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