TACC: Starting up job 6245021 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 1.449 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 32 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.019 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 480 c518-501.stampede.tacc.utexas.edu tg455591 Info: Running on 480 processors, 32 nodes, 32 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.107148 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1199.01 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 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 1450742564 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: 0.00571299 Info: Info: Entering startup at 0.197352 s, 1296.88 MB of memory in use Info: Startup phase 0 took 0.00619817 s, 1296.88 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.019326 s, 1297.22 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: 120 360 Info: OUTPUT PROC LOCATIONS: 240 Info: Startup phase 2 took 0.043503 s, 1298.13 MB of memory in use Info: Startup phase 3 took 0.100528 s, 1298.13 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 0.00691264 -0.00317126 -0.00179018 Info: Startup phase 4 took 0.0431209 s, 1418.57 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 0.059315 s, 1418.57 MB of memory in use Info: TORUS A SIZE 480 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 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 466 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.022109 s, 1429.05 MB of memory in use Info: PME using 20 x 22 x 19 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 10 11 13 ... Info: PME X PENCIL LOCATIONS: 1 2 3 4 5 7 8 9 11 12 ... Info: Startup phase 7 took 0.09357 s, 1436.12 MB of memory in use Info: Startup phase 8 took 0.0129061 s, 1436.12 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.050844 s, 1436.12 MB of memory in use Info: CREATING 46330 COMPUTE OBJECTS Info: Startup phase 10 took 0.027513 s, 1436.12 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 0.00861192 s, 1436.12 MB of memory in use Info: Startup phase 12 took 0.000193119 s, 1436.12 MB of memory in use Info: Finished startup at 0.68509 s, 1436.12 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 -4134759.4117 375583.0490 0.0000 0.0000 658178.0551 -2870583.6747 298.0563 -3528761.7299 -2868025.5326 298.0563 2252.9630 2340.7780 10194598.5131 2252.9630 2340.7780 LDB: ============= START OF LOAD BALANCING ============== 1.55466 LDB: ============== END OF LOAD BALANCING =============== 1.56294 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 1.56511 LDB: ============= START OF LOAD BALANCING ============== 4.5511 LDB: Largest compute 3671 load 0.152424 is 6.3% of average load 2.419546 LDB: Average compute 0.024142 is 1.0% of average load 2.419546 LDB: Partitioning computes with target load 0.241955 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023344 LDB: ============== END OF LOAD BALANCING =============== 4.60881 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 4.67674 Info: Initial time: 480 CPUs 0.0314188 s/step 0.181822 days/ns 1439.88 MB memory TIMING: 120 CPU: 3.13452, 0.0249795/step Wall: 4.09458, 0.0325554/step, 0.00976662 hours remaining, 1439.882812 MB of memory in use. ENERGY: 120 39532.1828 107524.5988 82006.3530 5161.7984 -4028074.9411 295907.0947 0.0000 0.0000 642170.9136 -2855771.9999 290.8074 -3497942.9134 -2853337.6736 289.9289 -25.7605 51.6986 10351963.6355 -2.2043 -1.2774 LDB: ============= START OF LOAD BALANCING ============== 5.43405 LDB: ============== END OF LOAD BALANCING =============== 5.43458 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 5.43667 LDB: ============= START OF LOAD BALANCING ============== 8.4309 LDB: Largest compute 3241 load 0.153261 is 6.4% of average load 2.407945 LDB: Average compute 0.024091 is 1.0% of average load 2.407945 LDB: TIME 8.47803 LOAD: AVG 2.40795 MAX 2.98286 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 None MEM: 1444.73 MB LDB: TIME 8.51314 LOAD: AVG 2.40795 MAX 2.60241 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 TorusLB MEM: 1444.73 MB LDB: ============== END OF LOAD BALANCING =============== 8.61493 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 8.68466 Info: Initial time: 480 CPUs 0.0312105 s/step 0.180616 days/ns 1440.42 MB memory TIMING: 240 CPU: 6.25205, 0.0259794/step Wall: 8.0966, 0.0333501/step, 0.00889337 hours remaining, 1440.417969 MB of memory in use. ENERGY: 240 39251.8959 107479.8783 82077.3110 5100.6782 -4015861.6742 292426.1672 0.0000 0.0000 644702.6850 -2844823.0585 291.9539 -3489525.7435 -2842241.0101 291.3727 -8.7155 66.1732 10348232.2510 -2.6695 -2.6603 LDB: ============= START OF LOAD BALANCING ============== 11.9728 LDB: Largest compute 2750 load 0.192969 is 6.4% of average load 3.031480 LDB: Average compute 0.030234 is 1.0% of average load 3.031480 LDB: TIME 12.0221 LOAD: AVG 3.03148 MAX 3.24699 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 None MEM: 1446.42 MB LDB: TIME 12.0274 LOAD: AVG 3.03148 MAX 3.24699 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 1446.42 MB LDB: TIME 12.0298 LOAD: AVG 3.03148 MAX 3.09642 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 1446.42 MB LDB: ============== END OF LOAD BALANCING =============== 12.0332 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 12.088 Info: Initial time: 480 CPUs 0.0273612 s/step 0.15834 days/ns 1446.42 MB memory TIMING: 360 CPU: 8.73867, 0.0207218/step Wall: 11.4953, 0.0283229/step, 0.00660868 hours remaining, 1446.421875 MB of memory in use. ENERGY: 360 39437.2483 107122.1415 82194.7008 5145.8441 -4008190.5706 290653.3363 0.0000 0.0000 647122.4775 -2836514.8220 293.0497 -3483637.2995 -2833903.6476 292.7353 -29.8624 45.6690 10347965.3946 0.2853 0.1352 LDB: ============= START OF LOAD BALANCING ============== 15.2946 LDB: Largest compute 3650 load 0.193227 is 6.4% of average load 3.034642 LDB: Average compute 0.030235 is 1.0% of average load 3.034642 LDB: TIME 15.3358 LOAD: AVG 3.03464 MAX 3.12226 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 None MEM: 1445.42 MB LDB: TIME 15.3411 LOAD: AVG 3.03464 MAX 3.12226 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 1445.42 MB LDB: TIME 15.3425 LOAD: AVG 3.03464 MAX 3.09984 PROXIES: TOTAL 8227 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 1445.42 MB LDB: ============== END OF LOAD BALANCING =============== 15.3458 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 15.4004 Info: Benchmark time: 480 CPUs 0.0267093 s/step 0.154568 days/ns 1445.42 MB memory TIMING: 480 CPU: 11.1473, 0.0200719/step Wall: 14.8065, 0.0275931/step, 0.00551863 hours remaining, 1445.417969 MB of memory in use. ENERGY: 480 39129.3881 107528.8942 82241.1716 5153.9356 -4000932.7607 286795.7626 0.0000 0.0000 648359.2776 -2831724.3310 293.6098 -3480083.6086 -2829179.9938 293.3456 -80.7856 -3.9930 10349617.1753 1.7887 1.8029 Info: Benchmark time: 480 CPUs 0.0266571 s/step 0.154266 days/ns 1445.42 MB memory TIMING: 600 CPU: 13.446, 0.0191554/step Wall: 18.0055, 0.0266583/step, 0.00444305 hours remaining, 1445.417969 MB of memory in use. ENERGY: 600 39269.6966 107541.0614 82109.5783 5081.3878 -3996358.8460 285471.4834 0.0000 0.0000 650248.2731 -2826637.3654 294.4653 -3476885.6385 -2824123.1935 293.9955 -78.4047 -2.5967 10352425.3828 0.0960 0.0710 Info: Benchmark time: 480 CPUs 0.0267735 s/step 0.154939 days/ns 1445.42 MB memory TIMING: 720 CPU: 15.7686, 0.0193554/step Wall: 21.2185, 0.0267747/step, 0.00356996 hours remaining, 1445.417969 MB of memory in use. ENERGY: 720 39037.4720 107487.0596 82097.4278 5168.2810 -3992504.4282 285389.4508 0.0000 0.0000 651583.6726 -2821741.0644 295.0700 -3473324.7370 -2819217.0463 294.6090 -81.0402 -8.1455 10354064.2127 6.9389 6.9036 Info: Benchmark time: 480 CPUs 0.0267804 s/step 0.154979 days/ns 1445.42 MB memory TIMING: 840 CPU: 18.0923, 0.0193637/step Wall: 24.4323, 0.0267815/step, 0.00267815 hours remaining, 1445.417969 MB of memory in use. ENERGY: 840 39238.0771 107512.8790 81841.1640 5114.1026 -3987193.8423 283229.9225 0.0000 0.0000 652455.0053 -2817802.6918 295.4646 -3470257.6971 -2815204.1698 295.1338 -82.5018 -9.1068 10358539.7204 4.2701 4.1310 Info: Benchmark time: 480 CPUs 0.0269875 s/step 0.156177 days/ns 1445.42 MB memory TIMING: 960 CPU: 20.4369, 0.0195387/step Wall: 27.6709, 0.0269886/step, 0.00179924 hours remaining, 1445.417969 MB of memory in use. ENERGY: 960 39138.7378 107461.2913 81977.3351 5094.6034 -3986474.0571 284439.1918 0.0000 0.0000 653579.2126 -2814783.6851 295.9737 -3468362.8977 -2812213.6588 295.4939 -20.6884 55.9119 10356760.2547 2.4008 2.4637 Info: Benchmark time: 480 CPUs 0.0269765 s/step 0.156114 days/ns 1445.42 MB memory TIMING: 1080 CPU: 22.7825, 0.019547/step Wall: 30.9082, 0.0269777/step, 0.000899256 hours remaining, 1445.417969 MB of memory in use. ENERGY: 1080 39126.6588 107364.2999 82119.7682 5104.0086 -3982556.8942 283308.8485 0.0000 0.0000 653748.2861 -2811785.0240 296.0502 -3465533.3101 -2809225.3714 295.9739 -30.3964 44.3313 10365115.9540 -2.9593 -3.0209 TIMING: 1200 CPU: 25.1232, 0.0195054/step Wall: 34.1389, 0.0269221/step, 0 hours remaining, 1445.417969 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 39353.1541 107465.9853 82093.3630 5170.1310 -3980682.7214 281645.4140 0.0000 0.0000 654118.7937 -2810835.8804 296.2180 -3464954.6741 -2808253.5938 296.2048 -117.9459 -42.8156 10364868.1877 0.9834 1.0433 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 0.093 seconds(file I/O: 0.092 secs), 1445.418 MB of memory in use The last velocity output (seq=-2) takes 0.241 seconds(file I/O: 0.155 secs), 1445.418 MB of memory in use ==================================================== WallClock: 35.131783 CPUTime: 26.075035 Memory: 1445.417969 MB TACC: Shutdown complete. Exiting.