TACC: Starting up job 6244939 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 1.263 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 1 unique compute nodes (16-way SMP). Charm++> cpu topology info is gathered in 0.011 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 15 c558-201.stampede.tacc.utexas.edu tg455591 Info: Running on 15 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.056603 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1157.32 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 1450737557 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: 0.0107431 Info: Info: Entering startup at 0.154059 s, 1255.14 MB of memory in use Info: Startup phase 0 took 0.00100899 s, 1255.14 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.00246191 s, 1255.27 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 0.0732911 s, 1402.63 MB of memory in use Info: Startup phase 3 took 0.190025 s, 1402.63 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 -0.00574638 0.000571591 0.0124192 Info: Startup phase 4 took 0.0663779 s, 1411.02 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 0.115505 s, 1411.02 MB of memory in use Info: TORUS A SIZE 15 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 0.018965 s, 1421.49 MB of memory in use Info: PME using 15 and 15 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 1 GRID NODES AND 1 TRANS NODES Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done. Info: Startup phase 7 took 0.194088 s, 1415.15 MB of memory in use Info: Startup phase 8 took 0.014245 s, 1415.15 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.00890708 s, 1415.28 MB of memory in use Info: CREATING 44015 COMPUTE OBJECTS Info: useSync: 0 useProxySync: 0 Info: Startup phase 10 took 0.287041 s, 1428.3 MB of memory in use Info: Startup phase 11 took 0.000945091 s, 1428.3 MB of memory in use Info: Startup phase 12 took 0.0195839 s, 1446.96 MB of memory in use Info: Finished startup at 1.1465 s, 1446.96 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 658421.1647 -2870340.5649 298.1664 -3528761.7296 -2867782.4733 298.1664 2253.3768 2341.2184 10194598.5131 2253.3768 2341.2184 LDB: ============= START OF LOAD BALANCING ============== 21.3925 LDB: ============== END OF LOAD BALANCING =============== 21.3954 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 21.3968 LDB: ============= START OF LOAD BALANCING ============== 97.5034 LDB: Largest compute 3671 load 0.151888 is 0.2% of average load 73.385605 LDB: Average compute 0.024253 is 0.0% of average load 73.385605 LDB: Partitioning computes with target load 7.338561 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023609 LDB: ============== END OF LOAD BALANCING =============== 97.5242 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 97.5308 Info: Initial time: 15 CPUs 0.794678 s/step 4.59883 days/ns 5011.96 MB memory TIMING: 120 CPU: 96.8923, 0.791021/step Wall: 98.1187, 0.794945/step, 0.238484 hours remaining, 5011.960938 MB of memory in use. ENERGY: 120 39531.3822 107479.6046 82058.6404 5136.4230 -4030640.3399 298215.4933 0.0000 0.0000 641739.3038 -2856479.4925 290.6120 -3498218.7963 -2853970.8831 289.9732 -3.3184 73.7619 10345393.7153 -6.6189 -5.6653 LDB: ============= START OF LOAD BALANCING ============== 116.695 LDB: ============== END OF LOAD BALANCING =============== 116.695 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 116.696 LDB: ============= START OF LOAD BALANCING ============== 192.615 LDB: Largest compute 2966 load 0.151250 is 0.2% of average load 73.234871 LDB: Average compute 0.024205 is 0.0% of average load 73.234871 LDB: TIME 192.631 LOAD: AVG 73.2349 MAX 75.9159 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 None MEM: 5031.59 MB LDB: TIME 192.655 LOAD: AVG 73.2349 MAX 74.7278 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 TorusLB MEM: 5031.59 MB LDB: ============== END OF LOAD BALANCING =============== 192.672 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 192.687 Info: Initial time: 15 CPUs 0.792437 s/step 4.58586 days/ns 5033.22 MB memory TIMING: 240 CPU: 191.7, 0.790063/step Wall: 193.286, 0.793061/step, 0.211483 hours remaining, 5033.222656 MB of memory in use. ENERGY: 240 39185.6504 107417.3226 82107.5895 5203.2148 -4017115.9686 291998.2082 0.0000 0.0000 645104.0625 -2846099.9205 292.1357 -3491203.9830 -2843585.8576 291.3866 -23.8278 50.2580 10347015.8394 -6.3853 -6.3543 LDB: ============= START OF LOAD BALANCING ============== 286.22 LDB: Largest compute 3154 load 0.192314 is 0.2% of average load 91.872644 LDB: Average compute 0.030351 is 0.0% of average load 91.872644 LDB: TIME 286.236 LOAD: AVG 91.8726 MAX 93.5279 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 None MEM: 5097.22 MB LDB: TIME 286.24 LOAD: AVG 91.8726 MAX 93.5279 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 RefineTorusLB MEM: 5097.22 MB LDB: TIME 286.247 LOAD: AVG 91.8726 MAX 92.8243 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 RefineTorusLB MEM: 5097.22 MB LDB: ============== END OF LOAD BALANCING =============== 286.25 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 286.255 Info: Initial time: 15 CPUs 0.779172 s/step 4.5091 days/ns 5097.22 MB memory TIMING: 360 CPU: 285.054, 0.777948/step Wall: 286.823, 0.779472/step, 0.181877 hours remaining, 5097.222656 MB of memory in use. ENERGY: 360 39194.6846 106970.7538 82005.9442 5106.2463 -4007399.5133 288290.5192 0.0000 0.0000 647425.7704 -2838405.5949 293.1871 -3485831.3652 -2835857.0001 292.4892 -89.0755 -14.7929 10348120.6247 0.8241 0.8035 LDB: ============= START OF LOAD BALANCING ============== 379.369 LDB: Largest compute 3085 load 0.191993 is 0.2% of average load 91.912477 LDB: Average compute 0.030367 is 0.0% of average load 91.912477 LDB: TIME 379.386 LOAD: AVG 91.9125 MAX 93.0896 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 None MEM: 5097.22 MB LDB: TIME 379.39 LOAD: AVG 91.9125 MAX 93.0896 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 RefineTorusLB MEM: 5097.22 MB LDB: TIME 379.391 LOAD: AVG 91.9125 MAX 92.8598 PROXIES: TOTAL 2315 MAXPE 176 MAXPATCH 3 RefineTorusLB MEM: 5097.22 MB LDB: ============== END OF LOAD BALANCING =============== 379.394 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 379.399 Info: Benchmark time: 15 CPUs 0.775958 s/step 4.4905 days/ns 5097.22 MB memory TIMING: 480 CPU: 377.999, 0.774541/step Wall: 379.968, 0.77621/step, 0.155242 hours remaining, 5097.222656 MB of memory in use. ENERGY: 480 39150.3979 107102.7050 82197.4519 5061.9838 -4000085.2836 287055.2937 0.0000 0.0000 647382.8757 -2832134.5756 293.1677 -3479517.4513 -2829525.0196 293.1343 -83.3098 -7.8156 10351544.7824 3.8090 3.7162 Info: Benchmark time: 15 CPUs 0.774033 s/step 4.47935 days/ns 5097.22 MB memory TIMING: 600 CPU: 470.707, 0.772574/step Wall: 472.852, 0.774034/step, 0.129006 hours remaining, 5097.222656 MB of memory in use. ENERGY: 600 39235.0193 107540.3644 82090.2373 5168.5681 -3993530.7178 284731.5780 0.0000 0.0000 650177.6996 -2824587.2512 294.4333 -3474764.9508 -2822075.9412 294.1127 -151.9578 -76.2964 10362890.9277 1.1619 1.2848 Info: Benchmark time: 15 CPUs 0.774539 s/step 4.48229 days/ns 5161.22 MB memory TIMING: 720 CPU: 563.482, 0.773124/step Wall: 565.797, 0.774541/step, 0.103272 hours remaining, 5161.222656 MB of memory in use. ENERGY: 720 39027.9752 107503.2370 82192.4418 5162.1366 -3988796.2678 283948.3873 0.0000 0.0000 650350.6955 -2820611.3944 294.5116 -3470962.0899 -2818043.7220 294.7369 -78.7276 -3.2520 10358608.0001 0.4743 0.5176 Info: Benchmark time: 15 CPUs 0.774295 s/step 4.48088 days/ns 5161.22 MB memory TIMING: 840 CPU: 656.164, 0.772349/step Wall: 658.713, 0.774297/step, 0.0774297 hours remaining, 5161.222656 MB of memory in use. ENERGY: 840 39454.2800 107556.4942 82042.1224 5153.8038 -3985837.0813 283221.8914 0.0000 0.0000 651593.0487 -2816815.4407 295.0742 -3468408.4894 -2814240.0410 295.1955 -69.7300 5.5737 10363386.2940 -0.5292 -0.5006 Info: Benchmark time: 15 CPUs 0.773899 s/step 4.47858 days/ns 5161.22 MB memory TIMING: 960 CPU: 748.859, 0.772458/step Wall: 751.581, 0.7739/step, 0.0515933 hours remaining, 5161.222656 MB of memory in use. ENERGY: 960 39251.4971 107634.2985 81827.8173 5125.7776 -3985666.5704 283859.0838 0.0000 0.0000 654309.1820 -2813658.9141 296.3043 -3467968.0961 -2811067.3454 295.6731 -29.8984 44.5588 10356874.5869 -0.7278 -0.7891 [c558-201.stampede.tacc.utexas.edu:mpirun_rsh][signal_processor] Caught signal 15, killing job