Running command: namd2 +idlepoll +devices 0,1 abeta_eq.conf +p48 Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 48 threads Charm++> Using recursive bisection (scheme 3) for topology aware partitions Converse/Charm++ Commit ID: v6.7.0-0-g46f867c-namd-charm-6.7.0-build-2015-Dec-21-45876 CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (24-way SMP). Charm++> cpu topology info is gathered in 0.020 seconds. Info: Built with CUDA version 10020 Pe 36 physical rank 36 will use CUDA device of pe 32 Pe 35 physical rank 35 will use CUDA device of pe 32 Pe 24 physical rank 24 will use CUDA device of pe 32 Pe 46 physical rank 46 will use CUDA device of pe 32 Pe 33 physical rank 33 will use CUDA device of pe 32 Pe 30 physical rank 30 will use CUDA device of pe 32 Pe 42 physical rank 42 will use CUDA device of pe 32 Pe 13 physical rank 13 will use CUDA device of pe 16 Pe 11 physical rank 11 will use CUDA device of pe 16 Pe 8 physical rank 8 will use CUDA device of pe 16 Pe 41 physical rank 41 will use CUDA device of pe 32 Pe 22 physical rank 22 will use CUDA device of pe 16 Pe 6 physical rank 6 will use CUDA device of pe 16 Pe 17 physical rank 17 will use CUDA device of pe 16 Pe 40 physical rank 40 will use CUDA device of pe 32 Pe 28 physical rank 28 will use CUDA device of pe 32 Pe 27 physical rank 27 will use CUDA device of pe 32 Pe 9 physical rank 9 will use CUDA device of pe 16 Pe 45 physical rank 45 will use CUDA device of pe 32 Pe 44 physical rank 44 will use CUDA device of pe 32 Pe 4 physical rank 4 will use CUDA device of pe 16 Pe 39 physical rank 39 will use CUDA device of pe 32 Pe 1 physical rank 1 will use CUDA device of pe 16 Pe 26 physical rank 26 will use CUDA device of pe 32 Pe 14 physical rank 14 will use CUDA device of pe 16 Pe 29 physical rank 29 will use CUDA device of pe 32 Pe 3 physical rank 3 will use CUDA device of pe 16 Pe 12 physical rank 12 will use CUDA device of pe 16 Pe 15 physical rank 15 will use CUDA device of pe 16 Pe 10 physical rank 10 will use CUDA device of pe 16 Pe 34 physical rank 34 will use CUDA device of pe 32 Pe 43 physical rank 43 will use CUDA device of pe 32 Pe 37 physical rank 37 will use CUDA device of pe 32 Pe 38 physical rank 38 will use CUDA device of pe 32 Pe 19 physical rank 19 will use CUDA device of pe 16 Pe 31 physical rank 31 will use CUDA device of pe 32 Pe 18 physical rank 18 will use CUDA device of pe 16 Pe 2 physical rank 2 will use CUDA device of pe 16 Pe 20 physical rank 20 will use CUDA device of pe 16 Pe 5 physical rank 5 will use CUDA device of pe 16 Pe 25 physical rank 25 will use CUDA device of pe 32 Pe 47 physical rank 47 will use CUDA device of pe 32 Pe 23 physical rank 23 will use CUDA device of pe 16 Pe 7 physical rank 7 will use CUDA device of pe 16 Pe 21 physical rank 21 will use CUDA device of pe 16 Pe 0 physical rank 0 will use CUDA device of pe 16 Charm++> Warning: the number of SMP threads (48) is greater than the number of physical cores (24), so threads will sleep while idling. Use +CmiSpinOnIdle or +CmiSleepOnIdle to control this directly. Pe 16 physical rank 16 binding to CUDA device 0 on gpu02: 'Tesla K40c' Mem: 12206MB Rev: 3.5 Pe 32 physical rank 32 binding to CUDA device 1 on gpu02: 'Tesla K40c' Mem: 12206MB Rev: 3.5 Info: NAMD 2.11 for Linux-x86_64-multicore-CUDA 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 multicore-linux64-gcc Info: Built Tue Mar 10 12:47:44 IST 2020 by locuz on gpu-login Info: 1 NAMD 2.11 Linux-x86_64-multicore-CUDA 48 gpu02 u.sudha Info: Running on 48 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 2.07587 s CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue Info: 73.7031 MB of memory in use based on /proc/self/stat Info: Configuration file is abeta_eq.conf Info: Working in the current directory /home/u.sudha/production2_LPL_2 TCL: Suspending until startup complete. Info: EXTENDED SYSTEM FILE ionized_prod1.restart.xsc Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 19573000 Info: STEPS PER CYCLE 20 Info: PERIODIC CELL BASIS 1 184.272 0 0 Info: PERIODIC CELL BASIS 2 0 190.122 0 Info: PERIODIC CELL BASIS 3 0 0 154.048 Info: PERIODIC CELL CENTER -2.1 -4 38 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 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: VELOCITY FILE ionized_prod1.restart.vel 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: DCD FILENAME ionized_prod2.dcd Info: DCD FREQUENCY 10000 Info: DCD FIRST STEP 19580000 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME ionized_prod2.xst Info: XST FREQUENCY 500 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME ionized_prod2 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME ionized_prod2.restart Info: RESTART FREQUENCY 1000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 Info: PAIRLIST DISTANCE 14 Info: PAIRLIST SHRINK RATE 0.01 Info: PAIRLIST GROW RATE 0.01 Info: PAIRLIST TRIGGER 0.3 Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.5 Info: ENERGY OUTPUT STEPS 1000 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 10000 Info: PRESSURE OUTPUT STEPS 1000 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 300 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS 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 192 192 160 Info: PME MAXIMUM GRID SPACING 1 Info: Attempting to read FFTW data from FFTW_NAMD_2.11_Linux-x86_64-multicore-CUDA.txt Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done. Info: Writing FFTW data to FFTW_NAMD_2.11_Linux-x86_64-multicore-CUDA.txt Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4 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 1585470114 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ionized.pdb Info: STRUCTURE FILE ionized.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all36m_prot.prm Info: PARAMETERS par_all36_carb.prm Info: PARAMETERS par_all36_lipid.prm Info: PARAMETERS par_all36_cgenff.prm Info: PARAMETERS par_all36_na.prm Info: PARAMETERS toppar_water_ions_namd.str Info: PARAMETERS ligand_beta_final.prm Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES ionized_prod1.restart.coor Info: FIRST TIMESTEP 19573000 Info: SKIPPING rtf SECTION IN STREAM FILE Info: SKIPPING rtf SECTION IN STREAM FILE Warning: SKIPPING PART OF PARAMETER FILE AFTER RETURN STATEMENT Info: SUMMARY OF PARAMETERS: Info: 972 BONDS Info: 2840 ANGLES Info: 6939 DIHEDRAL Info: 201 IMPROPER Info: 6 CROSSTERM Info: 355 VDW Info: 82 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 24.1735 Info: TIME FOR READING PDB FILE: 0.869169 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 556000 ATOMS Info: 405604 BONDS Info: 353425 ANGLES Info: 284864 DIHEDRALS Info: 2944 IMPROPERS Info: 360 CROSSTERMS Info: 0 EXCLUSIONS Info: 512415 RIGID BONDS Info: 1155585 DEGREES OF FREEDOM Info: 192952 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 192952 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 3.32985e+06 amu Info: TOTAL CHARGE = 4.25775e-05 e Info: MASS DENSITY = 1.02455 g/cm^3 Info: ATOM DENSITY = 0.103021 atoms/A^3 Info: ***************************** Info: Reading from binary file ionized_prod1.restart.coor Info: Info: Entering startup at 27.5043 s, 269.562 MB of memory in use Info: Startup phase 0 took 0.00586081 s, 269.574 MB of memory in use Info: ADDED 1043320 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0.336131 s, 394.801 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: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Updated CUDA LJ table with 355 x 355 elements. Info: Updated CUDA force table with 4096 elements. Info: Updated CUDA LJ table with 355 x 355 elements. Info: Updated CUDA force table with 4096 elements. Info: Startup phase 2 took 0.287262 s, 504.016 MB of memory in use Info: Startup phase 3 took 0.00194407 s, 504.402 MB of memory in use Info: Startup phase 4 took 0.0310969 s, 704.68 MB of memory in use Info: Startup phase 5 took 0.000734091 s, 704.68 MB of memory in use Info: PATCH GRID IS 11 (PERIODIC) BY 11 (PERIODIC) BY 9 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: Reading from binary file ionized_prod1.restart.vel Info: REMOVING COM VELOCITY 0.00199839 0.0116242 -0.00970334 Info: LARGEST PATCH (403) HAS 597 ATOMS Info: TORUS A SIZE 48 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 0.191842 s, 799.965 MB of memory in use Info: PME using 48 and 48 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 0.0418842 s, 822.188 MB of memory in use Info: Startup phase 8 took 0.018343 s, 826.191 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0.0174301 s, 830.406 MB of memory in use Info: CREATING 23205 COMPUTE OBJECTS CUDA device 1 stream priority range 0 -1 CUDA device 0 stream priority range 0 -1 Info: Found 303 unique exclusion lists needing 1772 bytes Pe 32 hosts 0 local and 22 remote patches for pe 32 Pe 4 hosts 0 local and 7 remote patches for pe 32 Pe 0 hosts 0 local and 23 remote patches for pe 32 Pe 25 hosts 0 local and 23 remote patches for pe 32 Pe 30 hosts 0 local and 23 remote patches for pe 32 Pe 28 hosts 0 local and 23 remote patches for pe 32 Pe 34 hosts 0 local and 23 remote patches for pe 32 Pe 41 hosts 0 local and 22 remote patches for pe 32 Pe 27 hosts 0 local and 22 remote patches for pe 32 Pe 33 hosts 0 local and 22 remote patches for pe 32 Pe 31 hosts 0 local and 23 remote patches for pe 32 Pe 40 hosts 0 local and 23 remote patches for pe 32 Pe 46 hosts 0 local and 23 remote patches for pe 32 Pe 43 hosts 0 local and 23 remote patches for pe 32 Pe 44 hosts 0 local and 23 remote patches for pe 32 Pe 23 hosts 0 local and 10 remote patches for pe 32 Pe 3 hosts 0 local and 23 remote patches for pe 32 Pe 39 hosts 0 local and 23 remote patches for pe 32 Pe 2 hosts 0 local and 23 remote patches for pe 32 Pe 24 hosts 0 local and 22 remote patches for pe 32 Pe 29 hosts 0 local and 22 remote patches for pe 32 Pe 37 hosts 0 local and 23 remote patches for pe 32 Pe 36 hosts 0 local and 22 remote patches for pe 32 Pe 35 hosts 0 local and 23 remote patches for pe 32 Pe 26 hosts 0 local and 22 remote patches for pe 32 Pe 47 hosts 0 local and 23 remote patches for pe 32 Pe 42 hosts 0 local and 23 remote patches for pe 32 Pe 38 hosts 0 local and 22 remote patches for pe 32 Pe 1 hosts 0 local and 23 remote patches for pe 32 Pe 45 hosts 0 local and 23 remote patches for pe 32 Info: Found 303 unique exclusion lists needing 1772 bytes Pe 16 hosts 0 local and 23 remote patches for pe 16 Pe 0 hosts 0 local and 23 remote patches for pe 16 Pe 6 hosts 0 local and 23 remote patches for pe 16 Pe 1 hosts 0 local and 23 remote patches for pe 16 Pe 8 hosts 0 local and 23 remote patches for pe 16 Pe 9 hosts 0 local and 23 remote patches for pe 16 Pe 10 hosts 0 local and 22 remote patches for pe 16 Pe 21 hosts 0 local and 23 remote patches for pe 16 Pe 24 hosts 0 local and 22 remote patches for pe 16 Pe 30 hosts 0 local and 13 remote patches for pe 16 Pe 13 hosts 0 local and 23 remote patches for pe 16 Pe 20 hosts 0 local and 23 remote patches for pe 16 Pe 17 hosts 0 local and 23 remote patches for pe 16 Pe 26 hosts 0 local and 12 remote patches for pe 16 Pe 29 hosts 0 local and 22 remote patches for pe 16 Pe 14 hosts 0 local and 23 remote patches for pe 16 Pe 23 hosts 0 local and 23 remote patches for pe 16 Pe 18 hosts 0 local and 23 remote patches for pe 16 Pe 5 hosts 0 local and 22 remote patches for pe 16 Pe 2 hosts 0 local and 23 remote patches for pe 16 Pe 28 hosts 0 local and 17 remote patches for pe 16 Pe 19 hosts 0 local and 22 remote patches for pe 16 Pe 15 hosts 0 local and 22 remote patches for pe 16 Pe 22 hosts 0 local and 22 remote patches for pe 16 Pe 3 hosts 0 local and 23 remote patches for pe 16 Pe 25 hosts 0 local and 23 remote patches for pe 16 Pe 7 hosts 0 local and 23 remote patches for pe 16 Pe 12 hosts 0 local and 22 remote patches for pe 16 Pe 11 hosts 0 local and 23 remote patches for pe 16 Pe 4 hosts 0 local and 23 remote patches for pe 16 Info: useSync: 0 useProxySync: 0 Info: Startup phase 10 took 0.296416 s, 911.078 MB of memory in use Info: Startup phase 11 took 0.000732183 s, 911.078 MB of memory in use Info: Startup phase 12 took 0.00107884 s, 911.277 MB of memory in use Info: Finished startup at 28.7351 s, 911.539 MB of memory in use TCL: Running for 200000000 steps Pe 32 has 0 local and 652 remote patches and 0 local and 7602 remote computes. Pe 16 has 0 local and 655 remote patches and 0 local and 7644 remote computes. PRESSURE: 19573000 -90.0088 17.0556 -21.1104 17.0559 -136.552 -31.4712 -21.1101 -31.4708 -124.101 GPRESSURE: 19573000 -0.624469 -5.79308 -28.1595 34.9199 -51.2411 4.44144 -14.5829 -8.72301 -48.6619 ENERGY: 19573000 12104.8730 61699.9347 43373.0700 744.1817 -1776571.7002 119221.1627 0.0000 0.0000 343504.6114 -1195923.8668 299.1721 -1539428.4782 -1195556.8222 299.1721 -116.8874 -33.5091 5396963.5667 -116.8874 -33.5091 OPENING EXTENDED SYSTEM TRAJECTORY FILE LDB: ============= START OF LOAD BALANCING ============== 31.481 LDB: ============== END OF LOAD BALANCING =============== 31.4825 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 31.4845 LDB: ============= START OF LOAD BALANCING ============== 36.214 LDB: Largest compute 20274 load 0.064214 is 2.5% of average load 2.529381 LDB: Average compute 0.004037 is 0.2% of average load 2.529381 LDB: Partitioning computes with target load 0.252938 LDB: Increased migratable compute count from 6534 to 6534 LDB: Largest unpartitionable compute is 0.064214 LDB: ============== END OF LOAD BALANCING =============== 36.2279 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 36.2356 Info: Initial time: 48 CPUs 0.0606327 s/step 0.701768 days/ns 1711.44 MB memory LDB: ============= START OF LOAD BALANCING ============== 37.3748 LDB: ============== END OF LOAD BALANCING =============== 37.3764 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 37.3786 LDB: ============= START OF LOAD BALANCING ============== 41.8769 LDB: Largest compute 20259 load 0.078446 is 3.4% of average load 2.302263 LDB: Average compute 0.004028 is 0.2% of average load 2.302263 LDB: TIME 41.8896 LOAD: AVG 2.30226 MAX 3.16549 PROXIES: TOTAL 2131 MAXPE 45 MAXPATCH 5 None MEM: 1734.45 MB LDB: TIME 41.8962 LOAD: AVG 2.30226 MAX 2.65336 PROXIES: TOTAL 2131 MAXPE 45 MAXPATCH 5 TorusLB MEM: 1734.45 MB LDB: ============== END OF LOAD BALANCING =============== 41.9097 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 41.9248 Info: Initial time: 48 CPUs 0.0562765 s/step 0.651349 days/ns 1765.75 MB memory LDB: ============= START OF LOAD BALANCING ============== 47.6028 LDB: Largest compute 20226 load 0.098116 is 3.5% of average load 2.833500 LDB: Average compute 0.005218 is 0.2% of average load 2.833500 LDB: TIME 47.6156 LOAD: AVG 2.8335 MAX 3.32395 PROXIES: TOTAL 2131 MAXPE 45 MAXPATCH 5 None MEM: 1775.71 MB LDB: TIME 47.617 LOAD: AVG 2.8335 MAX 3.32395 PROXIES: TOTAL 2131 MAXPE 45 MAXPATCH 5 RefineTorusLB MEM: 1775.71 MB LDB: TIME 47.6244 LOAD: AVG 2.8335 MAX 2.88264 PROXIES: TOTAL 2169 MAXPE 51 MAXPATCH 5 RefineTorusLB MEM: 1775.71 MB LDB: ============== END OF LOAD BALANCING =============== 47.6278 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 47.6357 Info: Initial time: 48 CPUs 0.0564768 s/step 0.653667 days/ns 1792.5 MB memory LDB: ============= START OF LOAD BALANCING ============== 53.1745 LDB: Largest compute 20274 load 0.096224 is 3.5% of average load 2.771683 LDB: Average compute 0.005070 is 0.2% of average load 2.771683 LDB: TIME 53.186 LOAD: AVG 2.77168 MAX 3.04045 PROXIES: TOTAL 2131 MAXPE 45 MAXPATCH 5 None MEM: 1794.76 MB LDB: TIME 53.1871 LOAD: AVG 2.77168 MAX 3.04045 PROXIES: TOTAL 2169 MAXPE 51 MAXPATCH 5 RefineTorusLB MEM: 1794.76 MB LDB: TIME 53.1958 LOAD: AVG 2.77168 MAX 2.81971 PROXIES: TOTAL 2186 MAXPE 52 MAXPATCH 5 RefineTorusLB MEM: 1794.76 MB LDB: ============== END OF LOAD BALANCING =============== 53.1989 Info: useSync: 0 useProxySync: 0 LDB: =============== DONE WITH MIGRATION ================ 53.2063 Info: Benchmark time: 48 CPUs 0.0556737 s/step 0.644372 days/ns 1799.73 MB memory