TACC: Starting up job 6245020 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 1.187 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 16 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.028 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 240 c451-601.stampede.tacc.utexas.edu tg455591 Info: Running on 240 processors, 16 nodes, 16 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0930588 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1196.73 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 1450742605 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: 0.00569081 Info: Info: Entering startup at 0.185383 s, 1294.57 MB of memory in use Info: Startup phase 0 took 0.00464106 s, 1294.57 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0148799 s, 1294.89 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: 60 180 Info: OUTPUT PROC LOCATIONS: 120 Info: Startup phase 2 took 0.0397069 s, 1295.86 MB of memory in use Info: Startup phase 3 took 0.0995162 s, 1295.86 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 -0.0056417 0.00462474 5.314e-05 Info: Startup phase 4 took 0.0420809 s, 1416.3 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 0.0553591 s, 1416.3 MB of memory in use Info: TORUS A SIZE 240 USING 0 15 30 45 60 75 90 105 120 135 150 165 180 195 210 225 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 226 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0198491 s, 1426.78 MB of memory in use Info: PME using 108 and 108 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 3 5 7 9 11 13 16 18 20 22 ... Info: PME TRANS LOCATIONS: 1 2 4 6 10 12 14 17 19 21 ... Info: PME USING 16 GRID NODES AND 16 TRANS NODES Info: Startup phase 7 took 0.0688298 s, 1433.66 MB of memory in use Info: Startup phase 8 took 0.00743508 s, 1433.66 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.0394151 s, 1433.66 MB of memory in use Info: CREATING 45135 COMPUTE OBJECTS Info: Startup phase 10 took 0.036217 s, 1433.66 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 0.00592184 s, 1433.66 MB of memory in use Info: Startup phase 12 took 0.000174046 s, 1433.66 MB of memory in use Info: Finished startup at 0.619409 s, 1433.66 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 657775.1642 -2870986.5653 297.8738 -3528761.7296 -2868428.2459 297.8738 2252.2285 2340.0378 10194598.5131 2252.2285 2340.0378 LDB: ============= START OF LOAD BALANCING ============== 2.19476 LDB: ============== END OF LOAD BALANCING =============== 2.20041 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 2.20237 LDB: ============= START OF LOAD BALANCING ============== 8.47675 LDB: Largest compute 3241 load 0.152761 is 3.2% of average load 4.785796 LDB: Average compute 0.024219 is 0.5% of average load 4.785796 LDB: Partitioning computes with target load 0.478580 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023467 LDB: ============== END OF LOAD BALANCING =============== 8.51117 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 8.57938 Info: Initial time: 240 CPUs 0.0644774 s/step 0.373133 days/ns 1449.92 MB memory TIMING: 120 CPU: 6.29304, 0.0508173/step Wall: 8.14827, 0.0653991/step, 0.0196197 hours remaining, 1449.917969 MB of memory in use. ENERGY: 120 39574.3768 107424.7210 81889.2190 5059.2275 -4027959.0427 295904.6897 0.0000 0.0000 640842.9546 -2857263.8541 290.2061 -3498106.8087 -2854834.4925 289.9534 -78.4091 -2.7176 10347441.6078 -7.2894 -6.3349 LDB: ============= START OF LOAD BALANCING ============== 10.2767 LDB: ============== END OF LOAD BALANCING =============== 10.2772 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 10.2789 LDB: ============= START OF LOAD BALANCING ============== 17.0056 LDB: Largest compute 3241 load 0.153793 is 3.2% of average load 4.778234 LDB: Average compute 0.024176 is 0.5% of average load 4.778234 LDB: TIME 17.0306 LOAD: AVG 4.77823 MAX 5.6924 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 None MEM: 1453.91 MB LDB: TIME 17.0639 LOAD: AVG 4.77823 MAX 4.95246 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 TorusLB MEM: 1453.91 MB LDB: ============== END OF LOAD BALANCING =============== 17.1498 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 17.2174 Info: Initial time: 240 CPUs 0.0703924 s/step 0.407364 days/ns 1450.41 MB memory TIMING: 240 CPU: 13.217, 0.0576996/step Wall: 16.8096, 0.0721778/step, 0.0192474 hours remaining, 1450.406250 MB of memory in use. ENERGY: 240 39198.3148 106947.1998 81942.3348 5109.6253 -4017198.8314 292673.8924 0.0000 0.0000 644957.0697 -2846370.3945 292.0691 -3491327.4642 -2843831.6653 291.1410 12.2458 88.5125 10338928.7157 1.7387 1.7728 LDB: ============= START OF LOAD BALANCING ============== 25.0039 LDB: Largest compute 3021 load 0.237538 is 3.9% of average load 6.021749 LDB: Average compute 0.030334 is 0.5% of average load 6.021749 LDB: TIME 25.0267 LOAD: AVG 6.02175 MAX 6.36179 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 None MEM: 1455.91 MB LDB: TIME 25.0324 LOAD: AVG 6.02175 MAX 6.36179 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 RefineTorusLB MEM: 1455.91 MB LDB: TIME 25.0349 LOAD: AVG 6.02175 MAX 6.11596 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 RefineTorusLB MEM: 1455.91 MB LDB: ============== END OF LOAD BALANCING =============== 25.0403 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 25.0981 Info: Initial time: 240 CPUs 0.0645318 s/step 0.373448 days/ns 1455.91 MB memory TIMING: 360 CPU: 19.2541, 0.050309/step Wall: 24.6479, 0.0653188/step, 0.0152411 hours remaining, 1455.914062 MB of memory in use. ENERGY: 360 39255.7691 107508.4242 82015.7122 5149.7531 -4006599.0642 288700.8546 0.0000 0.0000 647167.4903 -2836801.0607 293.0701 -3483968.5510 -2834252.9695 292.5532 -88.3983 -10.4440 10343379.3551 -3.7887 -3.8775 LDB: ============= START OF LOAD BALANCING ============== 32.8112 LDB: Largest compute 2750 load 0.198676 is 3.3% of average load 6.031307 LDB: Average compute 0.030349 is 0.5% of average load 6.031307 LDB: TIME 32.8322 LOAD: AVG 6.03131 MAX 6.33483 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 None MEM: 1459.92 MB LDB: TIME 32.838 LOAD: AVG 6.03131 MAX 6.33483 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 RefineTorusLB MEM: 1459.92 MB LDB: TIME 32.8402 LOAD: AVG 6.03131 MAX 6.12433 PROXIES: TOTAL 6631 MAXPE 33 MAXPATCH 8 RefineTorusLB MEM: 1459.92 MB LDB: ============== END OF LOAD BALANCING =============== 32.8482 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 32.9055 Info: Benchmark time: 240 CPUs 0.0643264 s/step 0.37226 days/ns 1459.92 MB memory TIMING: 480 CPU: 25.2632, 0.0500757/step Wall: 32.4616, 0.0651141/step, 0.0130228 hours remaining, 1459.917969 MB of memory in use. ENERGY: 480 39048.9275 107433.3552 82153.3613 5111.5500 -3996892.2489 284860.4959 0.0000 0.0000 647907.8840 -2830376.6751 293.4054 -3478284.5591 -2827762.0853 293.3863 -94.1548 -18.0356 10344961.2928 -1.5214 -1.4616 Info: Benchmark time: 240 CPUs 0.06572 s/step 0.380324 days/ns 1459.92 MB memory TIMING: 600 CPU: 31.3342, 0.0505923/step Wall: 40.3481, 0.0657213/step, 0.0109536 hours remaining, 1459.917969 MB of memory in use. ENERGY: 600 39231.5727 107348.0402 82133.4238 5080.1362 -3993484.2123 284172.0804 0.0000 0.0000 649569.1861 -2825949.7729 294.1577 -3475518.9589 -2823327.9565 294.0148 -113.1052 -41.2076 10348770.8136 3.5998 3.6367 Info: Benchmark time: 240 CPUs 0.0672972 s/step 0.389451 days/ns 1459.92 MB memory TIMING: 720 CPU: 37.5933, 0.0521587/step Wall: 48.4239, 0.0672985/step, 0.00897314 hours remaining, 1459.917969 MB of memory in use. ENERGY: 720 39380.4321 107139.9256 82130.6808 5095.2081 -3993180.8340 286433.0940 0.0000 0.0000 651408.5265 -2821592.9669 294.9907 -3473001.4934 -2818973.0381 294.6911 -10.0426 64.5727 10342932.9301 -2.3678 -2.3324 Info: Benchmark time: 240 CPUs 0.0599969 s/step 0.347204 days/ns 1459.92 MB memory TIMING: 840 CPU: 42.9955, 0.0450182/step Wall: 55.6238, 0.0599985/step, 0.00599985 hours remaining, 1459.917969 MB of memory in use. ENERGY: 840 39022.8083 107385.1410 82042.4459 5035.9334 -3986645.3122 283929.1748 0.0000 0.0000 651298.9567 -2817930.8519 294.9411 -3469229.8087 -2815287.1407 295.0490 -88.4850 -12.2718 10356188.6875 3.8810 3.8930 Info: Benchmark time: 240 CPUs 0.0534636 s/step 0.309396 days/ns 1459.92 MB memory TIMING: 960 CPU: 47.6358, 0.0386691/step Wall: 62.0396, 0.053465/step, 0.00356433 hours remaining, 1459.917969 MB of memory in use. ENERGY: 960 39241.4221 107768.7290 82047.9740 5209.7738 -3984350.9232 282505.0457 0.0000 0.0000 653548.2181 -2814029.7606 295.9596 -3467577.9787 -2811429.4800 295.5498 -42.3678 31.7372 10355267.3627 1.7368 1.7079 Info: Benchmark time: 240 CPUs 0.0532911 s/step 0.308397 days/ns 1459.92 MB memory TIMING: 1080 CPU: 52.2321, 0.0383025/step Wall: 68.4347, 0.0532925/step, 0.00177642 hours remaining, 1459.917969 MB of memory in use. ENERGY: 1080 39121.3623 107510.2570 82125.6813 5114.2022 -3983514.7078 282122.1100 0.0000 0.0000 655074.5896 -2812446.5053 296.6509 -3467521.0949 -2809798.9810 295.9638 -130.2822 -56.8480 10358055.4126 -0.0742 -0.1577 TIMING: 1200 CPU: 56.8484, 0.0384692/step Wall: 74.8261, 0.0532621/step, 0 hours remaining, 1459.917969 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 39134.5987 107495.1549 81950.4921 5072.3426 -3980656.8989 283221.5478 0.0000 0.0000 653897.6771 -2809885.0858 296.1179 -3463782.7629 -2807362.5903 296.2405 -9.1514 65.0489 10355545.3362 -1.6858 -1.7436 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 0.125 seconds(file I/O: 0.124 secs), 1459.918 MB of memory in use The last velocity output (seq=-2) takes 0.218 seconds(file I/O: 0.100 secs), 1459.918 MB of memory in use ==================================================== WallClock: 75.707382 CPUTime: 57.659233 Memory: 1459.917969 MB TACC: Shutdown complete. Exiting.