TACC: Starting up job 6245027 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 16.312 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 8 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 128 c466-102.stampede.tacc.utexas.edu tg455591 Info: Running on 128 processors, 128 nodes, 8 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0837359 s Info: 126.605 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 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 1450742557 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: 0.00578284 Info: Info: Entering startup at 0.177236 s, 222.25 MB of memory in use Info: Startup phase 0 took 0.00270915 s, 222.25 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.073468 s, 223.324 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: 32 96 Info: OUTPUT PROC LOCATIONS: 64 Info: Startup phase 2 took 0.0404398 s, 224.227 MB of memory in use Info: Startup phase 3 took 0.149794 s, 224.227 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 0.00189456 -0.00211891 -0.00675779 Info: Startup phase 4 took 0.0352659 s, 232.645 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 0.0540371 s, 233.648 MB of memory in use Info: TORUS A SIZE 128 USING 0 16 32 48 64 80 96 112 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 113 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0201521 s, 244.094 MB of memory in use Info: PME using 108 and 108 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 1 2 3 5 6 7 9 10 11 12 ... Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 8 9 10 11 ... Info: PME USING 108 GRID NODES AND 108 TRANS NODES Info: Startup phase 7 took 0.136205 s, 250.895 MB of memory in use Info: Startup phase 8 took 0.00580406 s, 250.895 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00996399 s, 250.895 MB of memory in use Info: CREATING 44575 COMPUTE OBJECTS Info: Startup phase 10 took 0.0180478 s, 250.895 MB of memory in use Info: useSync: 0 useProxySync: 0 Info: Startup phase 11 took 0.00144506 s, 250.895 MB of memory in use Info: Startup phase 12 took 0.00142598 s, 250.895 MB of memory in use Info: Finished startup at 0.725994 s, 250.895 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 -4134759.4114 375583.0490 0.0000 0.0000 658229.1467 -2870532.5829 298.0794 -3528761.7296 -2867973.9130 298.0794 2250.7043 2338.5746 10194598.5131 2250.7043 2338.5746 LDB: ============= START OF LOAD BALANCING ============== 3.21305 LDB: ============== END OF LOAD BALANCING =============== 3.22079 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 3.22228 LDB: ============= START OF LOAD BALANCING ============== 12.9126 LDB: Largest compute 3241 load 0.152935 is 1.8% of average load 8.684118 LDB: Average compute 0.024191 is 0.3% of average load 8.684118 LDB: Partitioning computes with target load 0.868412 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023928 LDB: ============== END OF LOAD BALANCING =============== 12.9388 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 13.0597 Info: Initial time: 128 CPUs 0.101107 s/step 0.585107 days/ns 252.613 MB memory TIMING: 120 CPU: 12.5201, 0.102126/step Wall: 12.5614, 0.10242/step, 0.0307259 hours remaining, 252.613281 MB of memory in use. ENERGY: 120 39669.9327 107331.8829 82018.7482 5135.7608 -4027095.8116 295618.3966 0.0000 0.0000 641734.0445 -2855587.0460 290.6096 -3497321.0904 -2853007.4362 289.9779 -69.8013 6.0793 10350051.1128 -4.5584 -3.6163 LDB: ============= START OF LOAD BALANCING ============== 15.4998 LDB: ============== END OF LOAD BALANCING =============== 15.5003 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 15.5018 LDB: ============= START OF LOAD BALANCING ============== 25.1675 LDB: Largest compute 3143 load 0.151704 is 1.8% of average load 8.663099 LDB: Average compute 0.024131 is 0.3% of average load 8.663099 LDB: TIME 25.1851 LOAD: AVG 8.6631 MAX 9.66236 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 None MEM: 252.613 MB LDB: TIME 25.2127 LOAD: AVG 8.6631 MAX 8.95239 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 TorusLB MEM: 252.613 MB LDB: ============== END OF LOAD BALANCING =============== 25.2386 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 25.3618 Info: Initial time: 128 CPUs 0.100759 s/step 0.583096 days/ns 254.641 MB memory TIMING: 240 CPU: 24.7802, 0.102168/step Wall: 24.8494, 0.102399/step, 0.0273065 hours remaining, 254.640625 MB of memory in use. ENERGY: 240 38946.1509 107298.6432 81977.1960 5043.2610 -4016916.8751 293582.0194 0.0000 0.0000 645424.8239 -2844644.7806 292.2810 -3490069.6045 -2842084.9166 291.2987 -1.8179 71.5693 10348277.4337 0.1115 0.2078 LDB: ============= START OF LOAD BALANCING ============== 36.7242 LDB: Largest compute 2966 load 0.195682 is 1.8% of average load 10.882487 LDB: Average compute 0.030266 is 0.3% of average load 10.882487 LDB: TIME 36.7438 LOAD: AVG 10.8825 MAX 11.3556 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 None MEM: 261.484 MB LDB: TIME 36.7487 LOAD: AVG 10.8825 MAX 11.3556 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 RefineTorusLB MEM: 261.484 MB LDB: TIME 36.7512 LOAD: AVG 10.8825 MAX 11.0224 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 RefineTorusLB MEM: 261.484 MB LDB: ============== END OF LOAD BALANCING =============== 36.7533 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 36.8693 Info: Initial time: 128 CPUs 0.0946532 s/step 0.547762 days/ns 261.484 MB memory TIMING: 360 CPU: 36.2555, 0.0956271/step Wall: 36.3533, 0.0958662/step, 0.0223688 hours remaining, 261.484375 MB of memory in use. ENERGY: 360 39265.9575 107616.0371 82095.3647 5128.0957 -4006306.2346 289662.6685 0.0000 0.0000 646582.6903 -2835955.4208 292.8053 -3482538.1111 -2833438.5945 292.6317 -12.3802 64.9746 10348225.9364 2.2134 2.2012 LDB: ============= START OF LOAD BALANCING ============== 48.0242 LDB: Largest compute 2966 load 0.192935 is 1.8% of average load 10.890522 LDB: Average compute 0.030278 is 0.3% of average load 10.890522 LDB: TIME 48.042 LOAD: AVG 10.8905 MAX 11.0881 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 None MEM: 261.484 MB LDB: TIME 48.0469 LOAD: AVG 10.8905 MAX 11.0881 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 RefineTorusLB MEM: 261.484 MB LDB: TIME 48.0483 LOAD: AVG 10.8905 MAX 11.0299 PROXIES: TOTAL 5002 MAXPE 42 MAXPATCH 8 RefineTorusLB MEM: 261.484 MB LDB: ============== END OF LOAD BALANCING =============== 48.0503 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 48.1674 Info: Benchmark time: 128 CPUs 0.0929542 s/step 0.537929 days/ns 261.484 MB memory TIMING: 480 CPU: 47.5228, 0.0938941/step Wall: 47.6516, 0.0941519/step, 0.0188304 hours remaining, 261.484375 MB of memory in use. ENERGY: 480 39238.5709 107176.1844 82006.5679 5217.6206 -3997871.7513 285873.2765 0.0000 0.0000 648178.7264 -2830180.8046 293.5281 -3478359.5310 -2827641.2385 293.3066 -65.6121 10.1838 10349629.6516 -2.9771 -3.0062 Info: Benchmark time: 128 CPUs 0.0930943 s/step 0.53874 days/ns 261.484 MB memory TIMING: 600 CPU: 58.6831, 0.0930025/step Wall: 58.8232, 0.0930971/step, 0.0155162 hours remaining, 261.484375 MB of memory in use. ENERGY: 600 39366.5332 107422.2202 82114.7672 5154.8191 -3993717.9503 285030.0992 0.0000 0.0000 650545.1584 -2824084.3530 294.5997 -3474629.5114 -2821515.5348 294.2411 -98.2173 -23.9368 10352660.1399 4.0015 3.9239 Info: Benchmark time: 128 CPUs 0.0930945 s/step 0.538742 days/ns 261.484 MB memory TIMING: 720 CPU: 69.8354, 0.0929359/step Wall: 69.9949, 0.0930972/step, 0.012413 hours remaining, 261.484375 MB of memory in use. ENERGY: 720 38822.9044 107468.6732 82155.0274 5112.3543 -3989557.8211 284872.0768 0.0000 0.0000 651176.5924 -2819950.1926 294.8857 -3471126.7849 -2817435.0949 294.8657 -3.1429 72.0542 10354835.7926 5.0280 5.0119 Info: Benchmark time: 128 CPUs 0.0932748 s/step 0.539785 days/ns 261.484 MB memory TIMING: 840 CPU: 81.0067, 0.0930942/step Wall: 81.1882, 0.0932774/step, 0.00932774 hours remaining, 261.484375 MB of memory in use. ENERGY: 840 39014.9178 107235.0056 82003.3569 5072.0634 -3986104.3105 282355.6152 0.0000 0.0000 653157.2100 -2817266.1416 295.7826 -3470423.3516 -2814659.8746 295.3567 -64.5158 10.0145 10348579.0844 -0.4782 -0.5745 Info: Benchmark time: 128 CPUs 0.09329 s/step 0.539873 days/ns 261.484 MB memory TIMING: 960 CPU: 92.167, 0.0930025/step Wall: 92.3833, 0.0932929/step, 0.00621953 hours remaining, 261.484375 MB of memory in use. ENERGY: 960 39126.5046 107573.4754 82086.7257 5154.8318 -3981757.6239 281583.2525 0.0000 0.0000 652805.0586 -2813427.7754 295.6231 -3466232.8339 -2810873.0750 295.5188 -93.0813 -18.3885 10357016.8625 0.6978 0.6996 Info: Benchmark time: 128 CPUs 0.0934602 s/step 0.540858 days/ns 261.484 MB memory TIMING: 1080 CPU: 103.355, 0.0932358/step Wall: 103.599, 0.0934631/step, 0.00311544 hours remaining, 261.484375 MB of memory in use. ENERGY: 1080 39366.7181 107277.0617 82212.2336 5111.8843 -3978578.6204 279867.1975 0.0000 0.0000 653732.2670 -2811011.2581 296.0430 -3464743.5252 -2808484.1471 296.0178 -142.5911 -69.2555 10359541.5357 -4.8187 -4.7728 TIMING: 1200 CPU: 114.554, 0.0933191/step Wall: 114.809, 0.0934153/step, 0 hours remaining, 261.484375 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 39019.1330 107437.1835 82120.5877 5139.6469 -3979170.6538 281917.8783 0.0000 0.0000 654579.6893 -2808956.5352 296.4268 -3463536.2244 -2806418.8791 296.4169 -38.3400 36.4141 10356099.9750 3.0680 2.9972 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 0.096 seconds(file I/O: 0.094 secs), 261.484 MB of memory in use The last velocity output (seq=-2) takes 0.172 seconds(file I/O: 0.082 secs), 261.484 MB of memory in use ==================================================== WallClock: 115.759308 CPUTime: 115.375458 Memory: 261.484375 MB