TACC: Starting up job 6244972 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 3.433 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 1 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.015 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 16 c552-501.stampede.tacc.utexas.edu tg455591 Info: Running on 16 processors, 16 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.073456 s Info: 110.32 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 1450737456 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: 0.0056622 Info: Info: Entering startup at 0.16015 s, 205.965 MB of memory in use Info: Startup phase 0 took 0.00165606 s, 205.965 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0622158 s, 207.031 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: 4 12 Info: OUTPUT PROC LOCATIONS: 8 Info: Startup phase 2 took 0.0354121 s, 208.008 MB of memory in use Info: Startup phase 3 took 0.158287 s, 208.008 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 -0.0010147 -0.0109313 0.000218885 Info: Startup phase 4 took 0.0324199 s, 216.426 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 0.052788 s, 217.426 MB of memory in use Info: TORUS A SIZE 16 USING 0 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.015799 s, 227.871 MB of memory in use Info: PME using 16 and 16 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: PME TRANS LOCATIONS: 0 1 2 3 4 5 6 7 8 9 ... Info: PME USING 16 GRID NODES AND 16 TRANS NODES Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 7 took 0.158301 s, 243.766 MB of memory in use Info: Startup phase 8 took 0.007514 s, 243.766 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00449705 s, 243.766 MB of memory in use Info: CREATING 44020 COMPUTE OBJECTS Info: Startup phase 10 took 0.022321 s, 253.098 MB of memory in use Info: useSync: 0 useProxySync: 0 Info: Startup phase 11 took 0.000375032 s, 253.098 MB of memory in use Info: Startup phase 12 took 0.00118995 s, 270.727 MB of memory in use Info: Finished startup at 0.712926 s, 270.727 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 -4134759.4112 375583.0490 0.0000 0.0000 658027.7007 -2870734.0287 297.9882 -3528761.7293 -2868175.6706 297.9882 2249.5791 2337.4752 10194598.5131 2249.5791 2337.4752 LDB: ============= START OF LOAD BALANCING ============== 19.1953 LDB: ============== END OF LOAD BALANCING =============== 19.1996 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 19.201 LDB: ============= START OF LOAD BALANCING ============== 91.2677 LDB: Largest compute 2966 load 0.151878 is 0.2% of average load 69.264569 LDB: Average compute 0.024244 is 0.0% of average load 69.264569 LDB: Partitioning computes with target load 6.926457 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023368 LDB: ============== END OF LOAD BALANCING =============== 91.2901 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 91.3975 Info: Initial time: 16 CPUs 0.752767 s/step 4.35629 days/ns 495.207 MB memory TIMING: 120 CPU: 91.6641, 0.750411/step Wall: 92.2092, 0.753907/step, 0.226172 hours remaining, 495.207031 MB of memory in use. ENERGY: 120 39390.6370 107335.4067 81919.3789 5083.7036 -4027221.8452 296539.3216 0.0000 0.0000 642451.3999 -2854501.9976 290.9344 -3496953.3974 -2852033.9240 290.0676 -27.1713 48.2658 10353986.5901 -7.2154 -6.1995 LDB: ============= START OF LOAD BALANCING ============== 109.547 LDB: ============== END OF LOAD BALANCING =============== 109.547 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 109.549 LDB: ============= START OF LOAD BALANCING ============== 181.403 LDB: Largest compute 3435 load 0.156409 is 0.2% of average load 69.131031 LDB: Average compute 0.024189 is 0.0% of average load 69.131031 LDB: TIME 181.42 LOAD: AVG 69.131 MAX 71.8354 PROXIES: TOTAL 2370 MAXPE 167 MAXPATCH 3 None MEM: 501.035 MB LDB: TIME 181.443 LOAD: AVG 69.131 MAX 70.1348 PROXIES: TOTAL 2370 MAXPE 167 MAXPATCH 3 TorusLB MEM: 501.035 MB LDB: ============== END OF LOAD BALANCING =============== 181.466 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 181.541 Info: Initial time: 16 CPUs 0.749966 s/step 4.34008 days/ns 501.035 MB memory TIMING: 240 CPU: 181.459, 0.748295/step Wall: 182.346, 0.751142/step, 0.200305 hours remaining, 501.035156 MB of memory in use. ENERGY: 240 39049.3014 106931.1909 82006.9882 5064.3921 -4014945.1644 292697.3404 0.0000 0.0000 645241.3536 -2843954.5978 292.1979 -3489195.9514 -2841300.6027 291.5462 -8.6077 68.3189 10346810.7239 -0.0688 0.1471 LDB: ============= START OF LOAD BALANCING ============== 270.055 LDB: Largest compute 3130 load 0.191958 is 0.2% of average load 86.676965 LDB: Average compute 0.030321 is 0.0% of average load 86.676965 LDB: TIME 270.072 LOAD: AVG 86.677 MAX 88.5029 PROXIES: TOTAL 2370 MAXPE 167 MAXPATCH 3 None MEM: 488.027 MB LDB: TIME 270.076 LOAD: AVG 86.677 MAX 88.5029 PROXIES: TOTAL 2370 MAXPE 167 MAXPATCH 3 RefineTorusLB MEM: 488.027 MB LDB: TIME 270.086 LOAD: AVG 86.677 MAX 87.5769 PROXIES: TOTAL 2373 MAXPE 167 MAXPATCH 3 RefineTorusLB MEM: 488.027 MB LDB: ============== END OF LOAD BALANCING =============== 270.088 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 270.148 Info: Initial time: 16 CPUs 0.737328 s/step 4.26694 days/ns 488.027 MB memory TIMING: 360 CPU: 269.688, 0.735238/step Wall: 270.919, 0.738109/step, 0.172226 hours remaining, 488.027344 MB of memory in use. ENERGY: 360 39166.0862 107429.9336 81974.0909 5194.3651 -4003547.5940 288097.8760 0.0000 0.0000 646359.9523 -2835325.2898 292.7044 -3481685.2422 -2832790.4449 292.5504 -80.3617 -5.8814 10353610.7893 4.9537 4.9151 LDB: ============= START OF LOAD BALANCING ============== 358.041 LDB: Largest compute 3998 load 0.195965 is 0.2% of average load 86.733036 LDB: Average compute 0.030338 is 0.0% of average load 86.733036 LDB: TIME 358.058 LOAD: AVG 86.733 MAX 87.829 PROXIES: TOTAL 2370 MAXPE 167 MAXPATCH 3 None MEM: 494.031 MB LDB: TIME 358.062 LOAD: AVG 86.733 MAX 87.829 PROXIES: TOTAL 2373 MAXPE 167 MAXPATCH 3 RefineTorusLB MEM: 494.031 MB LDB: TIME 358.086 LOAD: AVG 86.733 MAX 87.6336 PROXIES: TOTAL 2377 MAXPE 167 MAXPATCH 3 RefineTorusLB MEM: 494.031 MB LDB: ============== END OF LOAD BALANCING =============== 358.088 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 358.148 Info: Benchmark time: 16 CPUs 0.732464 s/step 4.2388 days/ns 494.031 MB memory TIMING: 480 CPU: 357.413, 0.731039/step Wall: 358.923, 0.733361/step, 0.146672 hours remaining, 494.031250 MB of memory in use. ENERGY: 480 39312.7767 107398.5770 81961.3073 5143.3610 -3997655.5318 286327.0448 0.0000 0.0000 649060.3708 -2828452.0941 293.9273 -3477512.4649 -2825963.5327 293.5708 -82.9531 -3.9751 10350171.4437 3.6516 3.7364 Info: Benchmark time: 16 CPUs 0.731866 s/step 4.23534 days/ns 494.031 MB memory TIMING: 600 CPU: 444.824, 0.728431/step Wall: 446.747, 0.731869/step, 0.121978 hours remaining, 494.031250 MB of memory in use. ENERGY: 600 39253.9327 107688.7264 82184.6188 5107.1476 -3992905.5659 284791.3118 0.0000 0.0000 650357.7563 -2823522.0724 294.5148 -3473879.8287 -2820993.9921 294.3358 -96.4085 -19.6181 10355507.6833 3.3442 3.1331 Info: Benchmark time: 16 CPUs 0.73173 s/step 4.23455 days/ns 500.398 MB memory TIMING: 720 CPU: 532.269, 0.728706/step Wall: 534.555, 0.731733/step, 0.0975644 hours remaining, 500.398438 MB of memory in use. ENERGY: 720 39271.0667 107118.9130 81908.2330 5174.6710 -3988677.2028 284206.1155 0.0000 0.0000 651551.0789 -2819447.1247 295.0552 -3470998.2036 -2816928.3428 294.8667 -91.0276 -13.9832 10360079.1159 2.6560 2.5690 Info: Benchmark time: 16 CPUs 0.73215 s/step 4.23698 days/ns 502.379 MB memory TIMING: 840 CPU: 619.779, 0.729247/step Wall: 622.413, 0.732152/step, 0.0732152 hours remaining, 502.378906 MB of memory in use. ENERGY: 840 39179.2808 107571.3735 82017.8994 5137.3921 -3986976.5936 284192.9345 0.0000 0.0000 652366.0501 -2816511.6632 295.4243 -3468877.7133 -2813966.0241 295.3433 -43.3020 33.2322 10363822.1845 -0.3811 -0.3494 Info: Benchmark time: 16 CPUs 0.732292 s/step 4.2378 days/ns 502.379 MB memory TIMING: 960 CPU: 707.215, 0.728639/step Wall: 710.289, 0.732295/step, 0.0488196 hours remaining, 502.378906 MB of memory in use. ENERGY: 960 39069.1216 107848.4037 82078.2578 5194.3718 -3983986.4497 282845.0240 0.0000 0.0000 653210.4504 -2813740.8204 295.8067 -3466951.2707 -2811112.3935 295.5923 -46.5767 27.7226 10365562.8546 4.8114 4.6783 Info: Benchmark time: 16 CPUs 0.733093 s/step 4.24243 days/ns 506.383 MB memory TIMING: 1080 CPU: 794.774, 0.729656/step Wall: 798.26, 0.733095/step, 0.0244365 hours remaining, 506.382812 MB of memory in use. ENERGY: 1080 39036.8924 107631.4549 82163.8544 5102.7007 -3980573.1201 281254.1621 0.0000 0.0000 653261.6253 -2812122.4303 295.8299 -3465384.0557 -2809524.4826 295.8981 -107.3253 -30.7040 10374254.9486 1.2414 1.2560 TIMING: 1200 CPU: 882.151, 0.728139/step Wall: 886.1, 0.732003/step, 0 hours remaining, 506.382812 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 38941.3885 107582.7949 81939.4817 5089.1134 -3981488.8857 282930.0607 0.0000 0.0000 653730.6270 -2811275.4197 296.0423 -3465006.0467 -2808661.1376 296.3013 -9.2707 67.6139 10363032.2984 -0.3040 -0.2279 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 0.135 seconds(file I/O: 0.064 secs), 506.383 MB of memory in use The last velocity output (seq=-2) takes 0.144 seconds(file I/O: 0.045 secs), 506.383 MB of memory in use ==================================================== WallClock: 887.080627 CPUTime: 882.858765 Memory: 506.382812 MB