namd-gpu +p8 +idlepoll +devices 0 conf/11-run-wat.conf | grep -v '^LDB\|WRITING COORDINATES\|The last' | tee out/11-run-wat/@log/00001.log Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 8 threads Charm++> Using recursive bisection (scheme 3) for topology aware partitions Charm++ warning> fences and atomic operations not available in native assembly Converse/Charm++ Commit ID: v6.7.0-0-g46f867c-namd-charm-6.7.0-build-2015-Dec-21-45876 [0] isomalloc.c> Disabling isomalloc because mmap() does not work 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 0.000 seconds. Info: Built with CUDA version 6050 Pe 7 physical rank 7 will use CUDA device of pe 4 Pe 2 physical rank 2 will use CUDA device of pe 4 Pe 3 physical rank 3 will use CUDA device of pe 4 Pe 6 physical rank 6 will use CUDA device of pe 4 Pe 1 physical rank 1 will use CUDA device of pe 4 Pe 5 physical rank 5 will use CUDA device of pe 4 Pe 0 physical rank 0 will use CUDA device of pe 4 Pe 4 physical rank 4 binding to CUDA device 0 on L12-IGOR: 'GeForce GTX 960' Mem: 2048MB Rev: 5.2 Info: NAMD 2.11 for Win64-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 60700 for multicore-win64 Info: Built Mon, Dec 21, 2015 10:32:11 AM by jim on europa Info: Running on 8 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.188 s Info: 28.668 MB of memory in use based on GetProcessMemoryInfo Info: Configuration file is conf/11-run-wat.conf Info: Changed directory to conf TCL: INPUTNAME: 'out/10-min-wat/00001' TCL: OUTPUTNAME: 'out/11-run-wat/00001' TCL: Restarting from out/10-min-wat/00001 TCL: running for 500000 TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE out/10-min-wat/00001.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 80.6578 0 0 Info: PERIODIC CELL BASIS 2 0 76.7707 0 Info: PERIODIC CELL BASIS 3 0 0 101.065 Info: PERIODIC CELL CENTER -19.5918 -9.75912 22.2998 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 out/10-min-wat/00001.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 out/11-run-wat/00001.dcd Info: DCD FREQUENCY 25000 Info: DCD FIRST STEP 25000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME out/11-run-wat/00001.xst Info: XST FREQUENCY 25000 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME out/11-run-wat/00001 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME out/11-run-wat/00001.restart Info: RESTART FREQUENCY 50000 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 0.495 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.995 Info: ENERGY OUTPUT STEPS 25000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 250000 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 300 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS Info: LANGEVIN DYNAMICS NOT 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 100 FS Info: PISTON TEMPERATURE IS 300 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS 3.60586e-006 3.60586e-006 3.60586e-006 Info: CELL FLUCTUATION IS ISOTROPIC Info: PARTICLE MESH EWALD (PME) ACTIVE Info: PME TOLERANCE 1e-006 Info: PME EWALD COEFFICIENT 0.257952 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 84 80 108 Info: PME MAXIMUM GRID SPACING 1 Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2 Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C2 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: RIGID BONDS TO HYDROGEN : ALL Info: ERROR TOLERANCE : 1e-005 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1458149380 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB struct/water.pdb Info: STRUCTURE FILE struct/water.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS FF/par_all22_prot.prm Info: PARAMETERS FF/par_all36_lipid.prm Info: PARAMETERS FF/par_all27_water.prm Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES out/10-min-wat/00001.restart.coor Info: SUMMARY OF PARAMETERS: Info: 175 BONDS Info: 455 ANGLES Info: 621 DIHEDRAL Info: 38 IMPROPER Info: 6 CROSSTERM Info: 89 VDW Info: 4 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 0.375 Info: TIME FOR READING PDB FILE: 0.11 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 63719 ATOMS Info: 45361 BONDS Info: 33776 ANGLES Info: 22452 DIHEDRALS Info: 1536 IMPROPERS Info: 533 CROSSTERMS Info: 0 EXCLUSIONS Info: 59494 RIGID BONDS Info: 131663 DEGREES OF FREEDOM Info: 22645 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 22645 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 391764 amu Info: TOTAL CHARGE = -4.99999 e Info: MASS DENSITY = 1.03954 g/cm^3 Info: ATOM DENSITY = 0.101818 atoms/A^3 Info: ***************************** Info: Reading from binary file out/10-min-wat/00001.restart.coor Info: Info: Entering startup at 0.688 s, 51.8945 MB of memory in use Info: Startup phase 0 took 0 s, 51.8945 MB of memory in use Info: ADDED 101348 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.0150001 s, 65.0117 MB of memory in use Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 1.05879e-022 AT 11.8295 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.56642e-014 AT 11.9138 Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.00179416 AT 12.039 Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.05879e-022 AT 11.8295 Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 2.90665e-016 AT 11.8295 Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.00154963 AT 11.8717 Info: INCONSISTENCY IN SLOW TABLE ENERGY VS FORCE: 0.000328258 AT 8.9687 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-032 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-014 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-032 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-015 AT 11.9138 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-025 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-015 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-026 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-016 AT 11.9138 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Updated CUDA LJ table with 89 x 89 elements. Info: Updated CUDA force table with 4096 elements. Info: Startup phase 2 took 0.172 s, 116.797 MB of memory in use Info: Startup phase 3 took 0 s, 118.262 MB of memory in use Info: Startup phase 4 took 0.016 s, 120.867 MB of memory in use Info: Startup phase 5 took 0 s, 120.867 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 out/10-min-wat/00001.restart.vel Info: REMOVING COM VELOCITY -0.00236361 0.00649183 -0.000624647 Info: LARGEST PATCH (5) HAS 838 ATOMS Info: TORUS A SIZE 8 USING 0 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0 s, 130.891 MB of memory in use Info: PME using 8 and 8 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 Info: PME USING 1 GRID NODES AND 1 TRANS NODES Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 7 took 0 s, 136.848 MB of memory in use Info: Startup phase 8 took 0 s, 136.848 MB of memory in use Info: Startup phase 9 took 0 s, 136.852 MB of memory in use Info: CREATING 1736 COMPUTE OBJECTS CUDA device 0 stream priority range 0 -1 Info: Found 329 unique exclusion lists needing 1052 bytes Pe 4 hosts 0 local and 10 remote patches for pe 4 Pe 6 hosts 0 local and 10 remote patches for pe 4 Pe 3 hosts 0 local and 10 remote patches for pe 4 Pe 0 hosts 0 local and 10 remote patches for pe 4 Pe 5 hosts 0 local and 10 remote patches for pe 4 Pe 2 hosts 0 local and 10 remote patches for pe 4 Pe 7 hosts 0 local and 10 remote patches for pe 4 Pe 1 hosts 0 local and 10 remote patches for pe 4 Info: useSync: 0 useProxySync: 0 Info: Startup phase 10 took 0.0150001 s, 141.844 MB of memory in use Info: Startup phase 11 took 0 s, 141.844 MB of memory in use Info: Startup phase 12 took 0 s, 153.219 MB of memory in use Info: Finished startup at 0.906 s, 153.219 MB of memory in use TCL: Running