Getting started

$ \renewcommand{\vec}[1]{ {\bf #1} } \newcommand{\bnabla}{ \vec{\nabla} } \newcommand{\Rey}{Re} \def\vechat#1{ \hat{ \vec{#1} } } \def\mat#1{#1} $

Overview of files

• Makefile will require modification for your compiler and libraries (see #Compiling_libraries). Sample commands for other compilers can be found near the top of the file.
• parallel.h Ensure _Np is set to 1 if you do not have MPI. This file contains macros for parallelisation that are only invoked if the number of processes Np is greater than 1.
• program/parameters.f90, where you’ll find parameters. See #Parameters
• utils/ contains a number of utilities. Almost anything can be done in a util, both post-processing and analysing data at runtime. There should be no need to alter the core code. See #Making_utils
• Matlab/, a few scripts. See Matlab/Readme.txt .

Parameters

./parallel.h:
_Np

Number of processors (set 1 for serial)
./program/parameters.f90:

i_N	Number of radial points $n\in[1,N]$
i_K	Maximum k (axial), $k\in(-K,\,K)$
i_M	Maximum m (azimuthal), $m\in[0,\,M)$
i_Mp	Azimuthal periodicity, i.e. $m=0,M_p,2M_p,\dots,(M-1)M_p$
	(set =1 for no symmetry assumption)
d_Re	Reynolds number $Re$ or $Rm_m$
d_alpha	Axial wavenumber $\alpha=2\pi/L_z$
b_const_flux	Enforce constant flux $U_b=\frac1{2}$.
i_save_rate1	Save frequency for snapshot data files
i_save_rate2	Save frequency for time-series data
i_maxtstep	Maximum number of timesteps (no limit if set $<0$)
d_cpuhours	Maximum number of cpu hours
d_time	Start time (taken from state.cdf.in if set $<0$)
d_timestep	Fixed timestep (typically 0.01 or dynamically controlled if set $<0$)
d_dterr	Maximum corrector norm, $\|f_{corr}\|$
d_courant	Courant number $\mathrm{C}$
d_implicit	Implicitness $c$

Input files

State files are stored in the NetCDF data format and can be transferred across different architectures safely. The program main.out runs with the compiled parameters (see main.info) but will load states of other truncations. Copy any state file e.g. state0018.cdf.dat to state.cdf.in It will interpolate if necessary.

ll

state.cdf.in:
$t$ & – Start time. Overridden by d_time if d_time$\ge$0
$\Delta t$ & – Timestep. Ignored, see parameter d_timestep.
$N, M_p, r_n$ & – Number of radial points, azimuthal periodicity,
& $\quad$ radial values of the input state.
& – If the radial points differ the fields are
& $\quad$ interpolated onto the new points.
$u_r,\,u_\theta,\, u_z$ & – Field vectors.
& – If $K\ne\,$K or $M\ne\,$M, harmonics are truncated or
& $\quad$ zeros appended.

Output

Snapshot data

Data saved every i_save_rate1 timesteps:

   state????.cdf.dat
   vel_spectrum.dat

All output is sent to the current directory, and state files are numbered 0000, 0001, 0002,…. Each file can be renamed state.cdf.in should a restart be necessary. To list times $t$ for each saved state file,
grep state OUT
The spectrum files are overwritten each save as they are retrievable from the state data. To verify sufficient truncation, a quick profile of the energy spectrum can be plotted with
gnuplot> set log
gnuplot> plot 'vel_spectrum.dat' w lp

Time-series data

Data saved every i_save_rate2 timesteps:

tim_step.dat	$t$, $\Delta t$, $\Delta t_{\|f\|}$, $\Delta t_{CFL}$	current and limiting step sizes
vel_energy.dat	$t$, $E$	energies and viscous dissipation
vel_friction.dat	$t$, $U_b$ or $\beta$, $\langle u_z(r=0)\rangle_z$, $u_\tau$	bulk velocites, pressure, friction vel.

Compiling libraries

Take a look at Makefile. The compiler and flags will probably need editing. There are suggested flags for many compilers at the top of this file.

Building the main code is successful if running make produces no errors, but this requires the necessary libraries to be present - LAPACK, netCDF and FFTW. Often it is necessary to build LAPACK and NetCDF with the compiler and compile flags that will be used for the main simulation code.

The default procedure for building a package (FFTW3, netCDF) is

tar -xvvzf package.tar.gz
cd package/
[set environment variables if necessary]
./configure --prefix=<path>
make
make install

– FFTW3. This usually requires no special treatment. Install with your package manager or build with the default settings.

– LAPACK. If using gfortran you might be able to use the binary version supplied for your linux distribution. Otherwise, edit the file make.inc that comes with LAPACK, setting the fortran compiler and flags to those you plan to use. Type ‘make’. Once finished, copy the following binaries into your library path (see Makefile LIBS -L$<$path$>$/lib/)
cp lapack.a <path>/lib/liblapack.a
cp blas.a <path>/lib/libblas.a

– netCDF. If using gfortran you might be able to use the supplied binary version for your linux distribution. Otherwise, typical environment variables required to build netCDF are
CXX=""
FC=/opt/intel/fc/10.1.018/bin/ifort
FFLAGS="-O3 -mcmodel=medium"
export CXX FC FFLAGS
After the ‘make install’, ensure that files netcdf.mod and typesizes.mod appear in your include path (see Makefile COMPFLAGS -I$<$path$>$/include/). Several versions can be found at http://www.unidata.ucar.edu/downloads/netcdf/current/index.jsp. Version 4.1.3 is relatively straight forward to install, the above flags should be sufficient.

Installation is trickier for more recent versions [2013-12-11 currently netcdf-4.3.0.tar.gz]. First
./configure --disable-netcdf-4 --prefix-<path>
which disables HDF5 support (not currently required in code). Fortran is no longer bundled, so get netcdf-fortran-4.2.tar.gz or a more recent version from here
http://www.unidata.ucar.edu/downloads/netcdf/index.jsp
Build with the above flags, and in addition
CPPFLAGS=-I<path>/include
export CPPFLAGS
Add the link flag -lnetcdff before -lnetcdf in the Makefile.

Compiling, starting and ending a run

• (See also the Tutorial.)

• For serial use set _Np to 1 in parallel.h (no MPI required). The compiler in Makefile might need altering if switching between parallel and serial use, or call mpirun -np 1 ....

• Set the parameters in program/parameters.f90.

• Compile

> make
> make install  

The second command creates the directory install/ and a text file main.info, which is a record of settings at compile time.

• Next an initial condition state.cdf.in is needed. NOTE: Any output state, e.g. state0012.cdf.dat can be copied to state.cdf.in to be used as an initial condition. If resolutions do not match, they are automatically interpolated or truncated.

> mv install ~/runs/job0001
> cd ~/runs/job0001/
> cp .../state0012.cdf.dat state.cdf.in

• To start the run (good to first double-check in main.info that the executable was compiled with correct parameters)

> nohup ./main.out > OUT 2> OUT.err &

After a few moments, press enter again to see if main.out stopped prematurely. If it has stopped there will be a message e.g. '[1]+ Done nohup...'; check OUT.err or OUT for clues why.

• To end the run

> rm RUNNING

This will terminate the job cleanly.

• NOTE: I generate almost all initial conditions by taking a state from a run with similar parameters. If there is a mismatch in i_Mp, use the utility changeMp.f90.

Monitoring a run

Immediately after starting a job, it’s a good idea to check for any warnings

> less OUT

To find out number of timesteps completed, or for possible diagnosis of an early exit,

> tail OUT

The code outputs timeseries data and snapshot data, the latter has a 4-digit number e.g. state0012.cdf.dat.

To see when the in the run each state was saved,

> grep state OUT | less   [OR]
> head -n 1 vel_spec* | less

I often monitor progress with tail vel_energy.dat or

> gnuplot
> plot 'vel_energy.dat' w l

Use rm RUNNING to end the job.

Making utils

The core of the code in program/ rarely needs to be changed. Almost anything can be done by creating a utility instead. There are many examples in utils/ and further information on the Utilities page.

In Makefile, set UTIL = utilname (omitting the .f90 extension), then type 'make util' which builds utilname.out.

It is good practice to do a 'make install' to generate a main.info file to keep alongside the executable.