TACC: Starting up job 6245025 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 3.803 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 2 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.017 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 32 c546-903.stampede.tacc.utexas.edu tg455591 Info: Running on 32 processors, 32 nodes, 2 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0767539 s Info: 112.648 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: 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 1450742552 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: 0.005548 Info: Info: Entering startup at 0.159404 s, 208.293 MB of memory in use Info: Startup phase 0 took 0.00210786 s, 208.293 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0702491 s, 209.367 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: 8 24 Info: OUTPUT PROC LOCATIONS: 16 Info: Startup phase 2 took 0.0404019 s, 210.27 MB of memory in use Info: Startup phase 3 took 0.157012 s, 210.27 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 -0.00760205 0.00522109 -0.00366287 Info: Startup phase 4 took 0.0326941 s, 218.66 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 0.0530429 s, 219.691 MB of memory in use Info: TORUS A SIZE 32 USING 0 16 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 17 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0165231 s, 230.133 MB of memory in use Info: PME using 31 and 31 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ... Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ... Info: PME USING 31 GRID NODES AND 31 TRANS NODES Info: Startup phase 7 took 0.164885 s, 236.863 MB of memory in use Info: Startup phase 8 took 0.00566602 s, 236.863 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00764608 s, 236.863 MB of memory in use Info: CREATING 44100 COMPUTE OBJECTS Info: Startup phase 10 took 0.0197179 s, 240.324 MB of memory in use Info: useSync: 0 useProxySync: 0 Info: Startup phase 11 took 0.00129914 s, 240.324 MB of memory in use Info: Startup phase 12 took 0.00129485 s, 249.246 MB of memory in use Info: Finished startup at 0.731944 s, 249.246 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 -4134759.4111 375583.0490 0.0000 0.0000 657247.8903 -2871513.8390 297.6350 -3528761.7293 -2868955.4211 297.6350 2249.0862 2336.8795 10194598.5131 2249.0862 2336.8795 LDB: ============= START OF LOAD BALANCING ============== 9.99762 LDB: ============== END OF LOAD BALANCING =============== 10.0034 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 10.0048 LDB: ============= START OF LOAD BALANCING ============== 46.3558 LDB: Largest compute 2966 load 0.154454 is 0.4% of average load 34.635007 LDB: Average compute 0.024192 is 0.1% of average load 34.635007 LDB: Partitioning computes with target load 3.463501 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023401 LDB: ============== END OF LOAD BALANCING =============== 46.3787 LDB: =============== DONE WITH MIGRATION ================ 46.4835 Info: useSync: 0 useProxySync: 0 Info: Initial time: 32 CPUs 0.379558 s/step 2.19652 days/ns 360.375 MB memory TIMING: 120 CPU: 46.4509, 0.380184/step Wall: 46.527, 0.380693/step, 0.114208 hours remaining, 360.375000 MB of memory in use. ENERGY: 120 39580.6203 106930.3379 81899.3010 5179.8287 -4029635.0506 296859.6900 0.0000 0.0000 641437.1760 -2857748.0967 290.4752 -3499185.2727 -2855269.6495 289.7851 -41.8374 35.6772 10352433.7529 -5.9295 -4.9030 LDB: ============= START OF LOAD BALANCING ============== 55.64 LDB: ============== END OF LOAD BALANCING =============== 55.6405 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 55.6419 LDB: ============= START OF LOAD BALANCING ============== 92.0005 LDB: Largest compute 3348 load 0.152834 is 0.4% of average load 34.551563 LDB: Average compute 0.024132 is 0.1% of average load 34.551563 LDB: TIME 92.0182 LOAD: AVG 34.5516 MAX 36.3505 PROXIES: TOTAL 3056 MAXPE 100 MAXPATCH 3 None MEM: 370.027 MB LDB: TIME 92.0432 LOAD: AVG 34.5516 MAX 35.0728 PROXIES: TOTAL 3056 MAXPE 100 MAXPATCH 3 TorusLB MEM: 370.027 MB LDB: ============== END OF LOAD BALANCING =============== 92.0647 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 92.1868 Info: Initial time: 32 CPUs 0.37927 s/step 2.19485 days/ns 370.027 MB memory TIMING: 240 CPU: 92.087, 0.380301/step Wall: 92.2281, 0.380843/step, 0.101558 hours remaining, 370.027344 MB of memory in use. ENERGY: 240 39187.3215 107499.8597 81997.6188 5145.6037 -4016208.8893 291573.7893 0.0000 0.0000 644637.4912 -2846167.2051 291.9244 -3490804.6963 -2843652.9187 291.1071 -94.1591 -18.0761 10350731.2681 2.1150 2.2238 LDB: ============= START OF LOAD BALANCING ============== 136.617 LDB: Largest compute 3609 load 0.191721 is 0.4% of average load 43.399593 LDB: Average compute 0.030264 is 0.1% of average load 43.399593 LDB: TIME 136.635 LOAD: AVG 43.3996 MAX 44.415 PROXIES: TOTAL 3056 MAXPE 100 MAXPATCH 3 None MEM: 392.039 MB LDB: TIME 136.64 LOAD: AVG 43.3996 MAX 44.415 PROXIES: TOTAL 3056 MAXPE 100 MAXPATCH 3 RefineTorusLB MEM: 392.039 MB LDB: TIME 136.656 LOAD: AVG 43.3996 MAX 43.8666 PROXIES: TOTAL 3059 MAXPE 100 MAXPATCH 3 RefineTorusLB MEM: 392.039 MB LDB: ============== END OF LOAD BALANCING =============== 136.658 LDB: =============== DONE WITH MIGRATION ================ 136.719 Info: useSync: 0 useProxySync: 0 Info: Initial time: 32 CPUs 0.370099 s/step 2.14178 days/ns 392.039 MB memory TIMING: 360 CPU: 136.542, 0.37046/step Wall: 136.742, 0.370948/step, 0.0865545 hours remaining, 392.039062 MB of memory in use. ENERGY: 360 39275.8326 107643.6711 82039.4855 5139.8597 -4006687.0905 288666.2877 0.0000 0.0000 646200.6277 -2837721.3263 292.6323 -3483921.9540 -2835259.0773 292.5689 -109.4137 -34.3026 10356018.4455 0.7039 0.5923 LDB: ============= START OF LOAD BALANCING ============== 180.866 LDB: Largest compute 3996 load 0.194848 is 0.4% of average load 43.429381 LDB: Average compute 0.030282 is 0.1% of average load 43.429381 LDB: TIME 180.883 LOAD: AVG 43.4294 MAX 44.0103 PROXIES: TOTAL 3056 MAXPE 100 MAXPATCH 3 None MEM: 395.016 MB LDB: TIME 180.888 LOAD: AVG 43.4294 MAX 44.0103 PROXIES: TOTAL 3059 MAXPE 100 MAXPATCH 3 RefineTorusLB MEM: 395.016 MB LDB: TIME 180.891 LOAD: AVG 43.4294 MAX 43.8929 PROXIES: TOTAL 3059 MAXPE 100 MAXPATCH 3 RefineTorusLB MEM: 395.016 MB LDB: ============== END OF LOAD BALANCING =============== 180.892 LDB: =============== DONE WITH MIGRATION ================ 181.005 Info: useSync: 0 useProxySync: 0 Info: Benchmark time: 32 CPUs 0.367884 s/step 2.12896 days/ns 395.016 MB memory TIMING: 480 CPU: 180.768, 0.368544/step Wall: 181.027, 0.369043/step, 0.0738086 hours remaining, 395.015625 MB of memory in use. ENERGY: 480 39176.6026 107188.9862 81893.5338 5091.5038 -3999494.9730 287164.8310 0.0000 0.0000 648658.0231 -2830321.4925 293.7451 -3478979.5156 -2827888.2725 293.1405 -44.4655 32.0507 10349664.1294 1.5068 1.4125 Info: Benchmark time: 32 CPUs 0.368096 s/step 2.13018 days/ns 395.016 MB memory TIMING: 600 CPU: 224.882, 0.367619/step Wall: 225.199, 0.368098/step, 0.0613497 hours remaining, 395.015625 MB of memory in use. ENERGY: 600 39075.1016 107671.0029 81990.9285 5083.6489 -3995340.6544 285584.1620 0.0000 0.0000 651437.8455 -2824497.9651 295.0040 -3475935.8106 -2821896.7892 294.1628 -42.2409 34.0501 10348317.6269 1.9574 1.9512 Info: Benchmark time: 32 CPUs 0.368163 s/step 2.13057 days/ns 395.266 MB memory TIMING: 720 CPU: 269.005, 0.367694/step Wall: 269.379, 0.368165/step, 0.0490887 hours remaining, 395.265625 MB of memory in use. ENERGY: 720 39603.3908 107759.7946 81843.1986 5177.9115 -3989226.5393 283650.6088 0.0000 0.0000 651481.8115 -2819709.8237 295.0239 -3471191.6352 -2817211.2259 294.8911 -153.5493 -79.0366 10359641.0060 -0.4779 -0.3875 Info: Benchmark time: 32 CPUs 0.368474 s/step 2.13238 days/ns 395.266 MB memory TIMING: 840 CPU: 313.163, 0.367986/step Wall: 313.596, 0.368477/step, 0.0368477 hours remaining, 395.265625 MB of memory in use. ENERGY: 840 39369.1858 107741.4143 82127.7039 5189.5747 -3985244.1037 282911.1107 0.0000 0.0000 651682.7630 -2816222.3514 295.1149 -3467905.1144 -2813630.7925 295.3430 -69.5834 4.8697 10360781.5686 2.2336 2.1646 Info: Benchmark time: 32 CPUs 0.368439 s/step 2.13217 days/ns 390.266 MB memory TIMING: 960 CPU: 357.318, 0.367952/step Wall: 357.809, 0.368442/step, 0.0245628 hours remaining, 390.265625 MB of memory in use. ENERGY: 960 39201.4019 107565.7829 82032.8507 5086.1147 -3985025.7103 284427.0411 0.0000 0.0000 652775.8038 -2813936.7153 295.6099 -3466712.5191 -2811449.7216 295.8433 -8.8397 66.1682 10357425.8696 0.3013 0.1098 Info: Benchmark time: 32 CPUs 0.368108 s/step 2.13026 days/ns 394.266 MB memory TIMING: 1080 CPU: 401.432, 0.367619/step Wall: 401.982, 0.368111/step, 0.0122704 hours remaining, 394.265625 MB of memory in use. ENERGY: 1080 39116.6920 107381.0564 81922.0122 5074.8596 -3980561.5465 282377.6797 0.0000 0.0000 654006.4844 -2810682.7622 296.1672 -3464689.2466 -2808099.6330 296.0359 -53.4584 21.4268 10363997.9367 0.1626 0.1283 TIMING: 1200 CPU: 445.406, 0.366453/step Wall: 446.012, 0.366918/step, 0 hours remaining, 396.265625 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 39183.3345 107242.9585 82061.2071 5198.0858 -3979012.9415 282113.0632 0.0000 0.0000 655193.7245 -2808020.5678 296.7048 -3463214.2923 -2805492.0618 296.5543 -58.2139 18.6469 10368206.9530 0.7624 0.7843 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 0.094 seconds(file I/O: 0.093 secs), 396.266 MB of memory in use The last velocity output (seq=-2) takes 0.174 seconds(file I/O: 0.087 secs), 396.266 MB of memory in use ==================================================== WallClock: 446.970917 CPUTime: 446.236176 Memory: 396.265625 MB