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Installing bout++
bendudson edited this page May 11, 2011
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BOUT++ needs, at the minimum:
- MPI
- FFTW
- NetCDF
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.
$ cd /path/to/bout++
$ ./configureElse, you may specify them manually:
$ ./configure MPICXX=/path/to/mpicxx --with-fftw=/path/to/fftw --with-netcdf=/path/to/netcdfThen do the usual
$ makeIf you are still in the bout++ directory, then
$ cd examples/advect1d
$ make
$ ./gas_compressYou 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