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999938825新虫 (初入文坛)
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[求助]
为什么我用namd 计算例子 cpu和 gpu占用率为0？
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我在win10 下用 namd 2.11 的 cuda版 进行测试 cpu i5 5500u gpu 830m 内存8gb 下面是log文件的信息 D:\namd-tutorial-files\NAMD>namd2 +idlepoll +devices 0 ubq_wb_eq.conf Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 1 threads Charm++> Using recursive bisection (scheme 3) for topology aware partitions Charm++ warning> fences and atomic operations not available in native assembly Converse/Charm++ Commit ID: v6.7.0-0-g46f867c-namd-charm-6.7.0-build-2015-Dec-21-45876 [0] isomalloc.c> Disabling isomalloc because mmap() does not work CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (4-way SMP). Charm++> cpu topology info is gathered in 0.016 seconds. Info: Built with CUDA version 6050 Pe 0 physical rank 0 binding to CUDA device 0 on K33: 'GeForce 830M' Mem: 2048MB Rev: 5.0 Info: NAMD 2.11 for Win64-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-win64 Info: Built Mon, Dec 21, 2015 10:32:11 AM by jim on europa Info: Running on 1 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 1.594 s Info: 24.1992 MB of memory in use based on GetProcessMemoryInfo Info: Configuration file is ubq_wb_eq.conf Info: Working in the current directory D:\namd-tutorial-files\NAMD TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 2 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 10 Info: PERIODIC CELL BASIS 1 42 0 0 Info: PERIODIC CELL BASIS 2 0 44 0 Info: PERIODIC CELL BASIS 3 0 0 47 Info: PERIODIC CELL CENTER 31 29 17.5 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT. Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 2000 steps Info: FIRST LDB TIMESTEP 50 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 310 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 ubq_wb_eq.dcd Info: DCD FREQUENCY 250 Info: DCD FIRST STEP 250 Info: DCD FILE WILL CONTAIN UNIT CELL DATA Info: XST FILENAME ubq_wb_eq.xst Info: XST FREQUENCY 250 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME ubq_wb_eq Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME ubq_wb_eq.restart Info: RESTART FREQUENCY 500 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 0.495 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 16.995 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: PRESSURE OUTPUT STEPS 100 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN USING BBK INTEGRATOR Info: LANGEVIN DAMPING COEFFICIENT IS 1 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 310 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-006 Info: PME EWALD COEFFICIENT 0.257952 Info: PME INTERPOLATION ORDER 4 Info: PME GRID DIMENSIONS 44 44 48 Info: PME MAXIMUM GRID SPACING 1 Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2 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-008 Info: MAX ITERATIONS : 100 Info: RIGID WATER USING SETTLE ALGORITHM Info: RANDOM NUMBER SEED 1478520185 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB ubq_wb.pdb Info: STRUCTURE FILE ubq_wb.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_lipid.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 180 BONDS Info: 447 ANGLES Info: 566 DIHEDRAL Info: 46 IMPROPER Info: 6 CROSSTERM Info: 119 VDW Info: 0 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Info: TIME FOR READING PSF FILE: 0.0779998 Info: TIME FOR READING PDB FILE: 0.0150001 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 7051 ATOMS Info: 5117 BONDS Info: 4197 ANGLES Info: 3293 DIHEDRALS Info: 204 IMPROPERS Info: 74 CROSSTERMS Info: 0 EXCLUSIONS Info: 6449 RIGID BONDS Info: 14704 DEGREES OF FREEDOM Info: 2542 HYDROGEN GROUPS Info: 4 ATOMS IN LARGEST HYDROGEN GROUP Info: 2542 MIGRATION GROUPS Info: 4 ATOMS IN LARGEST MIGRATION GROUP Info: TOTAL MASS = 43514.7 amu Info: TOTAL CHARGE = 1.00955e-006 e Info: MASS DENSITY = 0.831947 g/cm^3 Info: ATOM DENSITY = 0.0811803 atoms/A^3 Info: ***************************** Info: Info: Entering startup at 1.734 s, 26.9258 MB of memory in use Info: Startup phase 0 took 0 s, 26.9258 MB of memory in use Info: ADDED 12578 IMPLICIT EXCLUSIONS Info: Startup phase 1 took 0 s, 28.4375 MB of memory in use Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 769 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-023 AT 11.9138 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.40436e-016 AT 11.9138 Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556 Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 4.10282e-022 AT 11.9138 Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.56912e-015 AT 11.9138 Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556 Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-032 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-014 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-032 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-015 AT 11.9138 Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946 Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-025 AT 11.8295 Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-015 AT 11.9138 Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-026 AT 11.9138 Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-016 AT 11.9138 Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946 Info: Updated CUDA LJ table with 119 x 119 elements. Info: Updated CUDA force table with 4096 elements. Info: Startup phase 2 took 0.157 s, 93.957 MB of memory in use Info: Startup phase 3 took 0 s, 93.957 MB of memory in use Info: Startup phase 4 took 0 s, 93.957 MB of memory in use Info: Startup phase 5 took 0 s, 93.957 MB of memory in use Info: PATCH GRID IS 2 (PERIODIC) BY 2 (PERIODIC) BY 2 (PERIODIC) Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY Info: REMOVING COM VELOCITY -0.0232756 -0.0316902 0.0218916 Info: LARGEST PATCH (6) HAS 940 ATOMS Info: TORUS A SIZE 1 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 s, 95.5039 MB of memory in use Info: PME using 1 and 1 processors for FFT and reciprocal sum. Info: PME GRID LOCATIONS: 0 Info: PME TRANS LOCATIONS: 0 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 0.0149999 s, 95.5039 MB of memory in use Info: Startup phase 8 took 0 s, 95.5039 MB of memory in use LDB: Central LB being created... Info: Startup phase 9 took 0 s, 95.5039 MB of memory in use Info: CREATING 175 COMPUTE OBJECTS CUDA device 0 stream priority range 0 -1 Info: Found 223 unique exclusion lists needing 632 bytes Pe 0 hosts 0 local and 8 remote patches for pe 0 Info: Startup phase 10 took 0 s, 96.707 MB of memory in use Info: Startup phase 11 took 0 s, 96.707 MB of memory in use Info: Startup phase 12 took 0 s, 97.9609 MB of memory in use Info: Finished startup at 1.906 s, 97.9609 MB of memory in use TCL: Minimizing for 100 steps Pe 0 has 0 local and 8 remote patches and 0 local and 112 remote computes. 然后什么反应也没有了 这是怎么回事啊 |
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