TACC: Starting up job 6245026 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 4.034 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 4 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 64 c546-203.stampede.tacc.utexas.edu tg455591 Info: Running on 64 processors, 64 nodes, 4 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.168425 s Info: 117.234 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 1450742595 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: 0.005373 Info: Info: Entering startup at 0.254957 s, 212.879 MB of memory in use Info: Startup phase 0 took 0.0018959 s, 212.879 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0666981 s, 213.945 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: 16 48 Info: OUTPUT PROC LOCATIONS: 32 Info: Startup phase 2 took 0.039001 s, 214.922 MB of memory in use Info: Startup phase 3 took 0.146135 s, 214.922 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 0.00703294 0.0161654 0.00691062 Info: Startup phase 4 took 0.034574 s, 223.312 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 0.053216 s, 224.344 MB of memory in use Info: TORUS A SIZE 64 USING 0 16 32 48 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 49 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0186779 s, 234.789 MB of memory in use Info: PME using 54 and 54 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 54 GRID NODES AND 54 TRANS NODES Info: Startup phase 7 took 0.122476 s, 241.543 MB of memory in use Info: Startup phase 8 took 0.0052321 s, 241.543 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00755191 s, 241.543 MB of memory in use Info: CREATING 44260 COMPUTE OBJECTS Info: Startup phase 10 took 0.017844 s, 241.543 MB of memory in use Info: useSync: 0 useProxySync: 0 Info: Startup phase 11 took 0.00139904 s, 241.543 MB of memory in use Info: Startup phase 12 took 0.00129104 s, 245.387 MB of memory in use Info: Finished startup at 0.770949 s, 245.387 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 657480.5318 -2871281.1979 297.7404 -3528761.7297 -2868723.4472 297.7404 2251.7339 2339.5945 10194598.5131 2251.7339 2339.5945 LDB: ============= START OF LOAD BALANCING ============== 5.52056 LDB: ============== END OF LOAD BALANCING =============== 5.52657 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 5.52802 LDB: ============= START OF LOAD BALANCING ============== 24.0715 LDB: Largest compute 2966 load 0.154065 is 0.9% of average load 17.341370 LDB: Average compute 0.024240 is 0.1% of average load 17.341370 LDB: Partitioning computes with target load 1.734137 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023796 LDB: ============== END OF LOAD BALANCING =============== 24.0973 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 24.2164 Info: Initial time: 64 CPUs 0.193717 s/step 1.12105 days/ns 305.207 MB memory TIMING: 120 CPU: 23.7544, 0.194312/step Wall: 23.8533, 0.194996/step, 0.0584989 hours remaining, 305.207031 MB of memory in use. ENERGY: 120 39264.3850 107024.7353 82005.6068 5115.9711 -4026784.3845 295171.9006 0.0000 0.0000 641843.3586 -2856358.4272 290.6591 -3498201.7858 -2853947.7273 289.8321 -75.9886 -0.2408 10349635.7035 -3.6864 -2.5951 LDB: ============= START OF LOAD BALANCING ============== 28.903 LDB: ============== END OF LOAD BALANCING =============== 28.9035 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 28.905 LDB: ============= START OF LOAD BALANCING ============== 47.4531 LDB: Largest compute 2966 load 0.156750 is 0.9% of average load 17.302148 LDB: Average compute 0.024182 is 0.1% of average load 17.302148 LDB: TIME 47.4732 LOAD: AVG 17.3021 MAX 18.5267 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 None MEM: 312.879 MB LDB: TIME 47.4995 LOAD: AVG 17.3021 MAX 17.7917 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 TorusLB MEM: 312.879 MB LDB: ============== END OF LOAD BALANCING =============== 47.5229 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 47.645 Info: Initial time: 64 CPUs 0.193467 s/step 1.1196 days/ns 312.879 MB memory TIMING: 240 CPU: 47.0758, 0.194345/step Wall: 47.2638, 0.195087/step, 0.0520233 hours remaining, 312.878906 MB of memory in use. ENERGY: 240 39050.6903 106921.7022 82117.1301 5113.0944 -4015982.7225 292147.0184 0.0000 0.0000 645741.4292 -2844891.6579 292.4243 -3490633.0871 -2842317.0269 291.4405 -35.6229 41.4219 10343872.3298 0.1989 0.2382 LDB: ============= START OF LOAD BALANCING ============== 70.0685 LDB: Largest compute 2966 load 0.195836 is 0.9% of average load 21.727345 LDB: Average compute 0.030319 is 0.1% of average load 21.727345 LDB: TIME 70.0883 LOAD: AVG 21.7273 MAX 22.4112 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 None MEM: 328.887 MB LDB: TIME 70.0934 LOAD: AVG 21.7273 MAX 22.4112 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 RefineTorusLB MEM: 328.887 MB LDB: TIME 70.095 LOAD: AVG 21.7273 MAX 21.9465 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 RefineTorusLB MEM: 328.887 MB LDB: ============== END OF LOAD BALANCING =============== 70.097 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 70.2128 Info: Initial time: 64 CPUs 0.186811 s/step 1.08108 days/ns 328.887 MB memory TIMING: 360 CPU: 69.5704, 0.187455/step Wall: 69.8259, 0.188017/step, 0.0438706 hours remaining, 328.886719 MB of memory in use. ENERGY: 360 39112.9413 107118.6846 81918.7340 5153.6201 -4005963.4757 288688.5008 0.0000 0.0000 648490.6589 -2835480.3360 293.6693 -3483970.9949 -2832946.5154 292.7825 -43.9391 32.3991 10346958.3650 0.7796 0.7583 LDB: ============= START OF LOAD BALANCING ============== 92.3984 LDB: Largest compute 2778 load 0.193543 is 0.9% of average load 21.745514 LDB: Average compute 0.030344 is 0.1% of average load 21.745514 LDB: TIME 92.4167 LOAD: AVG 21.7455 MAX 22.0176 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 None MEM: 328.887 MB LDB: TIME 92.4218 LOAD: AVG 21.7455 MAX 22.0176 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 RefineTorusLB MEM: 328.887 MB LDB: TIME 92.4225 LOAD: AVG 21.7455 MAX 21.9887 PROXIES: TOTAL 4084 MAXPE 66 MAXPATCH 5 RefineTorusLB MEM: 328.887 MB LDB: ============== END OF LOAD BALANCING =============== 92.4244 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 92.5412 Info: Benchmark time: 64 CPUs 0.184879 s/step 1.0699 days/ns 328.887 MB memory TIMING: 480 CPU: 91.83, 0.185497/step Wall: 92.1545, 0.186072/step, 0.0372145 hours remaining, 328.886719 MB of memory in use. ENERGY: 480 38958.2870 107506.1506 81985.7427 5127.4690 -3996295.1822 284473.8523 0.0000 0.0000 649231.8866 -2829011.7940 294.0050 -3478243.6806 -2826464.2270 293.6103 -89.4218 -13.2072 10347799.2688 1.1597 1.1316 Info: Benchmark time: 64 CPUs 0.184447 s/step 1.0674 days/ns 328.887 MB memory TIMING: 600 CPU: 113.894, 0.183864/step Wall: 114.289, 0.18445/step, 0.0307416 hours remaining, 328.886719 MB of memory in use. ENERGY: 600 39471.9224 107394.6751 82072.0936 5065.5607 -3993449.6133 284916.3327 0.0000 0.0000 651219.9636 -2823309.0653 294.9053 -3474529.0288 -2820753.0911 294.4397 -85.9052 -11.2094 10353339.6707 -1.1776 -1.1957 Info: Benchmark time: 64 CPUs 0.184547 s/step 1.06798 days/ns 321.484 MB memory TIMING: 720 CPU: 135.973, 0.183997/step Wall: 136.434, 0.18455/step, 0.0246066 hours remaining, 321.484375 MB of memory in use. ENERGY: 720 39000.0807 107380.6713 82080.9193 5144.6969 -3989134.2409 283515.0530 0.0000 0.0000 651672.9277 -2820339.8920 295.1104 -3472012.8197 -2817752.3594 294.9097 -89.0675 -11.1929 10355753.3641 3.1858 3.3927 Info: Benchmark time: 64 CPUs 0.184545 s/step 1.06797 days/ns 325.484 MB memory TIMING: 840 CPU: 158.042, 0.183905/step Wall: 158.58, 0.184548/step, 0.0184548 hours remaining, 325.484375 MB of memory in use. ENERGY: 840 39196.7095 106995.4361 82347.3967 5141.9530 -3984822.0014 283393.2283 0.0000 0.0000 651663.9045 -2816083.3734 295.1063 -3467747.2779 -2813583.4835 295.4651 -85.3869 -8.7961 10367887.8198 -1.3556 -1.3200 Info: Benchmark time: 64 CPUs 0.184403 s/step 1.06715 days/ns 325.484 MB memory TIMING: 960 CPU: 180.122, 0.183997/step Wall: 180.709, 0.184405/step, 0.0122937 hours remaining, 325.484375 MB of memory in use. ENERGY: 960 39090.5651 108043.3299 82369.4820 5246.1097 -3983237.6301 282390.1322 0.0000 0.0000 652698.4628 -2813399.5483 295.5748 -3466098.0111 -2810867.1705 295.7330 -62.0387 14.4017 10360146.7861 2.9166 2.9640 Info: Benchmark time: 64 CPUs 0.184687 s/step 1.06879 days/ns 326.488 MB memory TIMING: 1080 CPU: 202.219, 0.184147/step Wall: 202.872, 0.18469/step, 0.00615633 hours remaining, 326.488281 MB of memory in use. ENERGY: 1080 39063.7487 107279.5523 82172.8350 5184.9818 -3983061.3421 283313.7612 0.0000 0.0000 655077.1149 -2810969.3482 296.6520 -3466046.4631 -2808451.7819 296.1104 -25.3379 50.6448 10357884.3537 5.2880 5.2911 TIMING: 1200 CPU: 224.235, 0.183464/step Wall: 224.986, 0.184287/step, 0 hours remaining, 326.488281 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 39127.6271 107812.6203 82167.9770 5194.9464 -3980534.0077 281509.8858 0.0000 0.0000 654622.3387 -2810098.6125 296.4461 -3464720.9512 -2807475.3161 296.3166 -139.1009 -64.3572 10368574.8079 1.3773 1.3317 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 0.164 seconds(file I/O: 0.163 secs), 326.488 MB of memory in use The last velocity output (seq=-2) takes 0.307 seconds(file I/O: 0.153 secs), 326.488 MB of memory in use ==================================================== WallClock: 226.088287 CPUTime: 225.105774 Memory: 326.488281 MB