: 0 VDW_PAIRS
Warning: Ignored 342 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
Warning: Ignored 342 angles with zero force constants.
Warning: Missing angles for 342 waters.
Warning: Obtained H-H distance from bond parameters for 342 waters.
Info: To read fep data from file: emo.fep
Info: To read fep flag data from column: 5
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 11031 ATOMS
Info: 9688 BONDS
Info: 8001 ANGLES
Info: 7000 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 6 EXCLUSIONS
Info: 2027 RIGID BONDS
Info: 2 ATOMS TO DISAPPEAR IN FINAL STATE
Info: 3 ATOMS TO APPEAR IN FINAL STATE
Info: 31066 DEGREES OF FREEDOM
Info: 9346 HYDROGEN GROUPS
Info: TOTAL MASS = 119307 amu
Info: TOTAL CHARGE = 0 e
Info: *****************************
Info: Entering startup phase 0 with 8136 kB of memory in use.
Info: Entering startup phase 1 with 8136 kB of memory in use.
FATAL ERROR: Tried to find atom type on node other than node 0
Stack Traceback:
[0] CmiAbort+0x33 [0x7f17f5]
[1] _Z8NAMD_diePKc+0x62 [0x4b2f62]
[2] _ZN8Molecule17build_atom_statusEv+0x1386 [0x696b3a]
[3] _ZN8Molecule16receive_MoleculeEP8MIStream+0xa81 [0x6a0f3d]
[4] _ZN4Node11namdOneRecvEv+0x45c [0x6b1d1e]
[5] _ZN4Node7startupEv+0x657 [0x6b1595]
[6] _ZN12CkIndex_Node18_call_startup_voidEPvP4Node+0x12 [0x6b0f3a]
[7] CkDeliverMessageFree+0x21 [0x7867eb]
[8] _Z15_processHandlerPvP11CkCoreState+0x455 [0x785df5]
[9] CsdScheduleForever+0xa2 [0x7f2492]
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu ======================================================================
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