TACC: Starting up job 6245031 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 16.997 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 128 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.049 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 2048 c477-802.stampede.tacc.utexas.edu tg455591 Info: Running on 2048 processors, 2048 nodes, 128 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.228878 s Info: 401.375 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 Hybrid Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4800 steps Info: FIRST LDB TIMESTEP 120 Info: HYBRIDLB GROUP SIZE 512 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 LOAD FROM NODE 1 Info: REMOVING PATCHES FROM PROCESSOR 0 Info: REMOVING PATCHES FROM PROCESSOR 1 Info: MAX SELF PARTITIONS 20 Info: MAX PAIR PARTITIONS 8 Info: SELF PARTITION ATOMS 154 Info: SELF2 PARTITION ATOMS 154 Info: PAIR PARTITION ATOMS 318 Info: PAIR2 PARTITION ATOMS 637 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 1450742388 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: 0.00572205 Info: Info: Entering startup at 0.351999 s, 497.035 MB of memory in use Info: Startup phase 0 took 0.019969 s, 497.035 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.119566 s, 497.57 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: 512 1536 Info: OUTPUT PROC LOCATIONS: 1024 Info: Startup phase 2 took 0.047302 s, 498.547 MB of memory in use Info: Startup phase 3 took 0.166942 s, 498.547 MB of memory in use Info: REDUCING NUMBER OF PATCHES TO IMPROVE LOAD BALANCE Info: PATCH GRID IS 13 (PERIODIC) BY 13 (PERIODIC) BY 12 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: LOADED 1810196 TOTAL EXCLUSIONS Info: REMOVING COM VELOCITY 0.00783551 -0.00243057 0.0172338 Info: Startup phase 4 took 0.0566099 s, 506.938 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 (1474) HAS 588 ATOMS Info: Startup phase 5 took 0.074352 s, 506.938 MB of memory in use Info: TORUS A SIZE 2048 USING 0 16 32 48 64 80 96 112 128 144 160 176 192 208 224 240 256 272 288 304 320 336 352 368 384 400 416 432 448 464 480 496 512 528 544 560 576 592 608 624 640 656 672 688 704 720 736 752 768 784 800 816 832 848 864 880 896 912 928 944 960 976 992 1008 1024 1040 1056 1072 1088 1104 1120 1136 1152 1168 1184 1200 1216 1232 1248 1264 1280 1296 1312 1328 1344 1360 1376 1392 1408 1424 1440 1456 1472 1488 1504 1520 1536 1552 1568 1584 1600 1616 1632 1648 1664 1680 1696 1712 1728 1744 1760 1776 1792 1808 1824 1840 1856 1872 1888 1904 1920 1936 1952 1968 1984 2000 2016 2032 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 2033 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.103326 s, 517.395 MB of memory in use Info: PME using 31 x 31 x 28 pencil grid for FFT and reciprocal sum. Info: PME Z PENCIL LOCATIONS: 1 3 5 7 9 11 13 15 17 19 ... Info: PME Y PENCIL LOCATIONS: 2 4 6 10 12 14 18 20 22 26 ... Info: PME X PENCIL LOCATIONS: 1 3 7 8 11 13 15 16 19 23 ... Info: Startup phase 7 took 0.430731 s, 529 MB of memory in use Info: Startup phase 8 took 0.03582 s, 529 MB of memory in use LDB: Hybrid LB being created... HybridBaseLB: ThreeLevelTree is created. Info: Startup phase 9 took 0.0422091 s, 529 MB of memory in use Info: CREATING 50700 COMPUTE OBJECTS Info: Startup phase 10 took 0.054132 s, 529 MB of memory in use Info: useSync: 1 useProxySync: 0 Info: Startup phase 11 took 0.00194788 s, 529 MB of memory in use Info: Startup phase 12 took 0.020705 s, 529 MB of memory in use Info: Finished startup at 1.52561 s, 529 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 659380.4314 -2869381.2983 298.6008 -3528761.7296 -2866822.6648 298.6008 2254.5227 2342.4104 10194598.5131 2254.5227 2342.4104 LDB: ============= START OF LOAD BALANCING ============== 1.98606 LDB: ============== END OF LOAD BALANCING =============== 2.02025 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 2.02807 LDB: ============= START OF LOAD BALANCING ============== 2.75886 LDB: Largest compute 2580 load 0.171980 is 29.2% of average load 0.588074 LDB: Average compute 0.025937 is 4.4% of average load 0.588074 LDB: Partitioning computes with target load 0.058807 LDB: Increased migratable compute count from 38532 to 48669 LDB: Largest unpartitionable compute is 0.025028 LDB: ============== END OF LOAD BALANCING =============== 2.83373 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 3.00425 Info: Initial time: 2048 CPUs 0.0079381 s/step 0.0459381 days/ns 529 MB memory TIMING: 120 CPU: 1.48977, 0.0101151/step Wall: 1.54686, 0.0103618/step, 0.00310855 hours remaining, 529.000000 MB of memory in use. ENERGY: 120 39522.7596 107164.2799 81911.5202 5102.0255 -4028297.4130 296278.9134 0.0000 0.0000 642582.5957 -2855735.3187 290.9939 -3498317.9144 -2853272.8908 290.1964 -53.8369 24.8624 10350853.5917 -1.4106 -0.3303 LDB: ============= START OF LOAD BALANCING ============== 3.19842 LDB: ============== END OF LOAD BALANCING =============== 3.20002 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 3.20358 LDB: ============= START OF LOAD BALANCING ============== 3.90997 LDB: Largest compute 2161 load 0.061276 is 10.9% of average load 0.563871 LDB: Average compute 0.020607 is 3.7% of average load 0.563871 LDB: TIME 3.91923 LOAD: AVG 0.563872 MAX 0.696869 PROXIES: TOTAL 14232 MAXPE 7 MAXPATCH 8 None MEM: 529 MB LDB: Reverting to original mapping on 1 balancers LDB: TIME 3.93057 LOAD: AVG 0.563872 MAX 0.677839 PROXIES: TOTAL 14490 MAXPE 12 MAXPATCH 9 TorusLB MEM: 529 MB LDB: ============== END OF LOAD BALANCING =============== 3.95906 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 4.15672 Info: Initial time: 2048 CPUs 0.00748817 s/step 0.0433343 days/ns 529 MB memory TIMING: 240 CPU: 2.6256, 0.00946523/step Wall: 2.69986, 0.00960835/step, 0.00256223 hours remaining, 529.000000 MB of memory in use. ENERGY: 240 39079.2070 107332.1269 81856.5808 5113.3212 -4015168.6210 292141.7859 0.0000 0.0000 644575.7192 -2845069.8800 291.8964 -3489645.5992 -2842513.4542 291.3345 20.6378 93.3726 10343455.5745 3.7149 3.7233 LDB: ============= START OF LOAD BALANCING ============== 5.07516 LDB: Largest compute 2161 load 0.081985 is 11.6% of average load 0.706874 LDB: Average compute 0.025855 is 3.7% of average load 0.706874 LDB: TIME 5.09324 LOAD: AVG 0.706875 MAX 0.890211 PROXIES: TOTAL 14490 MAXPE 12 MAXPATCH 9 None MEM: 529 MB LDB: TIME 5.12131 LOAD: AVG 0.706875 MAX 0.745252 PROXIES: TOTAL 16963 MAXPE 23 MAXPATCH 15 RefineTorusLB MEM: 529 MB LDB: ============== END OF LOAD BALANCING =============== 5.12824 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 5.29798 Info: Initial time: 2048 CPUs 0.00763738 s/step 0.0441978 days/ns 529 MB memory TIMING: 360 CPU: 3.75843, 0.00944023/step Wall: 3.84097, 0.00950923/step, 0.00221882 hours remaining, 529.000000 MB of memory in use. ENERGY: 360 39404.8049 107641.7452 81887.3058 5121.2468 -4004127.9509 288115.6112 0.0000 0.0000 647212.8501 -2834744.3870 293.0907 -3481957.2371 -2832177.2988 292.7221 -108.8168 -33.3695 10355632.1292 0.7063 0.7817 LDB: ============= START OF LOAD BALANCING ============== 6.15507 LDB: Largest compute 2161 load 0.083135 is 11.6% of average load 0.713893 LDB: Average compute 0.025894 is 3.6% of average load 0.713893 LDB: TIME 6.16794 LOAD: AVG 0.713896 MAX 0.808072 PROXIES: TOTAL 16963 MAXPE 23 MAXPATCH 15 None MEM: 529 MB LDB: TIME 6.17626 LOAD: AVG 0.713896 MAX 0.75389 PROXIES: TOTAL 16869 MAXPE 23 MAXPATCH 14 RefineTorusLB MEM: 529 MB LDB: ============== END OF LOAD BALANCING =============== 6.18222 Info: useSync: 1 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 6.34729 Info: Benchmark time: 2048 CPUs 0.00711594 s/step 0.0411802 days/ns 529 MB memory TIMING: 480 CPU: 4.79227, 0.00861536/step Wall: 4.8889, 0.00873278/step, 0.00174656 hours remaining, 529.000000 MB of memory in use. ENERGY: 480 39184.9424 107464.7094 82149.4390 5128.6790 -3997925.7766 286185.0357 0.0000 0.0000 649276.2660 -2828536.7050 294.0251 -3477812.9711 -2826000.3223 293.5550 -70.6650 6.1435 10353502.8290 -0.4380 -0.3448 Info: Benchmark time: 2048 CPUs 0.00713266 s/step 0.041277 days/ns 529 MB memory TIMING: 600 CPU: 5.64614, 0.00711558/step Wall: 5.74596, 0.00714212/step, 0.00119035 hours remaining, 529.000000 MB of memory in use. ENERGY: 600 39572.8033 107914.0843 81991.0213 5097.7549 -3994277.0176 285440.0005 0.0000 0.0000 650612.3712 -2823648.9821 294.6301 -3474261.3533 -2821098.7754 294.2361 -89.3143 -15.4090 10353059.6263 -0.0815 -0.0826 Info: Benchmark time: 2048 CPUs 0.00704832 s/step 0.0407889 days/ns 529 MB memory TIMING: 720 CPU: 6.49001, 0.00703226/step Wall: 6.59288, 0.00705772/step, 0.00094103 hours remaining, 529.000000 MB of memory in use. ENERGY: 720 39422.8729 107213.2654 82148.7319 5156.1540 -3986814.9563 281908.0935 0.0000 0.0000 651144.8223 -2819821.0163 294.8713 -3470965.8386 -2817246.3003 294.8593 -168.3571 -95.2311 10362192.0684 3.1371 3.0847 Info: Benchmark time: 2048 CPUs 0.0071169 s/step 0.0411858 days/ns 529 MB memory TIMING: 840 CPU: 7.34088, 0.00709059/step Wall: 7.44805, 0.00712636/step, 0.000712636 hours remaining, 529.000000 MB of memory in use. ENERGY: 840 39127.3340 107469.8369 82161.2099 5167.6154 -3985810.1297 283193.8181 0.0000 0.0000 652239.5691 -2816450.7462 295.3670 -3468690.3153 -2813873.4579 295.3614 -113.3693 -36.8329 10363957.8648 4.0842 4.0756 Info: Benchmark time: 2048 CPUs 0.00717461 s/step 0.0415197 days/ns 529 MB memory TIMING: 960 CPU: 8.19475, 0.00711558/step Wall: 8.31013, 0.00718406/step, 0.000478937 hours remaining, 529.000000 MB of memory in use. ENERGY: 960 39120.4576 107491.7899 82045.4528 5176.7051 -3983819.3093 283133.3249 0.0000 0.0000 653861.7774 -2812989.8015 296.1016 -3466851.5789 -2810425.0235 295.8049 -77.9765 -3.5244 10361819.3728 -0.6086 -0.6616 Info: Benchmark time: 2048 CPUs 0.00728512 s/step 0.0421592 days/ns 529 MB memory TIMING: 1080 CPU: 9.05162, 0.00714058/step Wall: 9.18548, 0.00729454/step, 0.000243151 hours remaining, 529.000000 MB of memory in use. ENERGY: 1080 39317.0749 107505.7749 82193.0641 5113.1268 -3979706.7660 281467.1404 0.0000 0.0000 652775.7061 -2811334.8788 295.6098 -3464110.5849 -2808744.3738 296.0770 -100.2120 -23.2235 10364930.2972 0.8031 0.7814 TIMING: 1200 CPU: 9.91849, 0.0072239/step Wall: 10.0544, 0.00724123/step, 0 hours remaining, 529.000000 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 39028.0938 107542.6189 82074.2789 5173.5740 -3979593.5875 282627.9463 0.0000 0.0000 654044.1643 -2809102.9113 296.1842 -3463147.0756 -2806566.7087 296.3424 -48.9338 27.9566 10364545.3580 0.7959 0.9712 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 0.094 seconds(file I/O: 0.093 secs), 529.000 MB of memory in use The last velocity output (seq=-2) takes 0.151 seconds(file I/O: 0.069 secs), 529.000 MB of memory in use ==================================================== WallClock: 12.868360 CPUTime: 12.060167 Memory: 529.000000 MB