Charm++> scheduler running in netpoll mode. Charm++> Running on 1 unique compute nodes (8-way SMP). Charm++> cpu topology info is gathered in 0.012 seconds. Info: NAMD 2.8 for Linux-x86_64-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 60303 for net-linux-x86_64-iccstatic Info: Built Sat May 28 11:30:15 CDT 2011 by jim on larissa.ks.uiuc.edu Info: 1 NAMD 2.8 Linux-x86_64-CUDA 8 bob deburg0 Info: Running on 8 processors, 8 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0175109 s Pe 4 sharing CUDA device 0 first 0 next 6 Pe 7 sharing CUDA device 1 first 1 next 1 Pe 4 physical rank 4 binding to CUDA device 0 on bob: 'Tesla C2050' Mem: 2687MB Rev: 2.0 Pe 0 sharing CUDA device 0 first 0 next 2 Pe 5 sharing CUDA device 1 first 1 next 7 Pe 7 physical rank 7 binding to CUDA device 1 on bob: 'Quadro 4000' Mem: 2047MB Rev: 2.0 Pe 5 physical rank 5 binding to CUDA device 1 on bob: 'Quadro 4000' Mem: 2047MB Rev: 2.0 Pe 0 physical rank 0 binding to CUDA device 0 on bob: 'Tesla C2050' Mem: 2687MB Rev: 2.0 Pe 3 sharing CUDA device 1 first 1 next 5 Pe 2 sharing CUDA device 0 first 0 next 4 Pe 2 physical rank 2 binding to CUDA device 0 on bob: 'Tesla C2050' Mem: 2687MB Rev: 2.0 Pe 3 physical rank 3 binding to CUDA device 1 on bob: 'Quadro 4000' Mem: 2047MB Rev: 2.0 Pe 6 sharing CUDA device 0 first 0 next 0 Pe 6 physical rank 6 binding to CUDA device 0 on bob: 'Tesla C2050' Mem: 2687MB Rev: 2.0 Pe 1 sharing CUDA device 1 first 1 next 3 Pe 1 physical rank 1 binding to CUDA device 1 on bob: 'Quadro 4000' Mem: 2047MB Rev: 2.0 Info: 1.63689 MB of memory in use based on CmiMemoryUsage Info: Configuration file is kcsa_T85A_popcwieq-09.conf Info: Working in the current directory /scratch/deburg0/kcsa_T85A/03-MINEQ TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE kcsa_T85A-popcwieq-08.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 6753000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 69.8064 0 0 Info: PERIODIC CELL BASIS 2 0 68.5168 0 Info: PERIODIC CELL BASIS 3 0 0 95.7835 Info: PERIODIC CELL CENTER 0.285712 0.299353 6.22171 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 kcsa_T85A-popcwieq-08.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 kcsa_T85A-popcwieq-09.dcd Info: DCD FREQUENCY 1000 Info: DCD FIRST STEP 6754000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME kcsa_T85A-popcwieq-09.xst Info: XST FREQUENCY 1000 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME kcsa_T85A-popcwieq-09 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME kcsa_T85A-popcwieq-09.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 0.96 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.96 Info: ENERGY OUTPUT STEPS 1000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 10000 Info: PRESSURE OUTPUT STEPS 1000 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 -0.000114122 -2.0068e-05 -5.86465e-05 Info: CELL FLUCTUATION IS ANISOTROPIC Info: CONSTANT AREA PRESSURE CONTROL ACTIVE 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 100 100 90 Info: PME MAXIMUM GRID SPACING 1.5 Info: Attempting to read FFTW data from FFTW_NAMD_2.8_Linux-x86_64-CUDA.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.8_Linux-x86_64-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 1310496122 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ../02-MEMBRANE/kcsa_T85A_popcwi.pdb Info: STRUCTURE FILE ../02-MEMBRANE/kcsa_T85A_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 kcsa_T85A-popcwieq-08.restart.coor Info: FIRST TIMESTEP 6753000 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: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 1.10855 Info: TIME FOR READING PDB FILE: 0.127645 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 47264 ATOMS Info: 38348 BONDS Info: 47914 ANGLES Info: 55156 DIHEDRALS Info: 1164 IMPROPERS Info: 404 CROSSTERMS Info: 0 EXCLUSIONS Info: 38478 RIGID BONDS Info: 103314 DEGREES OF FREEDOM Info: 17604 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 17604 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 287309 amu Info: TOTAL CHARGE = 1.69501e-05 e Info: MASS DENSITY = 1.04142 g/cm^3 Info: ATOM DENSITY = 0.103169 atoms/A^3 Info: ***************************** Info: Reading from binary file kcsa_T85A-popcwieq-08.restart.coor Info: Info: Entering startup at 2.53031 s, 15.8227 MB of memory in use Info: Startup phase 0 took 0.000545025 s, 15.8193 MB of memory in use Info: Startup phase 1 took 0.388635 s, 26.2325 MB of memory in use Info: Startup phase 2 took 0.00106311 s, 26.6273 MB of memory in use Info: Startup phase 3 took 0.000216961 s, 26.6253 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 kcsa_T85A-popcwieq-08.restart.vel Info: REMOVING COM VELOCITY 0.0743183 -0.00994812 -0.013457 Info: LARGEST PATCH (51) HAS 638 ATOMS Info: Startup phase 4 took 0.021986 s, 32.9997 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: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 5 took 0.00254798 s, 33.984 MB of memory in use Info: Startup phase 6 took 0.0211079 s, 28.5823 MB of memory in use LDB: Central LB being created... Info: Startup phase 7 took 1.2045 s, 28.5318 MB of memory in use Info: CREATING 1664 COMPUTE OBJECTS Info: useSync: 1 useProxySync: 0 Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: Updated CUDA LJ table with 121 x 121 elements. Info: Updated CUDA force table with 4096 elements. Info: Found 292 unique exclusion lists needing 900 bytes Info: Startup phase 8 took 0.044291 s, 30.6604 MB of memory in use Info: Startup phase 9 took 0.000174046 s, 32.0484 MB of memory in use Info: Finished startup at 4.21538 s, 32.0484 MB of memory in use TCL: Running for 2000 steps PRESSURE: 6753000 -187.8 341.595 317.847 341.595 -388.423 -49.9537 317.849 -49.9533 -414.063 GPRESSURE: 6753000 -121.493 492.046 298.221 311.213 -369.073 -18.0881 207.721 100.732 -423.563 ENERGY: 6753000 2919.5378 12317.7411 6567.4183 252.5095 -120877.6582 1259.3367 0.0000 0.0000 31675.1314 -65885.9832 308.5671 -97561.1146 -65660.9956 308.5671 -330.0956 -304.7098 458123.9699 -330.0956 -304.7098 OPENING EXTENDED SYSTEM TRAJECTORY FILE LDB: ============= START OF LOAD BALANCING ============== 5.46196 LDB: ============== END OF LOAD BALANCING =============== 5.46243 LDB: =============== DONE WITH MIGRATION ================ 5.46381 LDB: ============= START OF LOAD BALANCING ============== 9.57352 LDB: Largest compute 1471 load 0.054981 is 1.9% of average load 2.848372 LDB: Average compute 0.010964 is 0.4% of average load 2.848372 LDB: Partitioning computes with target load 0.284837 LDB: Increased migratable compute count from 480 to 480 LDB: Largest unpartitionable compute is 0.054981 LDB: ============== END OF LOAD BALANCING =============== 9.5761 LDB: =============== DONE WITH MIGRATION ================ 9.57823 Info: Initial time: 8 CPUs 0.0518139 s/step 0.299849 days/ns 41.1353 MB memory LDB: ============= START OF LOAD BALANCING ============== 10.6519 LDB: ============== END OF LOAD BALANCING =============== 10.6523 LDB: =============== DONE WITH MIGRATION ================ 10.6535 LDB: ============= START OF LOAD BALANCING ============== 15.0561 LDB: Largest compute 1461 load 0.060251 is 2.1% of average load 2.879520 LDB: Average compute 0.010998 is 0.4% of average load 2.879520 LDB: TIME 15.057 LOAD: AVG 2.87952 MAX 3.2555 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 None MEM: 41.3436 MB LDB: TIME 15.0574 LOAD: AVG 2.87952 MAX 2.88168 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 TorusLB MEM: 41.3659 MB LDB: ============== END OF LOAD BALANCING =============== 15.0599 LDB: =============== DONE WITH MIGRATION ================ 15.0626 Info: Initial time: 8 CPUs 0.0545258 s/step 0.315543 days/ns 41.035 MB memory LDB: ============= START OF LOAD BALANCING ============== 20.0476 LDB: Largest compute 1443 load 0.073535 is 2.1% of average load 3.544346 LDB: Average compute 0.015490 is 0.4% of average load 3.544346 LDB: TIME 20.0484 LOAD: AVG 3.54435 MAX 3.60593 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 None MEM: 41.2388 MB LDB: TIME 20.0485 LOAD: AVG 3.54435 MAX 3.60593 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 RefineTorusLB MEM: 41.2534 MB LDB: TIME 20.0486 LOAD: AVG 3.54435 MAX 3.60593 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 RefineTorusLB MEM: 41.2534 MB LDB: ============== END OF LOAD BALANCING =============== 20.0498 LDB: =============== DONE WITH MIGRATION ================ 20.0516 Info: Initial time: 8 CPUs 0.0498954 s/step 0.288747 days/ns 41.216 MB memory LDB: ============= START OF LOAD BALANCING ============== 25.0123 LDB: Largest compute 1443 load 0.073493 is 2.1% of average load 3.555661 LDB: Average compute 0.015443 is 0.4% of average load 3.555661 LDB: TIME 25.013 LOAD: AVG 3.55566 MAX 3.64097 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 None MEM: 41.3633 MB LDB: TIME 25.0131 LOAD: AVG 3.55566 MAX 3.64097 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 RefineTorusLB MEM: 41.3779 MB LDB: TIME 25.0132 LOAD: AVG 3.55566 MAX 3.64097 PROXIES: TOTAL 180 MAXPE 24 MAXPATCH 4 RefineTorusLB MEM: 41.3779 MB LDB: ============== END OF LOAD BALANCING =============== 25.0144 LDB: =============== DONE WITH MIGRATION ================ 25.0163 Info: Benchmark time: 8 CPUs 0.0496685 s/step 0.287433 days/ns 41.2329 MB memory Info: Benchmark time: 8 CPUs 0.051312 s/step 0.296944 days/ns 41.313 MB memory Info: Benchmark time: 8 CPUs 0.0514999 s/step 0.298032 days/ns 41.3917 MB memory PRESSURE: 6754000 -395.046 84.5177 -333.777 84.5196 449.77 133.023 -333.777 133.018 -724.056 GPRESSURE: 6754000 -327.934 107.138 -278.254 -2.56576 351.391 54.3451 -363.013 168.42 -576.925 PRESSAVG: 6754000 -47.3271 7.73536 2.36406 7.73514 -32.0019 -16.0307 2.36393 -16.0308 -13.0564 GPRESSAVG: 6754000 -46.9005 7.49962 3.0645 8.39942 -32.8753 -17.7164 3.27911 -16.484 -12.6638 ENERGY: 6754000 2853.4290 12356.3748 6598.3795 275.6338 -121128.9262 1380.7442 0.0000 0.0000 31500.8624 -66163.5026 306.8694 -97664.3650 -65941.5601 308.6976 -223.1106 -184.4893 459119.8216 -30.7951 -30.8132 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6754000 OPENING COORDINATE DCD FILE WRITING COORDINATES TO DCD FILE AT STEP 6754000 WRITING COORDINATES TO RESTART FILE AT STEP 6754000 FINISHED WRITING RESTART COORDINATES The last position output (seq=6754000) takes 0.010 seconds, 45.180 MB of memory in use WRITING VELOCITIES TO RESTART FILE AT STEP 6754000 FINISHED WRITING RESTART VELOCITIES The last velocity output (seq=6754000) takes 0.002 seconds, 45.577 MB of memory in use PRESSURE: 6755000 -288.858 182.655 -321.807 182.654 -141.089 -325.639 -321.809 -325.636 -131.688 GPRESSURE: 6755000 -147.171 32.6015 -186.175 140.015 -168.415 -189.233 -162.926 -284.243 -144.698 PRESSAVG: 6755000 -93.5229 -28.6513 44.9715 -28.6512 -79.2868 -12.4006 44.9716 -12.4005 -0.627039 GPRESSAVG: 6755000 -92.9419 -29.5429 45.1868 -28.4347 -80.0064 -11.7108 44.6296 -12.6884 -0.611143 ENERGY: 6755000 2885.4891 12560.6808 6561.9570 274.0971 -121220.4369 1441.2003 0.0000 0.0000 31739.7387 -65757.2739 309.1965 -97497.0126 -65534.5125 308.3851 -187.2119 -153.4280 457978.6280 -57.8122 -57.8531 WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 6755000 WRITING COORDINATES TO DCD FILE AT STEP 6755000 WRITING COORDINATES TO RESTART FILE AT STEP 6755000 FINISHED WRITING RESTART COORDINATES The last position output (seq=6755000) takes 0.008 seconds, 45.886 MB of memory in use WRITING VELOCITIES TO RESTART FILE AT STEP 6755000 FINISHED WRITING RESTART VELOCITIES The last velocity output (seq=6755000) takes 0.002 seconds, 45.712 MB of memory in use WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 6755000 CLOSING EXTENDED SYSTEM TRAJECTORY FILE WRITING COORDINATES TO OUTPUT FILE AT STEP 6755000 CLOSING COORDINATE DCD FILE The last position output (seq=-2) takes 0.101 seconds, 44.597 MB of memory in use WRITING VELOCITIES TO OUTPUT FILE AT STEP 6755000 The last velocity output (seq=-2) takes 0.002 seconds, 44.438 MB of memory in use ==================================================== WallClock: 106.788857 CPUTime: 105.121017 Memory: 44.439194 MB