TACC: Starting up job 6245028 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 6.889 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 : 0-15 Charm++> Running on 16 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-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-iccstatic Info: Built Mon Dec 21 10:36:00 CST 2015 by tg455591 on login4.stampede.tacc.utexas.edu Info: 1 NAMD 2.11 Linux-x86_64-ibverbs-Stampede-memopt 256 c470-203.stampede.tacc.utexas.edu tg455591 Info: Running on 256 processors, 256 nodes, 16 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.10589 s Info: 144.883 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: 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 1450742549 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: 0.00561905 Info: Info: Entering startup at 0.207573 s, 240.531 MB of memory in use Info: Startup phase 0 took 0.00339508 s, 240.531 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0769141 s, 241.094 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: 64 192 Info: OUTPUT PROC LOCATIONS: 128 Info: Startup phase 2 took 0.04142 s, 242.07 MB of memory in use Info: Startup phase 3 took 0.144505 s, 242.07 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 0.00528706 0.0137613 0.00660118 Info: Startup phase 4 took 0.0375669 s, 250.461 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 0.0550361 s, 251.492 MB of memory in use Info: TORUS A SIZE 256 USING 0 16 32 48 64 80 96 112 128 144 160 176 192 208 224 240 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 241 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0223689 s, 261.938 MB of memory in use Info: PME using 108 and 108 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 3 5 7 11 13 15 19 21 23 25 ... Info: PME TRANS LOCATIONS: 1 2 6 9 10 12 14 17 18 20 ... Info: PME USING 108 GRID NODES AND 108 TRANS NODES Info: Startup phase 7 took 0.156 s, 268.836 MB of memory in use Info: Startup phase 8 took 0.00718284 s, 268.836 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.0107982 s, 268.836 MB of memory in use Info: CREATING 45215 COMPUTE OBJECTS Info: Startup phase 10 took 0.0192478 s, 268.836 MB of memory in use Info: useSync: 0 useProxySync: 0 Info: Startup phase 11 took 0.00153923 s, 268.836 MB of memory in use Info: Startup phase 12 took 0.00137687 s, 268.836 MB of memory in use Info: Finished startup at 0.784924 s, 268.836 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 658029.2489 -2870732.4809 297.9889 -3528761.7298 -2868174.4441 297.9889 2253.5343 2341.2771 10194598.5131 2253.5343 2341.2771 LDB: ============= START OF LOAD BALANCING ============== 2.10355 LDB: ============== END OF LOAD BALANCING =============== 2.11283 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 2.11448 LDB: ============= START OF LOAD BALANCING ============== 7.19043 LDB: Largest compute 2966 load 0.153460 is 3.5% of average load 4.372523 LDB: Average compute 0.024168 is 0.6% of average load 4.372523 LDB: Partitioning computes with target load 0.437252 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023782 LDB: ============== END OF LOAD BALANCING =============== 7.22235 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 7.3485 Info: Initial time: 256 CPUs 0.0529499 s/step 0.306423 days/ns 268.836 MB memory TIMING: 120 CPU: 6.66699, 0.0541834/step Wall: 6.69385, 0.0543698/step, 0.0163109 hours remaining, 268.835938 MB of memory in use. ENERGY: 120 39403.6601 107520.0895 81879.4229 5075.5945 -4027761.3574 296082.4084 0.0000 0.0000 642709.4138 -2855090.7682 291.0513 -3497800.1819 -2852611.1636 290.0889 -18.6350 58.0056 10345466.2081 -0.6769 0.3334 LDB: ============= START OF LOAD BALANCING ============== 8.64623 LDB: ============== END OF LOAD BALANCING =============== 8.64673 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 8.6484 LDB: ============= START OF LOAD BALANCING ============== 13.7428 LDB: Largest compute 2942 load 0.153234 is 3.5% of average load 4.359577 LDB: Average compute 0.024108 is 0.6% of average load 4.359577 LDB: TIME 13.7632 LOAD: AVG 4.35958 MAX 5.09134 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 None MEM: 268.965 MB LDB: TIME 13.7952 LOAD: AVG 4.35958 MAX 4.45469 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 TorusLB MEM: 268.965 MB LDB: ============== END OF LOAD BALANCING =============== 13.8315 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 13.9574 Info: Initial time: 256 CPUs 0.0531601 s/step 0.307639 days/ns 271.227 MB memory TIMING: 240 CPU: 13.243, 0.0548/step Wall: 13.2907, 0.0549734/step, 0.0146596 hours remaining, 271.226562 MB of memory in use. ENERGY: 240 39214.9827 107372.5664 81994.2434 5106.5891 -4016740.8667 292745.9533 0.0000 0.0000 645173.1081 -2845133.4237 292.1670 -3490306.5319 -2842612.5024 291.5085 31.7176 106.8854 10344658.1707 -0.1779 -0.1861 LDB: ============= START OF LOAD BALANCING ============== 19.6854 LDB: Largest compute 3180 load 0.194299 is 3.5% of average load 5.477624 LDB: Average compute 0.030248 is 0.6% of average load 5.477624 LDB: TIME 19.7058 LOAD: AVG 5.47762 MAX 5.69758 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 None MEM: 271.227 MB LDB: TIME 19.7118 LOAD: AVG 5.47762 MAX 5.69758 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 RefineTorusLB MEM: 271.227 MB LDB: TIME 19.7128 LOAD: AVG 5.47762 MAX 5.56556 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 RefineTorusLB MEM: 271.227 MB LDB: ============== END OF LOAD BALANCING =============== 19.715 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 19.8353 Info: Initial time: 256 CPUs 0.0477213 s/step 0.276165 days/ns 271.227 MB memory TIMING: 360 CPU: 19.1051, 0.0488509/step Wall: 19.1676, 0.0489748/step, 0.0114275 hours remaining, 271.226562 MB of memory in use. ENERGY: 360 39261.7050 107164.6099 82096.7505 5185.1082 -4006587.9800 288686.9829 0.0000 0.0000 647541.0901 -2836651.7333 293.2393 -3484192.8234 -2834115.4529 292.5783 -55.8025 18.6735 10345816.3338 -1.9675 -1.9481 LDB: ============= START OF LOAD BALANCING ============== 25.504 LDB: Largest compute 3130 load 0.191054 is 3.5% of average load 5.478858 LDB: Average compute 0.030251 is 0.6% of average load 5.478858 LDB: TIME 25.5244 LOAD: AVG 5.47886 MAX 5.61193 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 None MEM: 271.227 MB LDB: TIME 25.5304 LOAD: AVG 5.47886 MAX 5.61193 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 RefineTorusLB MEM: 271.227 MB LDB: TIME 25.5314 LOAD: AVG 5.47886 MAX 5.56549 PROXIES: TOTAL 6794 MAXPE 32 MAXPATCH 8 RefineTorusLB MEM: 271.227 MB LDB: ============== END OF LOAD BALANCING =============== 25.5335 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 25.6531 Info: Benchmark time: 256 CPUs 0.047229 s/step 0.273316 days/ns 271.227 MB memory TIMING: 480 CPU: 24.9082, 0.0483593/step Wall: 24.9848, 0.048476/step, 0.00969521 hours remaining, 271.226562 MB of memory in use. ENERGY: 480 39136.0361 107904.3895 82033.2444 5230.9864 -4001486.1271 287897.8977 0.0000 0.0000 648797.1750 -2830486.3980 293.8081 -3479283.5730 -2827916.4133 293.5522 -77.4838 -0.9157 10351631.4490 0.4631 0.4014 Info: Benchmark time: 256 CPUs 0.0470882 s/step 0.272501 days/ns 271.227 MB memory TIMING: 600 CPU: 30.5374, 0.0469095/step Wall: 30.6357, 0.0470915/step, 0.00784858 hours remaining, 271.226562 MB of memory in use. ENERGY: 600 39170.9726 107694.7261 81859.4907 5130.5479 -3995180.8407 285871.3245 0.0000 0.0000 650667.2892 -2824786.4897 294.6550 -3475453.7789 -2822262.3094 294.1176 -61.9704 12.5190 10351813.1455 0.3620 0.3238 Info: Benchmark time: 256 CPUs 0.0472645 s/step 0.273522 days/ns 271.227 MB memory TIMING: 720 CPU: 36.1975, 0.0471678/step Wall: 36.3079, 0.0472677/step, 0.00630236 hours remaining, 271.226562 MB of memory in use. ENERGY: 720 39423.1467 107874.1933 82046.1151 5248.6215 -3990372.4833 283881.1228 0.0000 0.0000 651513.2081 -2820386.0758 295.0381 -3471899.2839 -2817865.2927 294.8707 -79.1709 -4.5923 10355038.0730 0.3692 0.2961 Info: Benchmark time: 256 CPUs 0.0473632 s/step 0.274092 days/ns 271.227 MB memory TIMING: 840 CPU: 41.8676, 0.0472512/step Wall: 41.9918, 0.0473663/step, 0.00473663 hours remaining, 271.226562 MB of memory in use. ENERGY: 840 39114.3497 107466.1499 82124.1497 5130.7750 -3986931.3769 283583.9933 0.0000 0.0000 653338.2608 -2816173.6985 295.8646 -3469511.9593 -2813625.2763 295.3310 -46.1533 27.5587 10361152.4347 2.3140 2.1942 Info: Benchmark time: 256 CPUs 0.0474558 s/step 0.274628 days/ns 271.227 MB memory TIMING: 960 CPU: 47.5498, 0.0473511/step Wall: 47.6869, 0.0474589/step, 0.00316393 hours remaining, 271.226562 MB of memory in use. ENERGY: 960 39246.9287 107461.1399 82108.7693 5116.6732 -3983727.2344 282788.9066 0.0000 0.0000 652859.0903 -2814145.7263 295.6476 -3467004.8167 -2811504.6894 295.7399 -98.8648 -24.5242 10366033.0802 -0.1384 0.0049 Info: Benchmark time: 256 CPUs 0.0476579 s/step 0.275798 days/ns 271.227 MB memory TIMING: 1080 CPU: 53.2479, 0.0474845/step Wall: 53.4062, 0.0476611/step, 0.0015887 hours remaining, 271.226562 MB of memory in use. ENERGY: 1080 38994.9937 107489.8911 82064.9079 5155.4998 -3982662.5441 282759.4680 0.0000 0.0000 654163.9551 -2812033.8285 296.2385 -3466197.7836 -2809403.6692 295.9390 -41.4169 30.9246 10361784.5466 3.0701 3.0510 TIMING: 1200 CPU: 58.933, 0.0473761/step Wall: 59.099, 0.0474396/step, 0 hours remaining, 271.226562 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 38980.4923 107726.1423 81948.4383 5016.1442 -3983131.0534 284240.1624 0.0000 0.0000 653941.2025 -2811278.4714 296.1376 -3465219.6739 -2808705.0512 296.3217 11.1768 86.5311 10364572.5259 3.6528 3.6872 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 0.120 seconds(file I/O: 0.119 secs), 271.227 MB of memory in use The last velocity output (seq=-2) takes 0.199 seconds(file I/O: 0.086 secs), 271.227 MB of memory in use ==================================================== WallClock: 60.153694 CPUTime: 59.810905 Memory: 271.226562 MB