TACC: Starting up job 6245018 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 1.087 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 4 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.013 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 60 c403-903.stampede.tacc.utexas.edu tg455591 Info: Running on 60 processors, 4 nodes, 4 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0605249 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1195.04 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 1450742703 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: 0.0108421 Info: Info: Entering startup at 0.15774 s, 1292.86 MB of memory in use Info: Startup phase 0 took 0.00175095 s, 1292.86 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.098932 s, 1293.18 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: 15 45 Info: OUTPUT PROC LOCATIONS: 30 Info: Startup phase 2 took 0.0653162 s, 1294.16 MB of memory in use Info: Startup phase 3 took 0.20722 s, 1294.16 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 -0.00722551 0.0139406 -0.00363874 Info: Startup phase 4 took 0.0548301 s, 1414.6 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 0.101321 s, 1414.6 MB of memory in use Info: TORUS A SIZE 60 USING 0 15 30 45 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 46 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.017225 s, 1425.07 MB of memory in use Info: PME using 54 and 54 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ... Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 8 9 10 11 ... Info: PME USING 4 GRID NODES AND 4 TRANS NODES Info: Startup phase 7 took 0.0921309 s, 1431.82 MB of memory in use Info: Startup phase 8 took 0.00592399 s, 1431.82 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.031682 s, 1431.82 MB of memory in use Info: CREATING 44240 COMPUTE OBJECTS Info: Startup phase 10 took 0.0945561 s, 1431.82 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 0.00470805 s, 1431.82 MB of memory in use Info: Startup phase 12 took 0.00407386 s, 1435.12 MB of memory in use Info: Finished startup at 0.93741 s, 1435.12 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 658497.2013 -2870264.5283 298.2008 -3528761.7296 -2867705.9162 298.2008 2251.3777 2339.2433 10194598.5131 2251.3777 2339.2433 LDB: ============= START OF LOAD BALANCING ============== 6.19261 LDB: ============== END OF LOAD BALANCING =============== 6.19597 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 6.19744 LDB: ============= START OF LOAD BALANCING ============== 25.712 LDB: Largest compute 2751 load 0.152481 is 0.8% of average load 18.520686 LDB: Average compute 0.024229 is 0.1% of average load 18.520686 LDB: Partitioning computes with target load 1.852069 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023670 LDB: ============== END OF LOAD BALANCING =============== 25.7354 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 25.7802 Info: Initial time: 60 CPUs 0.203801 s/step 1.17941 days/ns 2269.36 MB memory TIMING: 120 CPU: 24.9072, 0.202486/step Wall: 25.347, 0.204413/step, 0.061324 hours remaining, 2269.363281 MB of memory in use. ENERGY: 120 39614.1726 107540.3125 81867.3366 5187.1492 -4029228.0605 296983.0334 0.0000 0.0000 641492.9609 -2856543.0953 290.5004 -3498036.0562 -2854002.9135 289.9632 -16.7912 60.7733 10349595.5815 -8.1257 -7.1218 LDB: ============= START OF LOAD BALANCING ============== 30.6847 LDB: ============== END OF LOAD BALANCING =============== 30.6852 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 30.6869 LDB: ============= START OF LOAD BALANCING ============== 50.1213 LDB: Largest compute 3481 load 0.152620 is 0.8% of average load 18.435773 LDB: Average compute 0.024160 is 0.1% of average load 18.435773 LDB: TIME 50.1409 LOAD: AVG 18.4358 MAX 19.3889 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 None MEM: 2382.82 MB LDB: TIME 50.1684 LOAD: AVG 18.4358 MAX 18.7028 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 TorusLB MEM: 2382.82 MB LDB: ============== END OF LOAD BALANCING =============== 50.2239 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 50.2709 Info: Initial time: 60 CPUs 0.202745 s/step 1.1733 days/ns 2377.42 MB memory TIMING: 240 CPU: 49.1805, 0.202278/step Wall: 49.8285, 0.204013/step, 0.0544034 hours remaining, 2377.417969 MB of memory in use. ENERGY: 240 39027.8198 107564.3091 82031.1640 5066.2431 -4015437.4710 292327.6132 0.0000 0.0000 644790.5118 -2844629.8101 291.9937 -3489420.3219 -2842092.6382 291.4674 -62.0591 13.7913 10351452.5581 -1.0505 -0.8243 LDB: ============= START OF LOAD BALANCING ============== 73.9487 LDB: Largest compute 3241 load 0.196927 is 0.8% of average load 23.195110 LDB: Average compute 0.030301 is 0.1% of average load 23.195110 LDB: TIME 73.966 LOAD: AVG 23.1951 MAX 23.5855 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 None MEM: 2435.4 MB LDB: TIME 73.971 LOAD: AVG 23.1951 MAX 23.5855 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 RefineTorusLB MEM: 2435.4 MB LDB: TIME 73.972 LOAD: AVG 23.1951 MAX 23.4497 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 RefineTorusLB MEM: 2435.4 MB LDB: ============== END OF LOAD BALANCING =============== 73.9746 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 74.0155 Info: Initial time: 60 CPUs 0.197304 s/step 1.14181 days/ns 2435.4 MB memory TIMING: 360 CPU: 72.7609, 0.196503/step Wall: 73.5721, 0.197863/step, 0.046168 hours remaining, 2435.398438 MB of memory in use. ENERGY: 360 39132.5229 107050.0067 81887.7756 5166.2751 -4005955.3365 289802.6365 0.0000 0.0000 647382.8900 -2835533.2297 293.1677 -3482916.1197 -2832971.6413 292.7222 -31.3047 44.5458 10346390.5263 -1.1225 -1.3034 LDB: ============= START OF LOAD BALANCING ============== 97.6585 LDB: Largest compute 3241 load 0.203104 is 0.9% of average load 23.210235 LDB: Average compute 0.030324 is 0.1% of average load 23.210235 LDB: TIME 97.6757 LOAD: AVG 23.2102 MAX 23.4816 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 None MEM: 2431.38 MB LDB: TIME 97.6807 LOAD: AVG 23.2102 MAX 23.4816 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 RefineTorusLB MEM: 2431.38 MB LDB: TIME 97.6812 LOAD: AVG 23.2102 MAX 23.4688 PROXIES: TOTAL 3958 MAXPE 69 MAXPATCH 4 RefineTorusLB MEM: 2431.38 MB LDB: ============== END OF LOAD BALANCING =============== 97.6838 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 97.7242 Info: Benchmark time: 60 CPUs 0.197023 s/step 1.14018 days/ns 2431.38 MB memory TIMING: 480 CPU: 96.2964, 0.196129/step Wall: 97.2808, 0.197573/step, 0.0395146 hours remaining, 2431.382812 MB of memory in use. ENERGY: 480 39439.7468 107393.4099 82084.1080 5122.5563 -3998881.0138 286115.2143 0.0000 0.0000 649757.1077 -2828968.8707 294.2428 -3478725.9785 -2826514.2085 293.5141 -86.1081 -10.5185 10353092.5062 2.6064 2.5058 Info: Benchmark time: 60 CPUs 0.196702 s/step 1.13832 days/ns 2427.38 MB memory TIMING: 600 CPU: 119.75, 0.195445/step Wall: 120.885, 0.196703/step, 0.0327839 hours remaining, 2427.375000 MB of memory in use. ENERGY: 600 39270.3994 107610.0802 82076.1862 5142.7227 -3992167.4622 283713.3053 0.0000 0.0000 649621.0747 -2824733.6937 294.1812 -3474354.7684 -2822189.6849 294.1370 -114.6983 -39.2924 10352211.8701 -0.3598 -0.3504 Info: Benchmark time: 60 CPUs 0.196582 s/step 1.13763 days/ns 2427.38 MB memory TIMING: 720 CPU: 143.184, 0.195287/step Wall: 144.475, 0.196584/step, 0.0262112 hours remaining, 2427.375000 MB of memory in use. ENERGY: 720 39230.0988 107108.8095 82115.2934 5075.9744 -3989782.3019 284959.8356 0.0000 0.0000 651053.0388 -2820239.2514 294.8297 -3471292.2902 -2817688.1434 294.7795 -13.3057 63.0214 10354880.7102 3.0564 3.0385 Info: Benchmark time: 60 CPUs 0.196802 s/step 1.1389 days/ns 2424.36 MB memory TIMING: 840 CPU: 166.645, 0.195504/step Wall: 168.092, 0.196803/step, 0.0196803 hours remaining, 2424.363281 MB of memory in use. ENERGY: 840 39327.9471 106953.4718 81951.6836 5120.1832 -3983722.0185 282085.1997 0.0000 0.0000 651815.2619 -2816468.2712 295.1749 -3468283.5331 -2813879.9166 295.1954 -170.8840 -96.3980 10361891.4230 -0.6633 -0.6151 Info: Benchmark time: 60 CPUs 0.19678 s/step 1.13877 days/ns 2423.36 MB memory TIMING: 960 CPU: 190.106, 0.195512/step Wall: 191.705, 0.196781/step, 0.0131188 hours remaining, 2423.359375 MB of memory in use. ENERGY: 960 39480.5722 107621.5822 82167.7151 5137.1399 -3983560.5902 282159.3490 0.0000 0.0000 654119.0508 -2812875.1811 296.2182 -3466994.2318 -2810265.1078 295.6452 -74.5522 -0.9286 10358041.5937 0.7790 0.7793 Info: Benchmark time: 60 CPUs 0.196845 s/step 1.13915 days/ns 2423.36 MB memory TIMING: 1080 CPU: 213.589, 0.195687/step Wall: 215.327, 0.196847/step, 0.00656155 hours remaining, 2423.359375 MB of memory in use. ENERGY: 1080 39210.9414 107657.6372 82093.0266 5014.2000 -3978712.7922 280700.2934 0.0000 0.0000 653551.3367 -2810485.3569 295.9611 -3464036.6936 -2807944.1799 296.1279 -184.8476 -109.2939 10369678.8915 -0.3469 -0.3734 TIMING: 1200 CPU: 237.049, 0.195504/step Wall: 238.944, 0.196812/step, 0 hours remaining, 2422.355469 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 39232.9959 107707.7115 81958.8903 5125.0101 -3977521.9097 280618.7873 0.0000 0.0000 654483.8630 -2808394.6515 296.3834 -3462878.5145 -2805883.8128 296.4169 -106.6489 -30.5847 10371543.8940 1.9794 1.8783 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 0.122 seconds(file I/O: 0.120 secs), 2422.355 MB of memory in use The last velocity output (seq=-2) takes 0.179 seconds(file I/O: 0.066 secs), 2422.355 MB of memory in use ==================================================== WallClock: 240.005417 CPUTime: 237.840836 Memory: 2422.355469 MB TACC: Shutdown complete. Exiting.