Data conversion program#

Simulations under the INCITE project were performed with the pre-released version of Rayleigh V.0.99 on ALCF `Mira <https://www.alcf.anl.gov/alcf-resources/mira>’_ configured with IBM Blue Gene/Q processors. Consequently, data conversion is required for post-processing and to continue simulations from the checkpoint file.

The data conversion tools consists of three programs. Conversion programs for: * parameter file main_input * output data except for checkpoints * the checkpoint data in the folder Checkpoints

Requirement#

The checkpoint data conversion program is written in Fortran95 and C. The other programs are written in Python 3. Consequently, the following compilers and libraries are required:

C
Fortran
Python 3
numpy (https://numpy.org)
matplotlib (https://matplotlib.org)

Installation of compiler and library#

The following are simple examples of the installation procedures for Linux (Ubuntu) and Mac OS. There are a number of package managers available for both Linux and Mac OS that can install the required compilers and libraries.

Ubuntu#

GCC, the GNU Compiler Collection (url{https://gcc.gnu.org}) is already installed in most Linux distributions. However, packages for development are need to be installed. For Ubuntu 20, for example, the required compilers and libraries can be installed by using verb|apt| command as following:

% sudo apt install build-essential gfortran python3
% sudo apt install pip

Then, Python libraries numpy and matplotlib are installed by pip:

% pip install numpy
% pip install matplotlib

Mac OS#

Xcode (Apple) does not have a fortran compiler. The easiest way to install a fortran compiler is by installing GCC by using a package manager such as macports (url{https://www.macports.org}) or homebrew (url{https://brew.sh/index}).

GCC in Homebrew includes the gfortran compiler. The compiler and packages can be installed as follows:

% brew install gcc

Directories#

The top directory for the source files, src, contains the following directories:

% ls src
.               C_src           Makefile.in     config.status   configure.ac
..              Fortran_src     confdb          config.sub      work
.DS_Store       INCITE_convert  config.guess    configure

C_src C source directory
Fortran_src Fortran source directory
work Work directory for build
INCITE_convert Python source directory

Build checkpoint converter program#

The configure script is used for configuration of the install. The simplest way to install programs is the following process. From the top directory.:

%pwd
[HOMEDIR]
% ./configure
...
% make
...

The program “INCITE_checkpoint_converter” can be found in [HOMEDIR]/bin directory as:

% ls bin
.                               INCITE_checkpoint_converter

After the build, object modules in the work directory can be deleted by the following command:

% make clean

To revert the initial repository structure, type the following command:

% make distclean

Convert parameter file#

The checkpoint converter program is performed by executing the following:

% INCITE_convert/convert_main_input.py [INCITE_MAIN_INPUT] [NEW_MAIN_INPUT] [START_STEP]  [END_STEP]

[INCITE_MAIN_INPUT] is the file name of the original parameter file.
[NEW_MAIN_INPUT] is the file name of the new parameter file.

Convert data file except for checkpoint#

CAUTION: This program overwrites the original data. Copy the data to a new directory before running the conversion program:

% INCITE_convert/convert.py [FILES_TO_CONVERT]

[FILES_TO_CONVERT] are the file names to be converted. Regular expressions for UNIX can be used for this file name list.

Convert checkpoint data file#

CAUTION: This program overwrites the original data. Copy the data to a new directory before running the conversion program.