TACC: Starting up job 6245023 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 2.621 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 64 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.027 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 960 c403-504.stampede.tacc.utexas.edu tg455591 Info: Running on 960 processors, 64 nodes, 64 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.138082 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1203.54 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 LOAD FROM NODE 0 Info: REMOVING LOAD FROM NODE 1 Info: REMOVING PATCHES FROM PROCESSOR 0 Info: REMOVING PATCHES FROM PROCESSOR 1 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 1450742589 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: 0.00567389 Info: Info: Entering startup at 0.231566 s, 1301.42 MB of memory in use Info: Startup phase 0 took 0.0108519 s, 1301.42 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0373671 s, 1301.76 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: 240 720 Info: OUTPUT PROC LOCATIONS: 480 Info: Startup phase 2 took 0.0570378 s, 1302.67 MB of memory in use Info: Startup phase 3 took 0.101217 s, 1302.67 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 -0.00571489 -0.00421279 0.00666847 Info: Startup phase 4 took 0.0472071 s, 1423.12 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 0.058404 s, 1423.12 MB of memory in use Info: TORUS A SIZE 960 USING 0 15 30 45 60 75 90 105 120 135 150 165 180 195 210 225 240 255 270 285 300 315 330 345 360 375 390 405 420 435 450 465 480 495 510 525 540 555 570 585 600 615 630 645 660 675 690 705 720 735 750 765 780 795 810 825 840 855 870 885 900 915 930 945 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 946 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.026866 s, 1433.6 MB of memory in use Info: PME using 27 x 31 x 28 pencil grid for FFT and reciprocal sum. Info: PME Z PENCIL LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ... Info: PME Y PENCIL LOCATIONS: 1 3 5 6 7 8 9 11 13 14 ... Info: PME X PENCIL LOCATIONS: 1 2 3 4 5 7 8 9 10 11 ... Info: Startup phase 7 took 0.116472 s, 1441.04 MB of memory in use Info: Startup phase 8 took 0.0228679 s, 1441.04 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.076545 s, 1441.04 MB of memory in use Info: CREATING 48730 COMPUTE OBJECTS Info: Startup phase 10 took 0.039371 s, 1441.04 MB of memory in use Info: Building spanning tree ... send: 1 recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 Info: Startup phase 11 took 0.0132122 s, 1441.04 MB of memory in use Info: Startup phase 12 took 0.000220776 s, 1441.04 MB of memory in use Info: Finished startup at 0.839206 s, 1441.04 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 -4134759.4118 375583.0490 0.0000 0.0000 658083.5960 -2870678.1339 298.0135 -3528761.7299 -2868119.5400 298.0135 2251.9685 2339.7757 10194598.5131 2251.9685 2339.7757 LDB: ============= START OF LOAD BALANCING ============== 1.55383 LDB: ============== END OF LOAD BALANCING =============== 1.5676 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 1.56985 LDB: ============= START OF LOAD BALANCING ============== 3.72879 LDB: Largest compute 3410 load 0.150950 is 11.5% of average load 1.312738 LDB: Average compute 0.024137 is 1.8% of average load 1.312738 LDB: Partitioning computes with target load 0.131274 LDB: Increased migratable compute count from 41743 to 42190 LDB: Largest unpartitionable compute is 0.023256 LDB: ============== END OF LOAD BALANCING =============== 3.86426 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 3.95967 Info: Initial time: 960 CPUs 0.023107 s/step 0.133721 days/ns 1442.23 MB memory TIMING: 120 CPU: 2.47162, 0.0192887/step Wall: 3.21661, 0.0251679/step, 0.00755038 hours remaining, 1442.230469 MB of memory in use. ENERGY: 120 39347.9866 107156.0940 81942.1526 5093.8633 -4027177.4214 295970.0818 0.0000 0.0000 643250.1870 -2854417.0562 291.2962 -3497667.2432 -2851887.1254 290.0516 -20.4860 55.5006 10348460.1410 -2.7055 -1.5671 LDB: ============= START OF LOAD BALANCING ============== 4.48424 LDB: ============== END OF LOAD BALANCING =============== 4.49275 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 4.49691 LDB: ============= START OF LOAD BALANCING ============== 6.62692 LDB: Largest compute 3572 load 0.139746 is 10.7% of average load 1.301916 LDB: Average compute 0.023839 is 1.8% of average load 1.301916 LDB: TIME 6.74465 LOAD: AVG 1.30192 MAX 1.90939 PROXIES: TOTAL 10545 MAXPE 17 MAXPATCH 8 None MEM: 1454.96 MB LDB: TIME 6.78451 LOAD: AVG 1.30192 MAX 1.38809 PROXIES: TOTAL 10545 MAXPE 17 MAXPATCH 8 TorusLB MEM: 1454.96 MB LDB: ============== END OF LOAD BALANCING =============== 6.90389 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 6.99299 Info: Initial time: 960 CPUs 0.022172 s/step 0.12831 days/ns 1446.5 MB memory TIMING: 240 CPU: 4.83626, 0.0197053/step Wall: 6.2564, 0.0253316/step, 0.00675509 hours remaining, 1446.496094 MB of memory in use. ENERGY: 240 39296.3129 107003.1873 82124.4195 5169.2240 -4011554.8105 289550.0381 0.0000 0.0000 644729.0525 -2843682.5762 291.9659 -3488411.6287 -2841227.2870 291.4932 -100.1165 -23.3540 10352251.9923 1.9867 1.9427 LDB: ============= START OF LOAD BALANCING ============== 9.73545 LDB: Largest compute 3208 load 0.179854 is 10.9% of average load 1.651886 LDB: Average compute 0.029910 is 1.8% of average load 1.651886 LDB: TIME 9.84919 LOAD: AVG 1.65189 MAX 1.92811 PROXIES: TOTAL 10545 MAXPE 17 MAXPATCH 8 None MEM: 1446.5 MB LDB: TIME 9.85487 LOAD: AVG 1.65189 MAX 1.92811 PROXIES: TOTAL 10545 MAXPE 17 MAXPATCH 8 RefineTorusLB MEM: 1446.5 MB LDB: TIME 9.86116 LOAD: AVG 1.65189 MAX 1.70594 PROXIES: TOTAL 10579 MAXPE 17 MAXPATCH 8 RefineTorusLB MEM: 1446.5 MB LDB: ============== END OF LOAD BALANCING =============== 9.86527 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 9.93273 Info: Initial time: 960 CPUs 0.022792 s/step 0.131898 days/ns 1446.5 MB memory TIMING: 360 CPU: 6.98794, 0.0179306/step Wall: 9.18896, 0.024438/step, 0.00570219 hours remaining, 1446.496094 MB of memory in use. ENERGY: 360 38956.8446 107399.7793 81920.2041 5113.0410 -4004957.7177 289067.4686 0.0000 0.0000 646573.5864 -2835926.7936 292.8012 -3482500.3800 -2833413.6429 292.5636 -35.8363 39.3616 10349958.8003 1.7661 1.7354 LDB: ============= START OF LOAD BALANCING ============== 12.614 LDB: Largest compute 2761 load 0.179636 is 10.9% of average load 1.653286 LDB: Average compute 0.029917 is 1.8% of average load 1.653286 LDB: TIME 12.7399 LOAD: AVG 1.65329 MAX 1.77216 PROXIES: TOTAL 10545 MAXPE 17 MAXPATCH 8 None MEM: 1444.49 MB LDB: TIME 12.7456 LOAD: AVG 1.65329 MAX 1.77216 PROXIES: TOTAL 10579 MAXPE 17 MAXPATCH 8 RefineTorusLB MEM: 1444.49 MB LDB: TIME 12.7508 LOAD: AVG 1.65329 MAX 1.70744 PROXIES: TOTAL 10605 MAXPE 18 MAXPATCH 8 RefineTorusLB MEM: 1444.49 MB LDB: ============== END OF LOAD BALANCING =============== 12.7547 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 12.8208 Info: Benchmark time: 960 CPUs 0.0223629 s/step 0.129415 days/ns 1444.49 MB memory TIMING: 480 CPU: 9.08262, 0.0174557/step Wall: 12.0797, 0.0240892/step, 0.00481784 hours remaining, 1444.492188 MB of memory in use. ENERGY: 480 39209.1852 107513.7666 81900.9217 5057.0248 -3999347.6225 286935.9278 0.0000 0.0000 649498.9823 -2829231.8142 294.1259 -3478730.7965 -2826691.2332 293.4837 -108.9718 -34.2799 10350986.9275 4.3685 4.4061 Info: Benchmark time: 960 CPUs 0.0221323 s/step 0.128081 days/ns 1444.49 MB memory TIMING: 600 CPU: 10.9503, 0.0155643/step Wall: 14.7357, 0.0221339/step, 0.00368899 hours remaining, 1444.492188 MB of memory in use. ENERGY: 600 39023.8473 107007.6467 81907.8969 5049.1742 -3993761.0162 285326.3936 0.0000 0.0000 651200.7631 -2824245.2944 294.8966 -3475446.0574 -2821649.6072 294.2247 -76.7061 -0.0454 10356105.4909 -2.4136 -2.4220 Info: Benchmark time: 960 CPUs 0.0220442 s/step 0.127571 days/ns 1444.49 MB memory TIMING: 720 CPU: 12.7881, 0.0153143/step Wall: 17.3812, 0.0220456/step, 0.00293941 hours remaining, 1444.492188 MB of memory in use. ENERGY: 720 38950.7134 107576.6746 81914.8465 5123.3631 -3989740.3220 283407.9331 0.0000 0.0000 652257.4790 -2820509.3123 295.3751 -3472766.7913 -2817950.9411 294.9267 -109.2860 -35.3417 10360485.4983 1.7714 1.7719 Info: Benchmark time: 960 CPUs 0.0218436 s/step 0.12641 days/ns 1444.49 MB memory TIMING: 840 CPU: 14.6268, 0.0153227/step Wall: 20.0026, 0.021845/step, 0.0021845 hours remaining, 1444.492188 MB of memory in use. ENERGY: 840 39390.5333 107021.7704 82103.3115 5139.9655 -3987459.6480 282752.5616 0.0000 0.0000 651709.1524 -2819342.3533 295.1268 -3471051.5057 -2816825.8173 295.2908 -141.9602 -67.5280 10356992.9027 1.8643 1.6167 Info: Benchmark time: 960 CPUs 0.0230317 s/step 0.133285 days/ns 1444.49 MB memory TIMING: 960 CPU: 16.5825, 0.0162975/step Wall: 22.7666, 0.023033/step, 0.00153553 hours remaining, 1444.492188 MB of memory in use. ENERGY: 960 39379.3274 106995.0518 82040.4978 5151.4466 -3986420.5546 283516.2726 0.0000 0.0000 653860.1410 -2815477.8174 296.1009 -3469337.9584 -2812855.7616 295.3162 -67.1865 7.3899 10356302.8882 4.9516 4.9059 Info: Benchmark time: 960 CPUs 0.0217015 s/step 0.125587 days/ns 1444.49 MB memory TIMING: 1080 CPU: 18.3962, 0.0151144/step Wall: 25.3709, 0.0217027/step, 0.000723423 hours remaining, 1444.492188 MB of memory in use. ENERGY: 1080 39121.5971 107694.4591 82150.4023 5168.3335 -3984234.4971 283325.8935 0.0000 0.0000 653126.5531 -2813647.2585 295.7687 -3466773.8117 -2811115.4505 295.6796 -63.2916 10.5673 10360790.0970 2.6416 2.7653 TIMING: 1200 CPU: 20.2829, 0.0157226/step Wall: 28.0483, 0.0223122/step, 0 hours remaining, 1444.492188 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 39065.2157 106973.7370 81943.1915 5097.9161 -3980660.6246 282382.9947 0.0000 0.0000 653592.4771 -2811605.0925 295.9797 -3465197.5696 -2809012.8056 295.7797 -20.2804 53.7103 10361945.0796 -1.9069 -1.9656 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 0.131 seconds(file I/O: 0.130 secs), 1444.492 MB of memory in use The last velocity output (seq=-2) takes 0.201 seconds(file I/O: 0.077 secs), 1444.492 MB of memory in use ==================================================== WallClock: 29.111973 CPUTime: 21.154783 Memory: 1444.492188 MB TACC: Shutdown complete. Exiting.