Charm++> Running on MPI version: 2.1 multi-thread support: 0 (max supported: -1) Charm++> Running on 2 unique compute nodes (12-way SMP). Charm++> Cpu topology info: PE to node map: 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 Node to PE map: Chip #0: 0 1 2 3 4 5 6 7 8 9 10 11 Chip #1: 12 13 14 15 16 17 18 19 20 21 22 23 Charm++> cpu topology info is gathered in 0.002 seconds. Info: NAMD 2.7b3 for Linux-x86_64-MPI Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@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 60200 for mpi-linux-x86_64-ifort-mpicxx Info: Built Fri Aug 20 16:50:00 BST 2010 by sjr20 on planck01 Info: 1 NAMD 2.7b3 Linux-x86_64-MPI 24 west-2-2 pc104 Info: Running on 24 processors. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.00470996 s Info: 459.324 MB of memory in use based on /proc/self/stat Info: Configuration file is dcdanalysis2.conf TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE nachr_popcwi_ae032.restart.xsc Warning: Setting outputEnergies to 1 due to Warning: pairInteraction calculations Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 20000000 Info: STEPS PER CYCLE 1 Info: PERIODIC CELL BASIS 1 115.701 0 0 Info: PERIODIC CELL BASIS 2 0 118.12 0 Info: PERIODIC CELL BASIS 3 0 0 239.229 Info: PERIODIC CELL CENTER 0.0337309 0.0193593 7.8075 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 -- ASB Info: LDB PERIOD 200 steps Info: FIRST LDB TIMESTEP 5 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: REMOVING LOAD FROM NODE 0 Info: MAX SELF PARTITIONS 20 Info: MAX PAIR PARTITIONS 8 Info: SELF PARTITION ATOMS 154 Info: SELF2 PARTITION ATOMS 154 Info: PAIR PARTITION ATOMS 318 Info: PAIR2 PARTITION ATOMS 637 Info: MIN ATOMS PER PATCH 100 Info: VELOCITY FILE nachr_popcwi_ae032.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 dcdanalysis2.dcd Info: DCD FREQUENCY 25 Info: DCD FIRST STEP 20000025 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME dcdanalysis2.xst Info: XST FREQUENCY 500 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME dcdanalysis2 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME dcdanalysis2.restart Info: RESTART FREQUENCY 500 Info: BINARY RESTART FILES WILL BE USED Info: CUTOFF 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 0.96 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.96 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 10 Info: PRESSURE OUTPUT STEPS 500 Info: PAIR INTERACTION CALCULATIONS ACTIVE Info: USING FLAG 1 FOR GROUP 1 Info: COMPUTING ONLY SELF INTERACTIONS FOR GROUP 1 ATOMS Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 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 310 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS 2.08154e-05 2.08154e-05 -1.12011e-05 Info: CELL FLUCTUATION IS ANISOTROPIC Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE Info: PRESSURE PROFILE CALCULATIONS ACTIVE Info: NUMBER OF SLABS: 1 Info: SLAB THICKNESS: 239.229 Info: TIMESTEPS BETWEEN DATA OUTPUT: 25 Info: NUMBER OF ATOM TYPES: 1 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 120 120 240 Info: PME MAXIMUM GRID SPACING 1 Info: Attempting to read FFTW data from FFTW_NAMD_2.7b3_Linux-x86_64-MPI.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.7b3_Linux-x86_64-MPI.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 1 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 1373642035 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB nachr_popcwi.pdb Info: STRUCTURE FILE nachr_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 nachr_popcwi_ae032.restart.coor Info: FIRST TIMESTEP 20000000 Info: SUMMARY OF PARAMETERS: Info: 185 BONDS Info: 467 ANGLES Info: 601 DIHEDRAL Info: 47 IMPROPER Info: 6 CROSSTERM Info: 121 VDW Info: 2 VDW_PAIRS Info: LONG-RANGE LJ: APPLYING ANALYTICAL CORRECTIONS TO ENERGY AND PRESSURE Info: LONG-RANGE LJ: AVERAGE A AND B COEFFICIENTS 1.61586e+07 AND 11941.7 Info: TIME FOR READING PSF FILE: 3.63906 Info: TIME FOR READING PDB FILE: 0.489826 Info: Info: Reading from binary file nachr_popcwi_ae032.restart.coor Info: To read alch data from file: selexample.pdb Info: To read alch flag data from column: 5 Info: **************************** Info: STRUCTURE SUMMARY: Info: 334777 ATOMS Info: 249850 BONDS Info: 236727 ANGLES Info: 216001 DIHEDRALS Info: 5637 IMPROPERS Info: 1823 CROSSTERMS Info: 0 EXCLUSIONS Info: 299616 RIGID BONDS Info: PAIR INTERACTION GROUP 1 CONTAINS 13 ATOMS Info: 704715 DEGREES OF FREEDOM Info: 119648 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 119648 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 2.03547e+06 amu Info: TOTAL CHARGE = 6.83554e-05 e Info: MASS DENSITY = 1.03383 g/cm^3 Info: ATOM DENSITY = 0.102396 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 4.70284 s, 589.734 MB of memory in use Info: Startup phase 0 took 0.00488997 s, 589.734 MB of memory in use Info: Startup phase 1 took 0.761579 s, 594.848 MB of memory in use Info: Startup phase 2 took 0.002244 s, 594.848 MB of memory in use Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 14 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: Reading from binary file nachr_popcwi_ae032.restart.vel Info: REMOVING COM VELOCITY 0.00766634 -0.0257313 -0.0168146 Info: LARGEST PATCH (215) HAS 741 ATOMS Info: Startup phase 3 took 0.131365 s, 664.359 MB of memory in use Info: PME using 24 and 24 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 4 took 0.00201607 s, 664.359 MB of memory in use Info: Startup phase 5 took 0.0330179 s, 666.645 MB of memory in use LDB: Measuring processor speeds ...Namd Central LB beign created... Done. Info: Startup phase 6 took 1.20415 s, 666.645 MB of memory in use Info: CREATING 18849 COMPUTE OBJECTS Info: useSync: 1 useProxySync: 0 Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.26218e-29 AT 11.9974 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.34106e-29 AT 11.9974 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 5.29396e-23 AT 11.9974 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 9.34714e-23 AT 11.9974 Info: Startup phase 7 took 0.0048039 s, 666.645 MB of memory in use Info: Startup phase 8 took 0.000195026 s, 666.645 MB of memory in use Info: Finished startup at 6.8471 s, 666.645 MB of memory in use dcdplugin) detected standard 32-bit DCD file of native endianness dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later) Info: Coordinate file nachr_popcwi_pi01.dcd opened for reading. Info: Reading timestep from file. Info: Updating unit cell from timestep. Info: Reading from binary file nachr_popcwi_ae032.restart.vel Info: REMOVING COM VELOCITY 0.00766634 -0.0257313 -0.0168146 TCL: Setting parameter firstTimestep to 25 TCL: Running for 0 steps [5] Stack Traceback: [5:0] _ZN9Sequencer14submitHalfstepEi+0x571 [0x981591] [5:1] _ZN9Sequencer9integrateEv+0x548 [0x97a978] [5:2] _ZN9Sequencer9threadRunEPS_+0x328 [0x987968] [5:3] CthStartThread+0x26 [0xa043f6] [5:4] setJcontext+0x81 [0xa03ee1] [5:5] swapJcontext+0x3e [0xa03e3e] [6] Charm++ Runtime: Resumed thread (CthResume+0xe0 [0xa04240]) [4] Stack Traceback: [4:0] _ZN9Sequencer14submitHalfstepEi+0x571 [0x981591] [4:1] _ZN9Sequencer9integrateEv+0x548 [0x97a978] [4:2] _ZN9Sequencer9threadRunEPS_+0x328 [0x987968] [4:3] CthStartThread+0x26 [0xa043f6] [4:4] setJcontext+0x81 [0xa03ee1] [4:5] swapJcontext+0x3e [0xa03e3e] [6] Charm++ Runtime: Resumed thread (CthResume+0xe0 [0xa04240]) WARNING: there are no tuned data files appropriate for your configuration: device = shm:dapl, np = 24, ppn = 12