TACC: Starting up job 6245030 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 14.153 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 64 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.031 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 1024 c402-303.stampede.tacc.utexas.edu tg455591 Info: Running on 1024 processors, 1024 nodes, 64 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.14468 s Info: 255.566 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 LOAD FROM NODE 1 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 1450742545 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: 0.00559306 Info: Info: Entering startup at 0.250709 s, 351.223 MB of memory in use Info: Startup phase 0 took 0.012969 s, 351.223 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.086504 s, 351.891 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: 256 768 Info: OUTPUT PROC LOCATIONS: 512 Info: Startup phase 2 took 0.04266 s, 352.793 MB of memory in use Info: Startup phase 3 took 0.160166 s, 352.793 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 -0.00402567 -0.00274994 -0.00952235 Info: Startup phase 4 took 0.043159 s, 361.184 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 0.0696762 s, 362.223 MB of memory in use Info: TORUS A SIZE 1024 USING 0 16 32 48 64 80 96 112 128 144 160 176 192 208 224 240 256 272 288 304 320 336 352 368 384 400 416 432 448 464 480 496 512 528 544 560 576 592 608 624 640 656 672 688 704 720 736 752 768 784 800 816 832 848 864 880 896 912 928 944 960 976 992 1008 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 1009 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0298169 s, 372.668 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 2 3 4 5 6 7 8 9 10 ... Info: PME Y PENCIL LOCATIONS: 1 2 3 5 6 7 9 10 11 13 ... Info: PME X PENCIL LOCATIONS: 1 3 4 5 6 7 8 9 11 12 ... Info: Startup phase 7 took 0.208223 s, 383.895 MB of memory in use Info: Startup phase 8 took 0.021534 s, 383.895 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.0204139 s, 383.895 MB of memory in use Info: CREATING 49050 COMPUTE OBJECTS Info: Startup phase 10 took 0.0330601 s, 383.895 MB of memory in use Info: useSync: 1 useProxySync: 0 Info: Startup phase 11 took 0.00176811 s, 383.895 MB of memory in use Info: Startup phase 12 took 0.00117493 s, 383.895 MB of memory in use Info: Finished startup at 0.981834 s, 383.895 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 -4134759.4116 375583.0490 0.0000 0.0000 657382.0760 -2871379.6538 297.6958 -3528761.7298 -2868821.1498 297.6958 2247.7536 2335.6034 10194598.5131 2247.7536 2335.6034 LDB: ============= START OF LOAD BALANCING ============== 1.5164 LDB: ============== END OF LOAD BALANCING =============== 1.53695 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 1.53948 LDB: ============= START OF LOAD BALANCING ============== 3.29506 LDB: Largest compute 3840 load 0.152569 is 13.5% of average load 1.129688 LDB: Average compute 0.024089 is 2.1% of average load 1.129688 LDB: Partitioning computes with target load 0.112969 LDB: Increased migratable compute count from 41743 to 43828 LDB: Largest unpartitionable compute is 0.023610 LDB: ============== END OF LOAD BALANCING =============== 3.45532 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 3.60524 Info: Initial time: 1024 CPUs 0.018381 s/step 0.106371 days/ns 383.895 MB memory TIMING: 120 CPU: 2.6666, 0.0209718/step Wall: 2.69754, 0.0211798/step, 0.00635395 hours remaining, 383.894531 MB of memory in use. ENERGY: 120 39385.5072 107500.2215 81824.6708 5138.4460 -4027566.7490 296787.1123 0.0000 0.0000 641336.4682 -2855594.3231 290.4296 -3496930.7913 -2853044.8135 289.7980 -4.2789 73.4165 10351907.1261 -2.5724 -1.5311 LDB: ============= START OF LOAD BALANCING ============== 4.04973 LDB: ============== END OF LOAD BALANCING =============== 4.05065 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 4.0532 LDB: ============= START OF LOAD BALANCING ============== 5.80672 LDB: Largest compute 3796 load 0.125933 is 11.3% of average load 1.115801 LDB: Average compute 0.022927 is 2.1% of average load 1.115801 LDB: TIME 5.93447 LOAD: AVG 1.1158 MAX 1.73968 PROXIES: TOTAL 10800 MAXPE 17 MAXPATCH 8 None MEM: 396.902 MB LDB: TIME 5.97447 LOAD: AVG 1.1158 MAX 1.18655 PROXIES: TOTAL 10800 MAXPE 17 MAXPATCH 8 TorusLB MEM: 396.902 MB LDB: ============== END OF LOAD BALANCING =============== 6.02904 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 6.18546 Info: Initial time: 1024 CPUs 0.0182109 s/step 0.105387 days/ns 377.957 MB memory TIMING: 240 CPU: 5.22321, 0.0213051/step Wall: 5.26685, 0.021411/step, 0.00570959 hours remaining, 377.957031 MB of memory in use. ENERGY: 240 39314.8714 107248.5228 81946.0289 5142.0154 -4015685.5272 291351.3029 0.0000 0.0000 644781.1984 -2845901.5874 291.9895 -3490682.7858 -2843388.8325 291.2653 -62.2990 12.0220 10343424.4677 1.0592 1.2702 LDB: ============= START OF LOAD BALANCING ============== 7.76871 LDB: Largest compute 4094 load 0.161073 is 11.5% of average load 1.402891 LDB: Average compute 0.028803 is 2.1% of average load 1.402891 LDB: TIME 7.89927 LOAD: AVG 1.40289 MAX 1.5365 PROXIES: TOTAL 10800 MAXPE 17 MAXPATCH 8 None MEM: 396.902 MB LDB: TIME 7.90528 LOAD: AVG 1.40289 MAX 1.5365 PROXIES: TOTAL 10800 MAXPE 17 MAXPATCH 8 RefineTorusLB MEM: 396.902 MB LDB: TIME 7.90781 LOAD: AVG 1.40289 MAX 1.44965 PROXIES: TOTAL 10801 MAXPE 17 MAXPATCH 8 RefineTorusLB MEM: 396.902 MB LDB: ============== END OF LOAD BALANCING =============== 7.91151 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 8.049 Info: Initial time: 1024 CPUs 0.0132077 s/step 0.0764335 days/ns 376.312 MB memory TIMING: 360 CPU: 7.08192, 0.0154893/step Wall: 7.13333, 0.0155539/step, 0.00362925 hours remaining, 376.312500 MB of memory in use. ENERGY: 360 39224.3861 107864.4054 81779.3285 5183.7258 -4007054.9839 288855.1850 0.0000 0.0000 646310.4484 -2837837.5048 292.6820 -3484147.9532 -2835329.8402 292.4836 -116.3523 -42.6806 10345652.0688 0.9055 0.7778 LDB: ============= START OF LOAD BALANCING ============== 9.56832 LDB: Largest compute 4197 load 0.162108 is 11.6% of average load 1.402736 LDB: Average compute 0.028802 is 2.1% of average load 1.402736 LDB: TIME 9.6993 LOAD: AVG 1.40274 MAX 1.48006 PROXIES: TOTAL 10800 MAXPE 17 MAXPATCH 8 None MEM: 396.902 MB LDB: TIME 9.70533 LOAD: AVG 1.40274 MAX 1.48006 PROXIES: TOTAL 10801 MAXPE 17 MAXPATCH 8 RefineTorusLB MEM: 396.902 MB LDB: TIME 9.70758 LOAD: AVG 1.40274 MAX 1.4494 PROXIES: TOTAL 10801 MAXPE 17 MAXPATCH 8 RefineTorusLB MEM: 396.902 MB LDB: ============== END OF LOAD BALANCING =============== 9.71162 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 9.8531 Info: Benchmark time: 1024 CPUs 0.0126264 s/step 0.0730692 days/ns 376.035 MB memory TIMING: 480 CPU: 8.87565, 0.0149477/step Wall: 8.93455, 0.0150102/step, 0.00300204 hours remaining, 376.035156 MB of memory in use. ENERGY: 480 39004.3073 106679.4049 81948.4079 5015.3282 -4001147.9922 287322.3479 0.0000 0.0000 649707.7333 -2831470.4627 294.2205 -3481178.1960 -2828896.3687 293.3984 -93.1039 -15.2469 10348112.1175 5.1807 5.0215 Info: Benchmark time: 1024 CPUs 0.0125849 s/step 0.0728295 days/ns 376.035 MB memory TIMING: 600 CPU: 10.3814, 0.0125481/step Wall: 10.4455, 0.0125913/step, 0.00209854 hours remaining, 376.035156 MB of memory in use. ENERGY: 600 38979.0415 106784.4939 81949.4735 5156.8608 -3993393.5894 284151.0436 0.0000 0.0000 649853.1578 -2826519.5185 294.2863 -3476372.6762 -2823961.2752 293.8855 -146.3869 -70.9058 10351606.1726 1.7805 1.6255 Info: Benchmark time: 1024 CPUs 0.0126557 s/step 0.0732391 days/ns 376.035 MB memory TIMING: 720 CPU: 11.8982, 0.0126397/step Wall: 11.965, 0.0126621/step, 0.00168828 hours remaining, 376.035156 MB of memory in use. ENERGY: 720 39027.6144 106852.8012 82026.1331 5133.9941 -3992825.8128 286014.7540 0.0000 0.0000 651003.6231 -2822766.8929 294.8073 -3473770.5160 -2820187.9216 294.3620 -6.6064 66.9590 10351134.1599 1.2000 1.0615 Info: Benchmark time: 1024 CPUs 0.0126202 s/step 0.0730337 days/ns 376.035 MB memory TIMING: 840 CPU: 13.409, 0.0125898/step Wall: 13.4801, 0.0126266/step, 0.00126266 hours remaining, 376.035156 MB of memory in use. ENERGY: 840 39185.9578 107310.2753 82129.5685 5146.8773 -3987127.5833 282825.6771 0.0000 0.0000 652941.3946 -2817587.8326 295.6848 -3470529.2272 -2814956.4382 294.9821 -96.4735 -20.9775 10355356.5743 -1.6120 -1.6632 Info: Benchmark time: 1024 CPUs 0.0127017 s/step 0.0735054 days/ns 376.035 MB memory TIMING: 960 CPU: 14.9307, 0.0126814/step Wall: 15.0051, 0.0127081/step, 0.000847205 hours remaining, 376.035156 MB of memory in use. ENERGY: 960 39374.1983 107288.2870 82088.0317 5245.7632 -3984456.0930 282297.4441 0.0000 0.0000 653163.4913 -2814998.8773 295.7854 -3468162.3686 -2812493.8334 295.6147 -139.0538 -63.4687 10363773.6385 2.5349 2.3390 Info: Benchmark time: 1024 CPUs 0.0128032 s/step 0.0740926 days/ns 376.035 MB memory TIMING: 1080 CPU: 16.4645, 0.0127814/step Wall: 16.5423, 0.0128095/step, 0.000426985 hours remaining, 376.035156 MB of memory in use. ENERGY: 1080 39622.1179 107588.2394 82088.1989 5203.3703 -3986380.5346 284977.9524 0.0000 0.0000 653808.4198 -2813092.2359 296.0775 -3466900.6558 -2810498.5947 295.9839 2.0217 74.9373 10355624.3359 3.9234 3.7168 TIMING: 1200 CPU: 18.0023, 0.0128147/step Wall: 18.0838, 0.012846/step, 0 hours remaining, 376.035156 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 39386.6225 107203.6074 81925.0026 5162.5324 -3983233.5325 282808.8398 0.0000 0.0000 655163.5038 -2811583.4240 296.6911 -3466746.9278 -2809036.3867 296.0822 -55.1492 19.5673 10361847.3588 -1.4092 -1.3749 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 0.376 seconds(file I/O: 0.375 secs), 376.035 MB of memory in use The last velocity output (seq=-2) takes 0.545 seconds(file I/O: 0.177 secs), 376.035 MB of memory in use ==================================================== WallClock: 19.644053 CPUTime: 19.340059 Memory: 376.035156 MB