From: Alberto Santana (asantana_at_uprm.edu)
Date: Sun Jul 04 2004 - 13:25:32 CDT
Thanks for the reply. That was part of the problem, I rsh to a different node and got the same message. I took a look at the nodelist file and removed the master node from it, and the message is now gone, the master node has no Myrinet port.
If I run a job it starts but then aborts, this is all I get
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.5 for Linux-i686-GM
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 050612 for net-linux-gm-icc
Info: Built Sat Jul 3 14:37:44 EDT 2004 by santana on master
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: 1 NAMD 2.5 Linux-i686-GM 4 node2 santana
Info: Running on 4 processors.
Info: 2326 kB of memory in use.
Measuring processor speeds... Done.
Info: Changed directory to ./src
Info: Configuration file is alanin
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 0.5
Info: NUMBER OF STEPS 9
Info: STEPS PER CYCLE 3
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 600 steps
Info: FIRST LDB TIMESTEP 15
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: INITIAL TEMPERATURE 0
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 0.4
Info: NO DCD TRAJECTORY OUTPUT
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME output
Info: BINARY OUTPUT FILES WILL BE USED
Info: NO RESTART FILE
Info: SWITCHING ACTIVE
Info: SWITCHING ON 7
Info: SWITCHING OFF 8
Info: PAIRLIST DISTANCE 9
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 1
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 12.5
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 1088948586
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB alanin.pdb
Info: STRUCTURE FILE alanin.psf
Info: PARAMETER file: XPLOR format! (default)
Info: PARAMETERS alanin.params
Info: SUMMARY OF PARAMETERS:
Info: 61 BONDS
Info: 179 ANGLES
Info: 38 DIHEDRAL
Info: 42 IMPROPER
Info: 21 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 66 ATOMS
Info: 65 BONDS
Info: 96 ANGLES
Info: 31 DIHEDRALS
Info: 32 IMPROPERS
Info: 0 EXCLUSIONS
Info: 195 DEGREES OF FREEDOM
Info: 55 HYDROGEN GROUPS
Info: TOTAL MASS = 783.886 amu
Info: TOTAL CHARGE = 8.19564e-08 e
Info: *****************************
[0] Assertion "CkMyPe()!=0" failed in file init.C line 389.
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason:
req_handle_abort called
Fatal error on PE 0>
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