TACC: Starting up job 6245024 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 2.309 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 128 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.046 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 1920 c402-303.stampede.tacc.utexas.edu tg455591 Info: Running on 1920 processors, 128 nodes, 128 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.206695 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1212.61 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 Hybrid Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4800 steps Info: FIRST LDB TIMESTEP 120 Info: HYBRIDLB GROUP SIZE 480 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: MAX SELF PARTITIONS 20 Info: MAX PAIR PARTITIONS 8 Info: SELF PARTITION ATOMS 154 Info: SELF2 PARTITION ATOMS 154 Info: PAIR PARTITION ATOMS 318 Info: PAIR2 PARTITION ATOMS 637 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 1450742403 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: 0.00571012 Info: Info: Entering startup at 0.309539 s, 1310.46 MB of memory in use Info: Startup phase 0 took 0.020771 s, 1310.46 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0678251 s, 1310.78 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: 480 1440 Info: OUTPUT PROC LOCATIONS: 960 Info: Startup phase 2 took 0.0595009 s, 1311.75 MB of memory in use Info: Startup phase 3 took 0.102146 s, 1311.75 MB of memory in use Info: REDUCING NUMBER OF PATCHES TO IMPROVE LOAD BALANCE Info: PATCH GRID IS 13 (PERIODIC) BY 12 (PERIODIC) BY 12 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: LOADED 1810196 TOTAL EXCLUSIONS Info: REMOVING COM VELOCITY -0.0124258 0.0119044 0.00282796 Info: Startup phase 4 took 0.067349 s, 1432.07 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 (1357) HAS 643 ATOMS Info: Startup phase 5 took 0.0578752 s, 1432.07 MB of memory in use Info: TORUS A SIZE 1920 USING 0 15 30 45 60 75 90 105 120 135 150 165 180 195 210 225 240 255 270 285 300 315 330 345 360 375 390 405 420 435 450 465 480 495 510 525 540 555 570 585 600 615 630 645 660 675 690 705 720 735 750 765 780 795 810 825 840 855 870 885 900 915 930 945 960 975 990 1005 1020 1035 1050 1065 1080 1095 1110 1125 1140 1155 1170 1185 1200 1215 1230 1245 1260 1275 1290 1305 1320 1335 1350 1365 1380 1395 1410 1425 1440 1455 1470 1485 1500 1515 1530 1545 1560 1575 1590 1605 1620 1635 1650 1665 1680 1695 1710 1725 1740 1755 1770 1785 1800 1815 1830 1845 1860 1875 1890 1905 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 1906 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0262039 s, 1442.63 MB of memory in use Info: PME using 31 x 31 x 28 pencil grid for FFT and reciprocal sum. Info: PME Z PENCIL LOCATIONS: 1 3 5 7 9 11 13 16 18 20 ... Info: PME Y PENCIL LOCATIONS: 2 4 6 8 10 12 14 17 19 21 ... Info: PME X PENCIL LOCATIONS: 1 3 5 7 9 11 13 15 18 20 ... Info: Startup phase 7 took 0.142592 s, 1449.77 MB of memory in use Info: Startup phase 8 took 0.031163 s, 1449.77 MB of memory in use LDB: Hybrid LB being created... HybridBaseLB: ThreeLevelTree is created. Info: Startup phase 9 took 0.131551 s, 1449.77 MB of memory in use Info: CREATING 46800 COMPUTE OBJECTS Info: Startup phase 10 took 0.0507009 s, 1449.77 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 0.02211 s, 1449.77 MB of memory in use Info: Startup phase 12 took 0.000212908 s, 1449.77 MB of memory in use Info: Finished startup at 1.08954 s, 1449.77 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 -4134759.4114 375583.0490 0.0000 0.0000 657448.2363 -2871313.4933 297.7258 -3528761.7295 -2868755.1154 297.7258 2249.8976 2337.7678 10194598.5131 2249.8976 2337.7678 LDB: ============= START OF LOAD BALANCING ============== 1.47556 LDB: ============== END OF LOAD BALANCING =============== 1.50024 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 1.50253 LDB: ============= START OF LOAD BALANCING ============== 2.36743 LDB: Largest compute 3229 load 0.197017 is 28.2% of average load 0.697416 LDB: Average compute 0.028075 is 4.0% of average load 0.697416 LDB: Partitioning computes with target load 0.069742 LDB: Increased migratable compute count from 35568 to 44883 LDB: Largest unpartitionable compute is 0.026148 LDB: ============== END OF LOAD BALANCING =============== 2.48313 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 2.58725 Info: Initial time: 1920 CPUs 0.00908183 s/step 0.0525569 days/ns 1449.77 MB memory TIMING: 120 CPU: 1.15282, 0.00769883/step Wall: 1.59223, 0.0111413/step, 0.00334238 hours remaining, 1449.769531 MB of memory in use. ENERGY: 120 39740.2446 107258.3804 81998.0297 5032.4913 -4027310.9564 296332.7448 0.0000 0.0000 641109.3007 -2855839.7648 290.3267 -3496949.0655 -2853320.4799 289.9286 -19.2463 58.5936 10351501.4720 -3.8788 -2.8697 LDB: ============= START OF LOAD BALANCING ============== 2.8063 LDB: ============== END OF LOAD BALANCING =============== 2.80723 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 2.80975 LDB: ============= START OF LOAD BALANCING ============== 3.68189 LDB: Largest compute 3079 load 0.076384 is 11.2% of average load 0.682584 LDB: Average compute 0.022315 is 3.3% of average load 0.682584 LDB: TIME 3.69626 LOAD: AVG 0.682586 MAX 0.856022 PROXIES: TOTAL 13197 MAXPE 7 MAXPATCH 8 None MEM: 1449.77 MB LDB: TIME 3.70661 LOAD: AVG 0.682586 MAX 0.821348 PROXIES: TOTAL 13528 MAXPE 10 MAXPATCH 9 TorusLB MEM: 1449.77 MB LDB: ============== END OF LOAD BALANCING =============== 3.74665 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 3.81205 Info: Initial time: 1920 CPUs 0.0090864 s/step 0.0525833 days/ns 1449.77 MB memory TIMING: 240 CPU: 1.9707, 0.00681564/step Wall: 2.81648, 0.0102021/step, 0.00272056 hours remaining, 1449.769531 MB of memory in use. ENERGY: 240 38999.9113 107328.6135 82021.5299 5144.2261 -4015429.4394 291783.7389 0.0000 0.0000 644288.1320 -2845863.2877 291.7662 -3490151.4197 -2843377.6876 291.1957 -3.4129 72.8470 10346663.1806 1.5573 1.6135 LDB: ============= START OF LOAD BALANCING ============== 4.94788 LDB: Largest compute 3352 load 0.097242 is 11.4% of average load 0.853484 LDB: Average compute 0.028014 is 3.3% of average load 0.853484 LDB: TIME 4.96269 LOAD: AVG 0.853485 MAX 1.07965 PROXIES: TOTAL 13528 MAXPE 10 MAXPATCH 9 None MEM: 1450.19 MB LDB: TIME 4.99102 LOAD: AVG 0.853485 MAX 0.902139 PROXIES: TOTAL 16265 MAXPE 23 MAXPATCH 17 RefineTorusLB MEM: 1450.19 MB LDB: ============== END OF LOAD BALANCING =============== 5.01899 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 5.07918 Info: Initial time: 1920 CPUs 0.00946755 s/step 0.0547891 days/ns 1450.19 MB memory TIMING: 360 CPU: 2.77958, 0.00674064/step Wall: 4.08409, 0.0105634/step, 0.0024648 hours remaining, 1450.191406 MB of memory in use. ENERGY: 360 39507.7186 106885.6352 82146.4385 5122.4192 -4006575.3498 288108.0573 0.0000 0.0000 647665.7590 -2837139.3220 293.2958 -3484805.0810 -2834615.2835 292.4294 -127.5519 -51.4352 10353285.0246 -0.7276 -0.8294 LDB: ============= START OF LOAD BALANCING ============== 6.17339 LDB: Largest compute 3352 load 0.099045 is 11.3% of average load 0.877071 LDB: Average compute 0.028053 is 3.2% of average load 0.877071 LDB: TIME 6.18523 LOAD: AVG 0.877074 MAX 1.00356 PROXIES: TOTAL 16265 MAXPE 23 MAXPATCH 17 None MEM: 1450.38 MB LDB: TIME 6.19888 LOAD: AVG 0.877074 MAX 0.926451 PROXIES: TOTAL 16150 MAXPE 23 MAXPATCH 17 RefineTorusLB MEM: 1450.38 MB LDB: ============== END OF LOAD BALANCING =============== 6.22277 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 6.28252 Info: Benchmark time: 1920 CPUs 0.00909524 s/step 0.0526345 days/ns 1450.38 MB memory TIMING: 480 CPU: 3.53446, 0.00629071/step Wall: 5.28484, 0.0100063/step, 0.00200125 hours remaining, 1450.375000 MB of memory in use. ENERGY: 480 39082.0664 107171.2503 81977.2106 5108.6792 -3998766.5380 286957.7544 0.0000 0.0000 648405.7759 -2830063.8014 293.6309 -3478469.5772 -2827458.6761 293.5185 -73.7260 2.4431 10354529.3185 -2.1634 -2.0979 Info: Benchmark time: 1920 CPUs 0.00896654 s/step 0.0518897 days/ns 1450.38 MB memory TIMING: 600 CPU: 4.16237, 0.00523253/step Wall: 6.36096, 0.00896767/step, 0.00149461 hours remaining, 1450.375000 MB of memory in use. ENERGY: 600 38983.7013 107664.9644 81989.1279 5053.3938 -3995160.1026 286496.6787 0.0000 0.0000 650610.3878 -2824361.8486 294.6293 -3474972.2364 -2821771.8749 294.1773 -45.3888 29.0385 10353870.6386 -2.0034 -1.9765 Info: Benchmark time: 1920 CPUs 0.00883847 s/step 0.0511486 days/ns 1450.38 MB memory TIMING: 720 CPU: 4.77427, 0.00509922/step Wall: 7.42171, 0.00883959/step, 0.00117861 hours remaining, 1450.375000 MB of memory in use. ENERGY: 720 39055.1063 107294.1697 82061.8298 5063.5042 -3988960.8310 283257.4531 0.0000 0.0000 652067.5854 -2820161.1825 295.2891 -3472228.7680 -2817637.6729 294.8910 -107.4579 -32.3955 10357881.8130 1.2361 1.2431 Info: Benchmark time: 1920 CPUs 0.00887271 s/step 0.0513467 days/ns 1450.38 MB memory TIMING: 840 CPU: 5.39118, 0.00514089/step Wall: 8.48661, 0.0088742/step, 0.00088742 hours remaining, 1450.375000 MB of memory in use. ENERGY: 840 39005.5394 107528.2309 81990.0477 5099.5106 -3985400.2739 282919.2854 0.0000 0.0000 653417.2448 -2815440.4152 295.9003 -3468857.6599 -2812885.3986 295.4693 -72.5336 3.2425 10364236.9134 0.5291 0.4979 Info: Benchmark time: 1920 CPUs 0.00870767 s/step 0.0503916 days/ns 1450.38 MB memory TIMING: 960 CPU: 5.99109, 0.00499923/step Wall: 9.5317, 0.00870902/step, 0.000580601 hours remaining, 1450.375000 MB of memory in use. ENERGY: 960 39118.7935 107519.2632 82133.5263 4986.5326 -3982327.9664 282125.7963 0.0000 0.0000 653850.2430 -2812593.8115 296.0964 -3466444.0545 -2810016.7788 296.0422 -79.3955 -4.6322 10361075.7863 0.8706 0.8822 Info: Benchmark time: 1920 CPUs 0.00881574 s/step 0.051017 days/ns 1450.38 MB memory TIMING: 1080 CPU: 6.602, 0.0050909/step Wall: 10.5897, 0.0088169/step, 0.000293897 hours remaining, 1450.375000 MB of memory in use. ENERGY: 1080 39217.7353 107379.4445 82185.6450 5184.1612 -3980877.1128 281526.4861 0.0000 0.0000 654779.3461 -2810604.2945 296.5172 -3465383.6406 -2808050.7766 296.1426 -97.9568 -22.1171 10365049.7927 -0.7881 -0.7849 TIMING: 1200 CPU: 7.2129, 0.00509088/step Wall: 11.6423, 0.00877143/step, 0 hours remaining, 1450.375000 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 38887.6755 107797.1022 82288.1409 5099.6564 -3977625.7815 280729.8250 0.0000 0.0000 653940.3996 -2808882.9818 296.1372 -3462823.3814 -2806356.8849 296.4014 -54.6931 20.0980 10368633.0314 -1.2205 -1.3565 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 0.187 seconds(file I/O: 0.186 secs), 1450.375 MB of memory in use The last velocity output (seq=-2) takes 0.273 seconds(file I/O: 0.093 secs), 1450.375 MB of memory in use ==================================================== WallClock: 13.958325 CPUTime: 9.295586 Memory: 1450.375000 MB TACC: Shutdown complete. Exiting.