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Installing bout++
seanfarley edited this page Oct 5, 2010
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BOUT++ needs, at the minimum:
- MPI
- FFTW
If the prerequsites are installed into common system locations (/usr, /usr/local, /opt/local, or $HOME/local [in that order]) then configure will pick these packages up automatically. Else, you may specify them manually:
$ cd /path/to/bout++ $ cd bout++ $ ./configure --with-fftw=/path/to/fftw MPICXX=/path/to/mpicxx
Then do the usual
$ make
If you are still in the bout++ directory, then
$ cd examples/advect1d $ make $ ./gas_compress
You should hopefully see the following output:
$ ./gas_compress BOUT++ version 0.85 Code compiled on Oct 5 2010 at 14:56:15 B.Dudson (University of York), M.Umansky (LLNL) 2007 Based on BOUT by Xueqiao Xu, 1999 Compile-time options: Checking enabled, level 3 Signal handling enabled PDB support disabled netCDF support enabled Processor number: 0 of 1 Reading options file data/BOUT.inp Checking command-line options Option nout = 10 Option timestep = 0.01 Option grid = data/advect.grd.cdl Option dump_float = 1 (default) Option non_uniform = 0 (default) Option restart = 0 (default) Option append = 0 (default) Option dump_format = nc Option StaggerGrids = 0 (default) Setting X differencing methods First : Option ddx_first = c4 Fourth order central (C4) Second : Option ddx_second = c4 Fourth order central (C4) Upwind : Option ddx_upwind = u1 First order upwinding (U1) Setting Y differencing methods First : Option ddy_first = c4 Fourth order central (C4) Second : Option ddy_second = c2 Second order central (C2) Upwind : Option ddy_upwind = u1 First order upwinding (U1) Setting Z differencing methods First : Option ddz_first = c4 Fourth order central (C4) Second : Option ddz_second = c2 Second order central (C2) Upwind : Option ddz_upwind = u1 First order upwinding (U1) Setting grid format Option grid_format = (default) Using NetCDF format for file 'data/advect.grd.cdl' Loading mesh Grid size: 5 by 128 Option mxg = 2 Option myg = 2 Option NXPE = 1 (default) Option mz = 17 Option twistshift = false Option TwistOrder = 0 (default) Option ShiftOrder = 0 (default) Option shiftxderivs = false Option IncIntShear = 0 (default) Option BoundaryOnCell = 0 (default) Option StaggerGrids = 0 (default) Option async_send = 0 (default) Option zperiod = 1 (default) Option zmin = 0 Option zmax = 0.25 WARNING: Branch-cut 'jyseps1_2' not found. Setting to 64 WARNING: Branch-cut 'jyseps2_1' not found. Setting to 64 WARNING: Number of inner y points 'ny_inner' not found. Setting to 64 EQUILIBRIUM IS SINGLE NULL (SND) Option xperiodic = 0 (default) Connection between top of Y processor 0 and bottom of 0 in range 0 <= x < 5 => This processor sending in up => This processor sending in down WARNING adding connection: poloidal index -1 out of range MYPE_IN_CORE = 1 DXS = 5, DIN = 0. DOUT = -1 UXS = 5, UIN = 0. UOUT = -1 XIN = -1, XOUT = -1 Twist-shift: DI UI WARNING: Could not read 'g11' from grid. Setting to 1.000000e+00 WARNING: Could not read 'g22' from grid. Setting to 1.000000e+00 WARNING: Could not read 'g33' from grid. Setting to 1.000000e+00 WARNING: Could not read 'g12' from grid. Setting to 0.000000e+00 WARNING: Could not read 'g13' from grid. Setting to 0.000000e+00 WARNING: Could not read 'g23' from grid. Setting to 0.000000e+00 WARNING: Could not read 'zShift' from grid. Setting to 0.000000e+00 WARNING: Z shift for radial derivatives not found WARNING: Twist-shift angle 'ShiftAngle' not found. Setting from zShift Option twistshift_pf = 0 (default) Maximum error in diagonal inversion is 0.000000e+00 Maximum error in off-diagonal inversion is 0.000000e+00 WARNING: Could not read 'J' from grid. Setting to 0.000000e+00 WARNING: Jacobian 'J' not found. Calculating from metric tensor WARNING: Could not read 'Bxy' from grid. Setting to 0.000000e+00 WARNING: Magnitude of B field 'Bxy' not found. Calculating from metric tensor Calculating differential geometry terms Communicating connection terms Boundary regions in this processor: core, sol, done Setting file formats Using NetCDF format for file 'data/BOUT.dmp.0.nc' Initialising Laplacian inversion routines Option async = 1 (default) Option filter = 0.2 (default) Option low_mem = 0 (default) Option use_pdd = 0 (default) Option all_terms = 0 (default) Option laplace_nonuniform = 0 (default) Using serial algorithm Option max_mode = 6 (default) Initialising physics module Option solver_type = (default) Reading contravariant vector v WARNING: Could not read 'vx' from grid. Setting to 0.000000e+00 WARNING: Could not read 'vz' from grid. Setting to 0.000000e+00 Reading contravariant vector g WARNING: Could not read 'gx' from grid. Setting to 0.000000e+00 WARNING: Could not read 'gy' from grid. Setting to 0.000000e+00 WARNING: Could not read 'gz' from grid. Setting to 0.000000e+00 Option gamma = 1.66667 (default) Option gas_viscosity = 0 Option gas_include_viscosity = false Option gas_v0_multiply = -1 Setting boundary for variable density core region: Option density_bndry_core = (default) Option density_bndry_xin = (default) Option density_bndry_all = (default) Option all_bndry_core = (default) Option all_bndry_xin = (default) Option all_bndry_all = neumann neumann sol region: Option density_bndry_sol = (default) Option density_bndry_xout = (default) Option density_bndry_all = (default) Option all_bndry_sol = (default) Option all_bndry_xout = (default) Option all_bndry_all = neumann neumann Initial profile global options Option twistshift = false Option Ballooning = 0 (default) Option ShiftInitial = 0 (default) Option density_scale = 0.5 Option all_xs_opt = 0 Option all_ys_opt = 1 Option all_zs_opt = 2 Option all_xs_mode = 4 (default) Option all_ys_mode = 4 (default) Option all_zs_mode = 1 Option all_xs_phase = 0 (default) Option all_ys_phase = 0 (default) Option all_zs_phase = 0 (default) Option all_xs_s0 = 0.5 (default) Option all_ys_s0 = 0.5 Option all_zs_s0 = 0.5 (default) Option all_xs_wd = 0.2 (default) Option all_ys_wd = 0.1 Option all_zs_wd = 0.2 (default) Setting boundary for variable pressure core region: Option pressure_bndry_core = (default) Option pressure_bndry_xin = (default) Option pressure_bndry_all = (default) Option all_bndry_core = (default) Option all_bndry_xin = (default) Option all_bndry_all = neumann neumann sol region: Option pressure_bndry_sol = (default) Option pressure_bndry_xout = (default) Option pressure_bndry_all = (default) Option all_bndry_sol = (default) Option all_bndry_xout = (default) Option all_bndry_all = neumann neumann Option all_scale = 0 Option all_xs_opt = 0 Option all_ys_opt = 1 Option all_zs_opt = 2 Option all_xs_mode = 4 (default) Option all_ys_mode = 4 (default) Option all_zs_mode = 1 Option all_xs_phase = 0 (default) Option all_ys_phase = 0 (default) Option all_zs_phase = 0 (default) Option all_xs_s0 = 0.5 (default) Option all_ys_s0 = 0.5 Option all_zs_s0 = 0.5 (default) Option all_xs_wd = 0.2 (default) Option all_ys_wd = 0.1 Option all_zs_wd = 0.2 (default) Setting boundary for variable v core region: Option v_bndry_core = (default) Option v_bndry_xin = (default) Option v_bndry_all = (default) Option all_bndry_core = (default) Option all_bndry_xin = (default) Option all_bndry_all = neumann neumann sol region: Option v_bndry_sol = (default) Option v_bndry_xout = (default) Option v_bndry_all = (default) Option all_bndry_sol = (default) Option all_bndry_xout = (default) Option all_bndry_all = neumann neumann Setting boundary for variable vx core region: Option vx_bndry_core = (default) Option vx_bndry_xin = (default) Option vx_bndry_all = (default) Option all_bndry_core = (default) Option all_bndry_xin = (default) Option all_bndry_all = neumann neumann sol region: Option vx_bndry_sol = (default) Option vx_bndry_xout = (default) Option vx_bndry_all = (default) Option all_bndry_sol = (default) Option all_bndry_xout = (default) Option all_bndry_all = neumann neumann Option all_scale = 0 Option all_xs_opt = 0 Option all_ys_opt = 1 Option all_zs_opt = 2 Option all_xs_mode = 4 (default) Option all_ys_mode = 4 (default) Option all_zs_mode = 1 Option all_xs_phase = 0 (default) Option all_ys_phase = 0 (default) Option all_zs_phase = 0 (default) Option all_xs_s0 = 0.5 (default) Option all_ys_s0 = 0.5 Option all_zs_s0 = 0.5 (default) Option all_xs_wd = 0.2 (default) Option all_ys_wd = 0.1 Option all_zs_wd = 0.2 (default) Setting boundary for variable vy core region: Option vy_bndry_core = (default) Option vy_bndry_xin = (default) Option vy_bndry_all = (default) Option all_bndry_core = (default) Option all_bndry_xin = (default) Option all_bndry_all = neumann neumann sol region: Option vy_bndry_sol = (default) Option vy_bndry_xout = (default) Option vy_bndry_all = (default) Option all_bndry_sol = (default) Option all_bndry_xout = (default) Option all_bndry_all = neumann neumann Option all_scale = 0 Option all_xs_opt = 0 Option all_ys_opt = 1 Option all_zs_opt = 2 Option all_xs_mode = 4 (default) Option all_ys_mode = 4 (default) Option all_zs_mode = 1 Option all_xs_phase = 0 (default) Option all_ys_phase = 0 (default) Option all_zs_phase = 0 (default) Option all_xs_s0 = 0.5 (default) Option all_ys_s0 = 0.5 Option all_zs_s0 = 0.5 (default) Option all_xs_wd = 0.2 (default) Option all_ys_wd = 0.1 Option all_zs_wd = 0.2 (default) Setting boundary for variable vz core region: Option vz_bndry_core = (default) Option vz_bndry_xin = (default) Option vz_bndry_all = (default) Option all_bndry_core = (default) Option all_bndry_xin = (default) Option all_bndry_all = neumann neumann sol region: Option vz_bndry_sol = (default) Option vz_bndry_xout = (default) Option vz_bndry_all = (default) Option all_bndry_sol = (default) Option all_bndry_xout = (default) Option all_bndry_all = neumann neumann Option all_scale = 0 Option all_xs_opt = 0 Option all_ys_opt = 1 Option all_zs_opt = 2 Option all_xs_mode = 4 (default) Option all_ys_mode = 4 (default) Option all_zs_mode = 1 Option all_xs_phase = 0 (default) Option all_ys_phase = 0 (default) Option all_zs_phase = 0 (default) Option all_xs_s0 = 0.5 (default) Option all_ys_s0 = 0.5 Option all_zs_s0 = 0.5 (default) Option all_xs_wd = 0.2 (default) Option all_ys_wd = 0.1 Option all_zs_wd = 0.2 (default) Initialising solver Option archive = -1 (default) Option dump_format = nc Option restart_format = nc (default) Using NetCDF format for file 'nc' Initialising SUNDIALS' CVODE solver Boundary region inner X Boundary region outer X 3d fields = 5, 2d fields = 0 neq=51200, local_N=51200 Option mudq = 15 (default) Option mldq = 15 (default) Option mukeep = 5 (default) Option mlkeep = 5 (default) Option solver_atol = 1e-10 Option solver_rtol = 1e-05 Option maxl = 5 (default) Option use_precon = 0 (default) Option use_jacobian = 0 (default) Option max_timestep = -1 (default) Option pvode_mxstep = 500 (default) Option adams_moulton = 0 (default) Using BDF method Option func_iter = 0 (default) Using Newton iteration No preconditioning Using difference quotient approximation for Jacobian Running simulation Run started at : Tue Oct 5 23:21:10 2010 Option wall_limit = -1 (default) Sim Time | RHS evals | Wall Time | Calc Inv Comm I/O SOLVER 1.000e-02 29 - - - - - - 2.000e-02 13 2.34e-01 88.4 0.0 0.3 2.2 9.1 3.000e-02 8 1.50e-01 87.6 0.0 0.3 3.4 8.7 4.000e-02 7 1.30e-01 86.3 0.0 0.3 3.7 9.7 5.000e-02 8 1.54e-01 87.0 0.0 0.3 3.2 9.4 6.000e-02 5 9.62e-02 85.5 0.0 0.3 5.4 8.8 7.000e-02 5 9.38e-02 85.0 0.0 0.3 5.9 8.8 8.000e-02 4 7.69e-02 84.0 0.0 0.3 6.4 9.3 9.000e-02 4 7.78e-02 83.9 0.0 0.3 6.5 9.3 1.000e-01 4 7.85e-02 84.0 0.0 0.3 6.5 9.2 / Step 10 of 10. Elapsed 0:00:01.1 ETA 0:00:00.0 Run finished at : Tue Oct 5 23:21:12 2010 Run time : 2 s