TACC: Starting up job 6245019 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 1.611 seconds. Charmrun> scalable start enabled. Charmrun> IBVERBS version of charmrun Converse/Charm++ Commit ID: v6.7.0-0-g46f867c-namd-charm-6.7.0-build-2015-Dec-21-45876 Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'. Charm++> scheduler running in netpoll mode. CharmLB> Load balancer assumes all CPUs are same. Charm++> cpu affinity enabled. Charm++> cpuaffinity PE-core map : 1-15 Charm++> set comm 0 on node 0 to core #0 Charm++> Running on 8 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.013 seconds. Info: NAMD 2.11 for Linux-x86_64-ibverbs-smp-Stampede-memopt Warning: Warning: *** EXPERIMENTAL MEMORY OPTIMIZED VERSION *** Warning: 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 net-linux-x86_64-ibverbs-smp-iccstatic Info: Built Mon Dec 21 10:36:06 CST 2015 by tg455591 on login4.stampede.tacc.utexas.edu Info: 1 NAMD 2.11 Linux-x86_64-ibverbs-smp-Stampede-memopt 120 c406-804.stampede.tacc.utexas.edu tg455591 Info: Running on 120 processors, 8 nodes, 8 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.082221 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1195.6 MB of memory in use based on /proc/self/stat Info: Configuration file is /work/00288/tg455591/stmv/stmv2fs.namd Info: Changed directory to /work/00288/tg455591/stmv TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 1200 Info: STEPS PER CYCLE 24 Info: PERIODIC CELL BASIS 1 216.832 0 0 Info: PERIODIC CELL BASIS 2 0 216.832 0 Info: PERIODIC CELL BASIS 3 0 0 216.832 Info: PERIODIC CELL CENTER 0 0 0 Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4800 steps Info: FIRST LDB TIMESTEP 120 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: PME BACKGROUND SCALING 1 Info: REMOVING PATCHES FROM PROCESSOR 0 Info: MIN ATOMS PER PATCH 40 Info: INITIAL TEMPERATURE 298 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: NO DCD TRAJECTORY OUTPUT Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME /scratch/00288/tg455591/stmv-output Info: BINARY OUTPUT FILES WILL BE USED Info: NO RESTART FILE 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 4 Info: PAIRLISTS ENABLED Info: MARGIN 0.48 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.48 Info: ENERGY OUTPUT STEPS 120 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 120 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 298 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 5 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 100 FS Info: DECAY TIME IS 50 FS Info: PISTON TEMPERATURE IS 298 K Info: PRESSURE CONTROL IS GROUP-BASED Info: INITIAL STRAIN RATE IS 0 0 0 Info: CELL FLUCTUATION IS ISOTROPIC 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 216 216 216 Info: PME MAXIMUM GRID SPACING 1.5 Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 3 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 1450742633 Info: USE HYDROGEN BONDS? NO Info: STRUCTURE FILE stmv.psf.inter Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_na.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES stmv.coor Info: SUMMARY OF PARAMETERS: Info: 250 BONDS Info: 622 ANGLES Info: 1049 DIHEDRAL Info: 73 IMPROPER Info: 0 CROSSTERM Info: 130 VDW Info: 0 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 0.00584579 Info: Info: Entering startup at 0.171322 s, 1293.45 MB of memory in use Info: Startup phase 0 took 0.00237179 s, 1293.45 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.00894618 s, 1293.77 MB of memory in use 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: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 4.59334e-32 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 7.4108e-17 AT 11.9974 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 1.53481e-26 AT 11.9974 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.96691e-18 AT 11.9974 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Running with 2 input processors. Info: Running with 1 output processors (1 of them will output simultaneously). Info: INPUT PROC LOCATIONS: 30 90 Info: OUTPUT PROC LOCATIONS: 60 Info: Startup phase 2 took 0.0389769 s, 1294.74 MB of memory in use Info: Startup phase 3 took 0.098197 s, 1294.74 MB of memory in use Info: PATCH GRID IS 13 (PERIODIC) BY 13 (PERIODIC) BY 13 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: LOADED 1810196 TOTAL EXCLUSIONS Info: REMOVING COM VELOCITY -0.0124328 -3.78475e-05 0.00116403 Info: Startup phase 4 took 0.0375249 s, 1415.18 MB of memory in use Info: **************************** Info: STRUCTURE SUMMARY: Info: 1066628 ATOMS Info: 769956 BONDS Info: 605872 ANGLES Info: 450875 DIHEDRALS Info: 24578 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 977416 RIGID BONDS Info: 2222468 DEGREES OF FREEDOM Info: 389067 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 389067 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 6.69877e+06 amu Info: TOTAL CHARGE = 0.000168104 e Info: MASS DENSITY = 1.09115 g/cm^3 Info: ATOM DENSITY = 0.104627 atoms/A^3 Info: ***************************** Info: LARGEST PATCH (1044) HAS 541 ATOMS Info: Startup phase 5 took 0.055465 s, 1415.18 MB of memory in use Info: TORUS A SIZE 120 USING 0 15 30 45 60 75 90 105 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 106 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0180311 s, 1425.66 MB of memory in use Info: PME using 108 and 108 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ... Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 8 9 10 11 ... Info: PME USING 8 GRID NODES AND 8 TRANS NODES Info: Startup phase 7 took 0.07867 s, 1432.45 MB of memory in use Info: Startup phase 8 took 0.00617194 s, 1432.45 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.0339491 s, 1432.45 MB of memory in use Info: CREATING 44535 COMPUTE OBJECTS Info: Startup phase 10 took 0.056021 s, 1432.45 MB of memory in use Info: Building spanning tree ... send: 1 recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 Info: Startup phase 11 took 0.00516391 s, 1432.45 MB of memory in use Info: Startup phase 12 took 0.000190973 s, 1432.45 MB of memory in use Info: Finished startup at 0.611002 s, 1432.45 MB of memory in use ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 0 37737.0490 105740.7918 81950.2970 4986.4950 -4134759.4115 375583.0490 0.0000 0.0000 659233.5371 -2869528.1925 298.5342 -3528761.7296 -2866969.3681 298.5342 2254.2632 2342.1274 10194598.5131 2254.2632 2342.1274 LDB: ============= START OF LOAD BALANCING ============== 3.50819 LDB: ============== END OF LOAD BALANCING =============== 3.51272 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 3.51452 LDB: ============= START OF LOAD BALANCING ============== 13.9242 LDB: Largest compute 2966 load 0.153541 is 1.6% of average load 9.482901 LDB: Average compute 0.024240 is 0.3% of average load 9.482901 LDB: Partitioning computes with target load 0.948290 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023347 LDB: ============== END OF LOAD BALANCING =============== 13.9482 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 14.0023 Info: Initial time: 120 CPUs 0.108792 s/step 0.629581 days/ns 1458.73 MB memory TIMING: 120 CPU: 10.2964, 0.0830874/step Wall: 13.6814, 0.109498/step, 0.0328494 hours remaining, 1458.730469 MB of memory in use. ENERGY: 120 39238.0372 107657.9099 82121.1849 5042.5548 -4028138.2276 295881.4815 0.0000 0.0000 642238.8384 -2855958.2208 290.8382 -3498197.0593 -2853489.9974 290.2810 -102.1677 -25.4368 10357126.2755 -3.3806 -2.3582 LDB: ============= START OF LOAD BALANCING ============== 16.6267 LDB: ============== END OF LOAD BALANCING =============== 16.6271 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 16.6289 LDB: ============= START OF LOAD BALANCING ============== 28.7733 LDB: Largest compute 3946 load 0.157337 is 1.7% of average load 9.512158 LDB: Average compute 0.024230 is 0.3% of average load 9.512158 LDB: TIME 28.7932 LOAD: AVG 9.51216 MAX 10.7675 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 None MEM: 1464.11 MB LDB: TIME 28.8229 LOAD: AVG 9.51216 MAX 9.77656 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 TorusLB MEM: 1464.11 MB LDB: ============== END OF LOAD BALANCING =============== 28.8869 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 28.9543 Info: Initial time: 120 CPUs 0.123345 s/step 0.713803 days/ns 1463.58 MB memory TIMING: 240 CPU: 22.1156, 0.0984934/step Wall: 28.6664, 0.124875/step, 0.0333001 hours remaining, 1463.578125 MB of memory in use. ENERGY: 240 39087.6752 107345.9705 82010.8962 5088.5800 -4014942.3233 291572.8371 0.0000 0.0000 645523.5520 -2844312.8123 292.3257 -3489836.3643 -2841778.8453 291.5796 -52.8343 20.6098 10349747.9746 1.8578 1.9621 LDB: ============= START OF LOAD BALANCING ============== 43.8719 LDB: Largest compute 3613 load 0.197779 is 1.7% of average load 11.931824 LDB: Average compute 0.030411 is 0.3% of average load 11.931824 LDB: TIME 43.8955 LOAD: AVG 11.9318 MAX 12.5116 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 None MEM: 1533.62 MB LDB: TIME 43.9011 LOAD: AVG 11.9318 MAX 12.5116 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 RefineTorusLB MEM: 1533.62 MB LDB: TIME 43.9092 LOAD: AVG 11.9318 MAX 12.0853 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 RefineTorusLB MEM: 1533.62 MB LDB: ============== END OF LOAD BALANCING =============== 43.9154 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 43.9709 Info: Initial time: 120 CPUs 0.12427 s/step 0.719152 days/ns 1533.62 MB memory TIMING: 360 CPU: 35.6216, 0.11255/step Wall: 43.678, 0.125096/step, 0.0291892 hours remaining, 1533.625000 MB of memory in use. ENERGY: 360 38946.0315 107516.9272 82016.2945 5066.2225 -4006080.4059 289468.4138 0.0000 0.0000 647430.8236 -2835635.6928 293.1894 -3483066.5164 -2833138.3711 292.6135 6.3616 79.4069 10344583.1012 5.2550 5.1530 LDB: ============= START OF LOAD BALANCING ============== 58.8504 LDB: Largest compute 3806 load 0.211510 is 1.8% of average load 11.969055 LDB: Average compute 0.030444 is 0.3% of average load 11.969055 LDB: TIME 58.8683 LOAD: AVG 11.9691 MAX 12.3598 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 None MEM: 1529 MB LDB: TIME 58.8739 LOAD: AVG 11.9691 MAX 12.3598 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 RefineTorusLB MEM: 1529 MB LDB: TIME 58.8781 LOAD: AVG 11.9691 MAX 12.1222 PROXIES: TOTAL 4874 MAXPE 45 MAXPATCH 8 RefineTorusLB MEM: 1529 MB LDB: ============== END OF LOAD BALANCING =============== 58.8854 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 58.941 Info: Benchmark time: 120 CPUs 0.12374 s/step 0.716087 days/ns 1529 MB memory TIMING: 480 CPU: 49.0385, 0.111808/step Wall: 58.6177, 0.124498/step, 0.0248996 hours remaining, 1529.003906 MB of memory in use. ENERGY: 480 39201.4023 107211.3406 82214.8665 5152.0053 -3997604.7393 285413.3950 0.0000 0.0000 648982.3078 -2829429.4218 293.8920 -3478411.7295 -2826836.6870 293.5487 -142.3040 -64.6707 10352597.5310 -2.1040 -2.1207 Info: Benchmark time: 120 CPUs 0.115631 s/step 0.669158 days/ns 1525 MB memory TIMING: 600 CPU: 61.4697, 0.103593/step Wall: 72.4935, 0.115632/step, 0.019272 hours remaining, 1524.996094 MB of memory in use. ENERGY: 600 39180.8797 107591.1089 82057.1908 5167.9994 -3995039.7927 286859.8143 0.0000 0.0000 650307.3037 -2823875.4960 294.4920 -3474182.7997 -2821382.2150 294.4815 -24.8936 50.8260 10353672.5445 -1.7944 -1.7423 Info: Benchmark time: 120 CPUs 0.103891 s/step 0.601222 days/ns 1522.99 MB memory TIMING: 720 CPU: 72.525, 0.0921277/step Wall: 84.9606, 0.103892/step, 0.0138523 hours remaining, 1522.992188 MB of memory in use. ENERGY: 720 39076.2370 107092.9885 81925.1616 5184.4683 -3989818.0129 284791.5029 0.0000 0.0000 651544.7291 -2820202.9256 295.0524 -3471747.6548 -2817539.8046 294.8771 -58.1809 18.2330 10356524.3494 1.3746 1.2280 Info: Benchmark time: 120 CPUs 0.103711 s/step 0.600178 days/ns 1516.98 MB memory TIMING: 840 CPU: 83.5963, 0.092261/step Wall: 97.4061, 0.103712/step, 0.0103712 hours remaining, 1516.980469 MB of memory in use. ENERGY: 840 39135.7997 107083.4624 82011.2760 5140.9387 -3987681.8496 283706.6253 0.0000 0.0000 652450.7930 -2818152.9544 295.4627 -3470603.7475 -2815534.2629 295.2721 -45.6390 29.9420 10354937.3441 2.4081 2.4403 Info: Benchmark time: 120 CPUs 0.10396 s/step 0.601623 days/ns 1516.98 MB memory TIMING: 960 CPU: 94.6566, 0.0921693/step Wall: 109.882, 0.103962/step, 0.00693078 hours remaining, 1516.980469 MB of memory in use. ENERGY: 960 39222.3814 107409.1552 82314.5337 5119.1399 -3985738.4881 282585.4907 0.0000 0.0000 652976.5991 -2816111.1881 295.7008 -3469087.7872 -2813546.2122 295.5347 -71.5411 5.3400 10356162.9987 2.2760 2.1374 Info: Benchmark time: 120 CPUs 0.103808 s/step 0.600743 days/ns 1516.98 MB memory TIMING: 1080 CPU: 105.724, 0.0922276/step Wall: 122.339, 0.10381/step, 0.00346033 hours remaining, 1516.980469 MB of memory in use. ENERGY: 1080 39285.8559 108018.7269 82250.4968 5095.2665 -3982076.6385 280666.1714 0.0000 0.0000 653526.8892 -2813233.2317 295.9500 -3466760.1209 -2810696.9772 295.8225 -141.9833 -64.7310 10362144.8759 1.2755 1.2947 TIMING: 1200 CPU: 116.79, 0.0922193/step Wall: 134.812, 0.103946/step, 0 hours remaining, 1516.980469 MB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG ENERGY: 1200 39093.6291 107159.8072 82116.3158 5125.6480 -3979329.5960 281651.1672 0.0000 0.0000 652753.9042 -2811429.1245 295.5999 -3464183.0287 -2808835.6650 295.9741 -69.1378 4.2542 10365456.0543 1.5838 1.5299 WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 1200 WRITING COORDINATES TO OUTPUT FILE AT STEP 1200 WRITING VELOCITIES TO OUTPUT FILE AT STEP 1200 The last position output (seq=-2) takes 0.081 seconds(file I/O: 0.080 secs), 1516.980 MB of memory in use The last velocity output (seq=-2) takes 0.164 seconds(file I/O: 0.089 secs), 1516.980 MB of memory in use ==================================================== WallClock: 135.563660 CPUTime: 117.505135 Memory: 1516.980469 MB TACC: Shutdown complete. Exiting.