TACC: Starting up job 6245029 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 9.390 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 32 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.024 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 512 c403-804.stampede.tacc.utexas.edu tg455591 Info: Running on 512 processors, 512 nodes, 32 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.107163 s Info: 182.336 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 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 1450742551 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: 0.00580311 Info: Info: Entering startup at 0.207921 s, 277.984 MB of memory in use Info: Startup phase 0 took 0.00658679 s, 277.984 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0775781 s, 278.656 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: 128 384 Info: OUTPUT PROC LOCATIONS: 256 Info: Startup phase 2 took 0.0387371 s, 279.559 MB of memory in use Info: Startup phase 3 took 0.144715 s, 279.559 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 0.00553334 -0.0106231 -0.00329478 Info: Startup phase 4 took 0.0382679 s, 287.949 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 0.0542791 s, 287.949 MB of memory in use Info: TORUS A SIZE 512 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 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 497 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0254819 s, 298.426 MB of memory in use Info: PME using 22 x 22 x 22 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 4 5 6 7 9 10 11 ... Info: PME X PENCIL LOCATIONS: 1 2 3 5 6 7 8 9 10 11 ... Info: Startup phase 7 took 0.171902 s, 305.52 MB of memory in use Info: Startup phase 8 took 0.0145121 s, 305.52 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.01331 s, 305.52 MB of memory in use Info: CREATING 46490 COMPUTE OBJECTS Info: Startup phase 10 took 0.0234041 s, 305.52 MB of memory in use Info: useSync: 0 useProxySync: 0 Info: Startup phase 11 took 0.00158787 s, 305.52 MB of memory in use Info: Startup phase 12 took 0.000866175 s, 305.52 MB of memory in use Info: Finished startup at 0.819149 s, 305.52 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 -4134759.4115 375583.0490 0.0000 0.0000 656751.6810 -2872010.0486 297.4103 -3528761.7296 -2869452.2854 297.4103 2248.1429 2336.0019 10194598.5131 2248.1429 2336.0019 LDB: ============= START OF LOAD BALANCING ============== 1.60035 LDB: ============== END OF LOAD BALANCING =============== 1.61415 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 1.6161 LDB: ============= START OF LOAD BALANCING ============== 4.51933 LDB: Largest compute 2751 load 0.149541 is 6.8% of average load 2.206867 LDB: Average compute 0.024146 is 1.1% of average load 2.206867 LDB: Partitioning computes with target load 0.220687 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023399 LDB: ============== END OF LOAD BALANCING =============== 4.58828 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 4.72164 Info: Initial time: 512 CPUs 0.030283 s/step 0.175249 days/ns 309.312 MB memory TIMING: 120 CPU: 3.9684, 0.0319868/step Wall: 3.98844, 0.0321151/step, 0.00963454 hours remaining, 309.312500 MB of memory in use. ENERGY: 120 39513.2361 107392.7038 81819.7196 5068.1281 -4028008.8698 296651.6863 0.0000 0.0000 641780.8065 -2855782.5895 290.6308 -3497563.3960 -2853385.8235 289.8694 -19.6140 57.7846 10347029.1021 0.3254 1.3774 LDB: ============= START OF LOAD BALANCING ============== 5.45244 LDB: ============== END OF LOAD BALANCING =============== 5.45594 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 5.45787 LDB: ============= START OF LOAD BALANCING ============== 8.35054 LDB: Largest compute 3241 load 0.151931 is 6.9% of average load 2.194784 LDB: Average compute 0.024085 is 1.1% of average load 2.194784 LDB: TIME 8.40255 LOAD: AVG 2.19478 MAX 2.88905 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 None MEM: 309.312 MB LDB: TIME 8.43646 LOAD: AVG 2.19478 MAX 2.36378 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 TorusLB MEM: 309.312 MB LDB: ============== END OF LOAD BALANCING =============== 8.48586 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 8.62116 Info: Initial time: 512 CPUs 0.0301003 s/step 0.174191 days/ns 309.312 MB memory TIMING: 240 CPU: 7.84581, 0.0323118/step Wall: 7.87762, 0.0324098/step, 0.0086426 hours remaining, 309.312500 MB of memory in use. ENERGY: 240 39189.9152 107029.6536 82018.0389 5127.8752 -4015852.8594 293263.1077 0.0000 0.0000 645035.4032 -2844188.8656 292.1046 -3489224.2688 -2841644.7460 291.4586 31.5664 105.8713 10344002.5663 1.8590 1.8657 LDB: ============= START OF LOAD BALANCING ============== 11.6035 LDB: Largest compute 2750 load 0.194083 is 7.0% of average load 2.756573 LDB: Average compute 0.030240 is 1.1% of average load 2.756573 LDB: TIME 11.6542 LOAD: AVG 2.75657 MAX 2.96066 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 None MEM: 309.312 MB LDB: TIME 11.6595 LOAD: AVG 2.75657 MAX 2.96066 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 309.312 MB LDB: TIME 11.6625 LOAD: AVG 2.75657 MAX 2.81776 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 309.312 MB LDB: ============== END OF LOAD BALANCING =============== 11.6649 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 11.7872 Info: Initial time: 512 CPUs 0.0248264 s/step 0.143671 days/ns 309.312 MB memory TIMING: 360 CPU: 11.0023, 0.0263043/step Wall: 11.0413, 0.0263639/step, 0.00615159 hours remaining, 309.312500 MB of memory in use. ENERGY: 360 39393.1336 107430.7001 81942.9270 5156.9182 -4004763.6119 287655.2716 0.0000 0.0000 647534.3205 -2835650.3408 293.2363 -3483184.6613 -2833099.2731 292.6389 -116.7988 -43.8918 10350383.0895 1.1984 1.1217 LDB: ============= START OF LOAD BALANCING ============== 14.6963 LDB: Largest compute 2750 load 0.193611 is 7.0% of average load 2.757507 LDB: Average compute 0.030240 is 1.1% of average load 2.757507 LDB: TIME 14.7474 LOAD: AVG 2.75751 MAX 2.85299 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 None MEM: 309.312 MB LDB: TIME 14.7527 LOAD: AVG 2.75751 MAX 2.85299 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 309.312 MB LDB: TIME 14.7545 LOAD: AVG 2.75751 MAX 2.8184 PROXIES: TOTAL 8376 MAXPE 23 MAXPATCH 8 RefineTorusLB MEM: 309.312 MB LDB: ============== END OF LOAD BALANCING =============== 14.7569 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 14.8799 Info: Benchmark time: 512 CPUs 0.0242558 s/step 0.140369 days/ns 309.312 MB memory TIMING: 480 CPU: 14.0909, 0.0257377/step Wall: 14.1364, 0.0257926/step, 0.00515852 hours remaining, 309.312500 MB of memory in use. ENERGY: 480 39136.7821 107877.6756 82206.6370 5146.4138 -3997366.7070 285092.1339 0.0000 0.0000 647762.2635 -2830144.8010 293.3395 -3477907.0645 -2827571.8047 293.5208 -134.0796 -59.0596 10350188.4993 6.4192 6.3021 Info: Benchmark time: 512 CPUs 0.0241416 s/step 0.139708 days/ns 309.312 MB memory TIMING: 600 CPU: 16.9844, 0.024113/step Wall: 17.0339, 0.0241459/step, 0.00402431 hours remaining, 309.312500 MB of memory in use. ENERGY: 600 39063.1737 107762.9052 81996.6392 5114.1688 -3994077.7899 285011.1823 0.0000 0.0000 651009.0961 -2824120.6247 294.8098 -3475129.7208 -2821513.4114 294.1073 -83.9256 -7.3724 10350585.7981 -0.8441 -0.8036 Info: Benchmark time: 512 CPUs 0.0242964 s/step 0.140604 days/ns 309.312 MB memory TIMING: 720 CPU: 19.897, 0.0242713/step Wall: 19.95, 0.0243007/step, 0.00324009 hours remaining, 309.312500 MB of memory in use. ENERGY: 720 38971.5425 107712.7392 82068.5762 5213.1826 -3992152.2146 285962.4975 0.0000 0.0000 651409.9046 -2820813.7721 294.9913 -3472223.6767 -2818305.1016 294.8527 10.1074 85.3998 10350692.5865 4.4927 4.4802 Info: Benchmark time: 512 CPUs 0.0243138 s/step 0.140705 days/ns 309.312 MB memory TIMING: 840 CPU: 22.8095, 0.0242713/step Wall: 22.8682, 0.0243182/step, 0.00243182 hours remaining, 309.312500 MB of memory in use. ENERGY: 840 39310.1397 107359.2968 82196.2652 5088.7966 -3986362.4457 283165.8073 0.0000 0.0000 652424.1092 -2816818.0309 295.4506 -3469242.1401 -2814175.3663 295.2018 -103.9965 -26.6270 10359607.2161 -0.6278 -0.6766 Info: Benchmark time: 512 CPUs 0.0243754 s/step 0.141062 days/ns 309.312 MB memory TIMING: 960 CPU: 25.7311, 0.0243463/step Wall: 25.7937, 0.0243797/step, 0.00162531 hours remaining, 309.312500 MB of memory in use. ENERGY: 960 39050.5459 107838.3633 82017.2414 5211.6665 -3984549.3520 282819.3768 0.0000 0.0000 652850.7529 -2814761.4052 295.6438 -3467612.1581 -2812225.6659 295.6678 -61.5365 12.8057 10360927.5099 0.9838 1.0067 Info: Benchmark time: 512 CPUs 0.0243867 s/step 0.141127 days/ns 309.312 MB memory TIMING: 1080 CPU: 28.6546, 0.024363/step Wall: 28.7207, 0.024391/step, 0.000813032 hours remaining, 309.312500 MB of memory in use. ENERGY: 1080 39194.2637 107378.8276 81823.1938 5178.9601 -3982134.2385 281687.7623 0.0000 0.0000 653726.9125 -2813144.3186 296.0406 -3466871.2311 -2810568.6934 295.7028 -137.9560 -62.1030 10363567.4621 2.1358 2.0437 TIMING: 1200 CPU: 31.5652, 0.0242547/step Wall: 31.6363, 0.0242971/step, 0 hours remaining, 309.312500 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 39336.3646 106911.1712 82075.6721 5123.3652 -3981254.5643 282881.9362 0.0000 0.0000 654357.2062 -2810568.8489 296.3260 -3464926.0550 -2807964.0856 296.1587 -61.0825 15.7177 10368296.0370 2.1227 2.1308 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 0.104 seconds(file I/O: 0.103 secs), 309.312 MB of memory in use The last velocity output (seq=-2) takes 0.175 seconds(file I/O: 0.079 secs), 309.312 MB of memory in use ==================================================== WallClock: 32.740532 CPUTime: 32.485062 Memory: 309.312500 MB