Job 199392 started at Tue Mar 19 21:09:58 EST 2013
Scratch directory /scratch/avoca/199392 has been allocated
1 Blue Gene/Q compute nodes have been allocated
Converse/Charm++ Commit ID: v6.3.0-723-g6148ae1
[0] isomalloc.c> Disabling isomalloc because isomalloc disabled by conv-mach
Info: NAMD 2.9 for BlueGeneQ
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60305 for pami-bluegeneq-xlc
Info: Built Tue Mar 5 12:47:30 EST 2013 by bobdanani on avoca-m
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information unavailable.
Info: Charm++/Converse parallel runtime startup completed at 0.00442912 s
Info: 127.875 MB of memory in use based on /proc/self/stat
Info: Configuration file is compress.namd
Info: Working in the current directory /vlsci/VR0224/sridhar/Multi_Pores/Big_pores/Compress
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        10000
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  403 0 0
Info: PERIODIC CELL BASIS 2  0 400 0
Info: PERIODIC CELL BASIS 3  0 0 100
Info: PERIODIC CELL CENTER   0 0 0
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCER  Centralized
Info: LOAD BALANCING STRATEGY  New Load Balancers -- DEFAULT
Info: LDB PERIOD             4000 steps
Info: FIRST LDB TIMESTEP     100
Info: LAST LDB TIMESTEP     -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MIN ATOMS PER PATCH    40
Info: INITIAL TEMPERATURE    0
Info: CENTER OF MASS MOVING INITIALLY? YES
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME           ionize_min.dcd
Info: DCD FREQUENCY          1000
Info: DCD FIRST STEP         1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           ionize_min.xst
Info: XST FREQUENCY          1000
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        ionize_min
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       ionize_min.restart
Info: RESTART FREQUENCY      1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      14
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
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16.5
Info: ENERGY OUTPUT STEPS    1000
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    1000
Info: PRESSURE OUTPUT STEPS  1000
Info: FIXED ATOMS ACTIVE
Info: CONJUGATE GRADIENT MINIMIZATION ACTIVE
Info: LINE MINIMIZATION GOAL = 0.001
Info: BABY STEP SIZE = 0.01
Info: TINY STEP SIZE = 1e-06
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         432 400 108
Info: PME MAXIMUM GRID SPACING    1
Info: Attempting to read FFTW data from FFTW_NAMD_2.9_BlueGeneQ.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.9_BlueGeneQ.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     1363687801
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         ionize.pdb
Info: STRUCTURE FILE         ionize.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             ../gra_ion_water.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 3 BONDS
Info: 1 ANGLES
Info: 0 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 6 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 107.099
FATAL ERROR: Memory allocation failed on processor 0.
------------- Processor 0 Exiting: Called CmiAbort ------------
{snd:0,rcv:0} Reason: FATAL ERROR: Memory allocation failed on processor 0.

namd2: machine.c:774: CmiAbort: Assertion `0' failed.
2013-03-19 21:28:09.911 (WARN ) [0xfff9e978bb0] 522847:ibm.runjob.client.Job: terminated by signal 6
2013-03-19 21:28:09.911 (WARN ) [0xfff9e978bb0] 522847:ibm.runjob.client.Job: abnormal termination by signal 6 from rank 0