TACC: Starting up job 6245017 TACC: Setting up parallel environment for MVAPICH2+mpispawn. TACC: Starting parallel tasks... Charmrun> started all node programs in 1.111 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 2 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 30 c466-202.stampede.tacc.utexas.edu tg455591 Info: Running on 30 processors, 2 nodes, 2 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0659399 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 1194.75 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 1450742816 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: 0.010793 Info: Info: Entering startup at 0.16512 s, 1292.62 MB of memory in use Info: Startup phase 0 took 0.00158906 s, 1292.62 MB of memory in use Warning: an empty exclusion signature with index 709! Info: Startup phase 1 took 0.0109279 s, 1292.78 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: 8 23 Info: OUTPUT PROC LOCATIONS: 15 Info: Startup phase 2 took 0.0668712 s, 1366.94 MB of memory in use Info: Startup phase 3 took 0.189125 s, 1366.94 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 -0.0121054 -0.00791405 -0.00331608 Info: Startup phase 4 took 0.0673559 s, 1375.33 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 0.110324 s, 1375.33 MB of memory in use Info: TORUS A SIZE 30 USING 0 15 Info: TORUS B SIZE 1 USING 0 Info: TORUS C SIZE 1 USING 0 Info: TORUS MINIMAL MESH SIZE IS 16 BY 1 BY 1 Info: Placed 100% of base nodes on same physical node as patch Info: Startup phase 6 took 0.0220251 s, 1385.8 MB of memory in use Info: PME using 27 and 27 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 2 GRID NODES AND 2 TRANS NODES Info: Startup phase 7 took 0.166742 s, 1381.1 MB of memory in use Info: Startup phase 8 took 0.00998497 s, 1381.1 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.0313358 s, 1381.23 MB of memory in use Info: CREATING 44090 COMPUTE OBJECTS Info: Startup phase 10 took 0.204087 s, 1322.44 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 0.00882316 s, 1322.57 MB of memory in use Info: Startup phase 12 took 0.00961685 s, 1332.04 MB of memory in use Info: Finished startup at 1.06393 s, 1332.04 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 -4134759.4113 375583.0490 0.0000 0.0000 656952.5203 -2871809.2091 297.5013 -3528761.7294 -2869251.5835 297.5013 2249.1680 2336.9580 10194598.5131 2249.1680 2336.9580 LDB: ============= START OF LOAD BALANCING ============== 11.3173 LDB: ============== END OF LOAD BALANCING =============== 11.3207 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 11.3222 LDB: ============= START OF LOAD BALANCING ============== 49.6781 LDB: Largest compute 2966 load 0.156247 is 0.4% of average load 36.767450 LDB: Average compute 0.024242 is 0.1% of average load 36.767450 LDB: Partitioning computes with target load 3.676745 LDB: Increased migratable compute count from 41743 to 41743 LDB: Largest unpartitionable compute is 0.023873 LDB: ============== END OF LOAD BALANCING =============== 49.6999 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 49.7324 Info: Initial time: 30 CPUs 0.400672 s/step 2.3187 days/ns 3254.67 MB memory TIMING: 120 CPU: 48.9786, 0.398539/step Wall: 49.6655, 0.401169/step, 0.120351 hours remaining, 3254.667969 MB of memory in use. ENERGY: 120 39245.9704 106975.6914 82019.1166 5153.6259 -4028155.3157 296120.5186 0.0000 0.0000 640869.9683 -2857770.4244 290.2183 -3498640.3927 -2855222.0020 289.6180 -49.8788 28.7295 10346343.5365 -3.9126 -2.9007 LDB: ============= START OF LOAD BALANCING ============== 59.3848 LDB: ============== END OF LOAD BALANCING =============== 59.3851 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 59.3868 LDB: ============= START OF LOAD BALANCING ============== 97.5559 LDB: Largest compute 2751 load 0.154822 is 0.4% of average load 36.659179 LDB: Average compute 0.024190 is 0.1% of average load 36.659179 LDB: TIME 97.5724 LOAD: AVG 36.6592 MAX 38.1601 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 None MEM: 3242.63 MB LDB: TIME 97.5977 LOAD: AVG 36.6592 MAX 37.1018 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 TorusLB MEM: 3242.63 MB LDB: ============== END OF LOAD BALANCING =============== 97.6406 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 97.6765 Info: Initial time: 30 CPUs 0.398389 s/step 2.30549 days/ns 3257.64 MB memory TIMING: 240 CPU: 96.6603, 0.397348/step Wall: 97.5952, 0.399415/step, 0.106511 hours remaining, 3257.636719 MB of memory in use. ENERGY: 240 39117.6838 107364.3253 82190.1812 5136.5708 -4019396.5643 294011.7954 0.0000 0.0000 644668.5293 -2846907.4785 291.9385 -3491576.0077 -2844403.3454 291.0541 -34.1906 44.2963 10339079.1110 3.4252 3.7692 LDB: ============= START OF LOAD BALANCING ============== 144.475 LDB: Largest compute 3956 load 0.195021 is 0.4% of average load 46.038043 LDB: Average compute 0.030348 is 0.1% of average load 46.038043 LDB: TIME 144.493 LOAD: AVG 46.038 MAX 46.7728 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 None MEM: 3256.99 MB LDB: TIME 144.498 LOAD: AVG 46.038 MAX 46.7728 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 RefineTorusLB MEM: 3256.99 MB LDB: TIME 144.5 LOAD: AVG 46.038 MAX 46.5216 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 RefineTorusLB MEM: 3256.99 MB LDB: ============== END OF LOAD BALANCING =============== 144.502 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 144.533 Info: Initial time: 30 CPUs 0.389863 s/step 2.25615 days/ns 3256.99 MB memory TIMING: 360 CPU: 143.359, 0.389158/step Wall: 144.438, 0.390353/step, 0.0910823 hours remaining, 3256.992188 MB of memory in use. ENERGY: 360 39365.3013 107077.2874 82040.1662 5173.7713 -4008320.5418 290301.5537 0.0000 0.0000 646939.1691 -2837423.2928 292.9667 -3484362.4619 -2834866.6483 292.3524 -4.5681 71.5582 10344300.2499 -0.0027 -0.0068 LDB: ============= START OF LOAD BALANCING ============== 191.288 LDB: Largest compute 3956 load 0.192309 is 0.4% of average load 46.066862 LDB: Average compute 0.030366 is 0.1% of average load 46.066862 LDB: TIME 191.304 LOAD: AVG 46.0669 MAX 46.6891 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 None MEM: 3262.61 MB LDB: TIME 191.309 LOAD: AVG 46.0669 MAX 46.6891 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 RefineTorusLB MEM: 3262.61 MB LDB: TIME 191.31 LOAD: AVG 46.0669 MAX 46.5501 PROXIES: TOTAL 2975 MAXPE 104 MAXPATCH 4 RefineTorusLB MEM: 3262.61 MB LDB: ============== END OF LOAD BALANCING =============== 191.313 Info: build node-aware spanning tree with send: 1, recv: 0 with branch factor 4 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 191.342 Info: Benchmark time: 30 CPUs 0.389632 s/step 2.25481 days/ns 3262.61 MB memory TIMING: 480 CPU: 190.018, 0.388824/step Wall: 191.248, 0.390088/step, 0.0780177 hours remaining, 3262.613281 MB of memory in use. ENERGY: 480 39322.9280 107137.2761 82056.1604 5235.6723 -4000823.7928 287174.2285 0.0000 0.0000 648134.7351 -2831762.7925 293.5081 -3479897.5275 -2829243.8407 293.3180 -82.1294 -7.0259 10351067.1302 0.8967 0.9116 Info: Benchmark time: 30 CPUs 0.388773 s/step 2.24984 days/ns 3262.61 MB memory TIMING: 600 CPU: 236.514, 0.387466/step Wall: 237.901, 0.388774/step, 0.0647957 hours remaining, 3262.613281 MB of memory in use. ENERGY: 600 39402.8705 107513.7377 81965.6370 5136.2721 -3994764.3961 285666.9199 0.0000 0.0000 648946.5464 -2826132.4126 293.8758 -3475078.9589 -2823557.3999 293.8984 -66.1317 7.0197 10352142.4637 2.7203 2.6141 Info: Benchmark time: 30 CPUs 0.38853 s/step 2.24844 days/ns 3262.61 MB memory TIMING: 720 CPU: 282.984, 0.387249/step Wall: 284.525, 0.388531/step, 0.0518041 hours remaining, 3262.613281 MB of memory in use. ENERGY: 720 39266.3207 107173.7736 81877.7105 5211.0537 -3990383.9209 284370.2975 0.0000 0.0000 650659.3772 -2821825.3876 294.6514 -3472484.7648 -2819275.9371 294.5885 -56.9691 19.1521 10353695.0955 0.6517 0.6435 Info: Benchmark time: 30 CPUs 0.388722 s/step 2.24955 days/ns 3262.61 MB memory TIMING: 840 CPU: 329.486, 0.387516/step Wall: 331.172, 0.388723/step, 0.0388723 hours remaining, 3262.613281 MB of memory in use. ENERGY: 840 39360.3051 107711.6920 82054.4060 5134.3150 -3986089.9885 282913.6242 0.0000 0.0000 651861.8264 -2817053.8197 295.1960 -3468915.6461 -2814467.3847 295.1344 -132.2050 -56.8056 10362826.3768 0.5352 0.6044 Info: Benchmark time: 30 CPUs 0.388679 s/step 2.2493 days/ns 3262.61 MB memory TIMING: 960 CPU: 375.965, 0.387324/step Wall: 377.813, 0.38868/step, 0.025912 hours remaining, 3262.613281 MB of memory in use. ENERGY: 960 39138.8381 107676.5431 82213.6325 5207.8252 -3984594.3049 283000.0830 0.0000 0.0000 652827.0788 -2814530.3042 295.6331 -3467357.3829 -2811950.5857 295.6563 -94.8377 -19.3639 10361598.7093 1.4843 1.5119 Info: Benchmark time: 30 CPUs 0.389034 s/step 2.25135 days/ns 3262.61 MB memory TIMING: 1080 CPU: 422.48, 0.387624/step Wall: 424.497, 0.389035/step, 0.0129678 hours remaining, 3262.613281 MB of memory in use. ENERGY: 1080 39205.9728 107557.0324 81988.9972 5073.6481 -3982794.7460 283319.1086 0.0000 0.0000 654072.9838 -2811577.0032 296.1973 -3465649.9871 -2809005.8935 296.0889 -79.2439 -3.9231 10365637.6509 2.7083 2.7280 TIMING: 1200 CPU: 468.911, 0.386925/step Wall: 471.081, 0.388199/step, 0 hours remaining, 3262.613281 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 39132.2046 107691.9957 82121.8724 5113.7353 -3982559.5385 284106.7238 0.0000 0.0000 655091.2321 -2809301.7747 296.6584 -3464393.0068 -2806746.9451 296.1714 13.1832 87.3431 10364879.1630 -1.4425 -1.6286 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 FATAL ERROR: Error on opening binary file /scratch/00288/tg455591/stmv-output.coor: No such file or directory ------------- Processor 15 Exiting: Called CmiAbort ------------ Reason: FATAL ERROR: Error on opening binary file /scratch/00288/tg455591/stmv-output.coor: No such file or directory [15] Stack Traceback: [15:0] [0x4b311a] [15:1] [0xb1bc8b] [15:2] [0x4cea67] [15:3] [0xc72535] [15:4] [0xc724d7] [15:5] [0xd0fe9f] [15:6] [0xe9aa8f] [15:7] [0x4bf9b0] [15:8] [0x4b7843] [15:9] __libc_start_main+0xfd [0x37ac41ed5d] [15:10] [0x40fbf9] Fatal error on PE 15> FATAL ERROR: Error on opening binary file /scratch/00288/tg455591/stmv-output.coor: No such file or directory TACC: Shutdown complete. Exiting.