Charm++: standalone mode (not using charmrun) Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21 CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (8-way SMP). Charm++> cpu topology info is gathered in 0.006 seconds. Info: NAMD CVS-2012-05-31 for Linux-x86_64-multicore-CUDA 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 60400 for multicore-linux64-iccstatic Info: Built Thu May 31 02:24:52 CDT 2012 by jim on lisboa.ks.uiuc.edu Info: 1 NAMD CVS-2012-05-31 Linux-x86_64-multicore-CUDA 4 localhost.localdomain Ian Info: Running on 4 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.011677 s Pe 3 physical rank 3 will use CUDA device of pe 2 Pe 2 physical rank 2 binding to CUDA device 0 on localhost.localdomain: 'GeForce GTX 680' Mem: 2047MB Rev: 3.0 Pe 1 physical rank 1 will use CUDA device of pe 2 Did not find +devices i,j,k,... argument, using all Pe 0 physical rank 0 will use CUDA device of pe 2 ComputeMsmMgr: (constructor) PE 2 ComputeMsmMgr: (constructor) PE 0 ComputeMsmMgr: (constructor) PE 3 ComputeMsmMgr: (constructor) PE 1 Info: 7.48438 MB of memory in use based on /proc/self/stat Info: Configuration file is 3EML_ADN_popcwimineq-02.conf Info: Working in the current directory /home/Ian/Escritorio/3EML_ADN_2_28 TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE 3EML_ADN_2_popcwimineq-01.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 251000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 87 0 0 Info: PERIODIC CELL BASIS 2 0 87 0 Info: PERIODIC CELL BASIS 3 0 0 98 Info: PERIODIC CELL CENTER -3.7614 -2.75091 -3.48826 Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. 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: VELOCITY FILE 3EML_ADN_2_popcwimineq-01.restart.vel Info: CENTER OF MASS MOVING INITIALLY? NO 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 3EML_ADN_2_popcwimineq-02.dcd Info: DCD FREQUENCY 1000 Info: DCD FIRST STEP 252000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME 3EML_ADN_2_popcwimineq-02.xst Info: XST FREQUENCY 1000 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME 3EML_ADN_2_popcwimineq-02 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME 3EML_ADN_2_popcwimineq-02.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 13.5 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 3 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 19 Info: ENERGY OUTPUT STEPS 50 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 500 Info: PRESSURE OUTPUT STEPS 50 Info: HARMONIC CONSTRAINTS ACTIVE Info: HARMONIC CONS EXP 2 Info: TCL GLOBAL FORCES ACTIVE Info: TCL GLOBAL FORCES SCRIPT keep_water_out.tcl Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 300 Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE Info: TARGET PRESSURE IS 1.01325 BAR Info: OSCILLATION PERIOD IS 200 FS Info: DECAY TIME IS 50 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 ANISOTROPIC 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 243 243 243 Info: PME MAXIMUM GRID SPACING 1 Info: Attempting to read FFTW data from FFTW_NAMD_CVS-2012-05-31_Linux-x86_64-multicore-CUDA.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_CVS-2012-05-31_Linux-x86_64-multicore-CUDA.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 1339180755 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB 3EML_ADN_2_popcwi.pdb Info: STRUCTURE FILE 3EML_ADN_2_popcwi.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_lipidNBFIX.prm Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES 3EML_ADN_2_popcwimineq-01.restart.coor Info: FIRST TIMESTEP 251000 Info: SUMMARY OF PARAMETERS: Info: 201 BONDS Info: 498 ANGLES Info: 668 DIHEDRAL Info: 60 IMPROPER Info: 6 CROSSTERM Info: 133 VDW Info: 2 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 0.788977 Info: TIME FOR READING PDB FILE: 0.0863829 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 66590 ATOMS Info: 53368 BONDS Info: 65041 ANGLES Info: 72985 DIHEDRALS Info: 1137 IMPROPERS Info: 306 CROSSTERMS Info: 0 EXCLUSIONS Info: 4885 CONSTRAINTS Info: 55333 RIGID BONDS Info: 144437 DEGREES OF FREEDOM Info: 24278 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 24278 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 399655 amu Info: TOTAL CHARGE = 2.47099e-05 e Info: MASS DENSITY = 0.894706 g/cm^3 Info: ATOM DENSITY = 0.0897727 atoms/A^3 Info: ***************************** Info: Reading from binary file 3EML_ADN_2_popcwimineq-01.restart.coor Info: Info: Entering startup at 1.01835 s, 41.7266 MB of memory in use Info: Startup phase 0 took 9.89437e-05 s, 41.7461 MB of memory in use Info: Startup phase 1 took 0.0561671 s, 49.4805 MB of memory in use Info: Startup phase 2 took 0.000447035 s, 51.0352 MB of memory in use Info: Startup phase 3 took 4.88758e-05 s, 51.0547 MB of memory in use Info: PATCH GRID IS 4 (PERIODIC) BY 4 (PERIODIC) BY 5 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: Reading from binary file 3EML_ADN_2_popcwimineq-01.restart.vel Info: REMOVING COM VELOCITY 1.01612e-07 3.73206e-09 -1.82795e-07 Info: LARGEST PATCH (29) HAS 945 ATOMS Info: Startup phase 4 took 0.0126472 s, 60.0664 MB of memory in use Info: PME using 4 and 4 processors for FFT and reciprocal sum. Info: PME USING 1 GRID NODES AND 1 TRANS NODES 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: Startup phase 5 took 0.0108969 s, 115.641 MB of memory in use Info: Startup phase 6 took 0.00863194 s, 115.781 MB of memory in use LDB: Central LB being created... Info: Startup phase 7 took 0.00191402 s, 116.559 MB of memory in use Info: CREATING 1716 COMPUTE OBJECTS Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556 Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946