install_unix

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Installing dismod_at in Unix

System Requirements

The following programs are required by dismod_at and should have standard system installs:

C++ Compiler

The dismod_at program can be compiled by any C++98 compliant compiler; e.g., g++ . (Note that a C++11 compiler would be better.)

Fortran Compiler

A fortran compiler is required by ipopt which in turn is required by dismod_at .

git

The git program, a source code version control system, is required by dismod_at .

cmake

The cmake program, which installs other programs, is required by dismod_at .

pkg-config

The pkg-config program must be installed.

python3

The python3, programming language. The packages listed in the standard library are assumed to be present. You need to have the following additional python packages: numpy , matplotlib , scipy , build .

sqlite3

The http://sqlite.org/ library, version 3.7.11 (released on 2012-03-20) or higher; see sqlite releases. Note that the development headers are required; e.g., on Fedora or Red-Hat one needs to install sqlite-devel .

gsl

gsl, the gnu scientific library. Note that the development headers are required; e.g., on Fedora or Red-Hat one needs to install gsl-devel .

suitesparse

The suitesparse sparse matrix package. Note that the development headers are required; e.g., on Fedora or Red-Hat one needs to install suitesparse-devel .

eigen

The eigen <https://libeigen.gitlab.io/eigen/docs-nightly/>_ linear algebra package.

Download dismod_at.git

After installing the requirements above, use the following command to get the current version of dismod_at:

      git clone https://github.com/bradbell/dismod_at.git dismod_at.git
      cd dismod_at.git

You can determine the git_hash and version number corresponding to this checkout of the master branch using the commands:

      git show-ref | grep 'refs/heads/master'
      grep ‘^ SET ( dismod_at_version ‘ CMakeLists.txt

You can checkout an old version corresponding to a specific git_hash , and check its version number, using the commands:

      git checkout -q git_hash
      grep ‘^ SET ( dismod_at_version ‘ CMakeLists.txt

Paths

This discussion is intended to help with the install of the special requirements and dismod_at (see below).

Adding to a Path

The instructions below may require you to add to a path_name . Use the command

echo $ path_name

to see if your initial path is empty. If it is empty, use the command

export path_name = directory

to add directory to the path. If it is non-empty, use

export path_name =” $ path_name : directory “

to add directory to the path.

PKG_CONFIG_PATH

After sqlite3 and gsl are installed the following commands should work:

pkg-config sqlite3 --modversion
pkg-config gsl     --modversion

If one of them fails, a corresponding directory is missing from the PKG_CONFIG_PATH environment variable. If prefix is the prefix where gsl was installed, the command

find -L prefix -name gsl.pc 2> /dev/null

should find the directory where gsl.pc is located. After cppad_mixed is installed (see below), the following command should work:

pkg-config pkg --modversion

where pkg is any of the required packages. (There is one exception, the eigen package uses eigen3 for pkg above.) If one of these commands fails,

find -L dismod_at_prefix -name pkg . pc 2> /dev/null

should find the directory where pkg . pc is located; see dismod_at_prefix .

LD_LIBRARY_PATH

The library locations are set at link time using cmake’s always full rpath commands. Hence, it should not be necessary to set LD_LIBRARY_PATH in order for dismod_at to work.

PATH

After you install dismod_at (see below) you should be able to execute the command

dismod_at

from any directory. If you get the error dismod_at: command not found , you will need to add the binary install directory to you path. Use the following command to find it:

find -L dismod_at_prefix -name dismod_at 2> /dev/null

see dismod_at_prefix .

PYTHONPATH

After you install dismod_at you should be able to execute the following commands:

      python3
      import dismod_at
      quit ()

where python3 is your python3_executable . If you get the error No module named 'dismod_at' , you will need to add the directory where the module is installed to your python path. Use the following command to find it:

find -L dismod_at_prefix -name site-packages 2> /dev/null

Special Requirements

The packages listed below are required by dismod_at and may not have standard system installs

install_settings.py

The settings in bin/install_settings.py are used by the scripts that install the special requirements. You must first change these settings to the appropriate values for your system before running the install scripts below:

ipopt

The Ipopt optimization package. The script bin/get_cppad_mixed.sh (see below) includes an install of ipopt.

cppad

The cppad C++ algorithmic differentiation package. The script bin/get_cppad_mixed.sh (see below) includes an install of cppad.

cppad_mixed

The cppad_mixed C++ random effects modeling package. Starting in the dismod_at.git directory, the command

bin/get_cppad_mixed.sh

can be used to install ipopt, and cppad_mixed. This script also serves as an example of how to install cppad_mixed.

dismod_at

The steps above should only need to be executed once, not for each new version of dismod_at (unless the release_notes say otherwise). The steps below will need to be executed each time you install a new version of dismod_at :

Setup

The file bin/install_settings.py has setting that you should change so they correspond to your machine.

Cmake Command

After changing bin/install_settings.py to work for your system, in the dismod_at.git directory execute the following command:

bin/run_cmake.sh

The script also serves as an example of how to install dismod_at.

Build

The following command is option and will just build the executable program build/devel/dismod_at :

cd build
make
cd ..

Test

The following commands are optional and will, build the dismod_at executable, build the examples and tests, and run the examples, correctness tests, and speed tests:

cd build
make check
make speed
cd ..

Some of the tests use different random number simulations each time they are run. If you get a correctness check failure during a make check or make speed , try running the make command again. If you get the same correctness check fails twice in a row, there probably is a problem and you should get help from the dismod_at development team.

Install

The following command will, build the dismod_at library and executable if necessary, and install dismod_at:

cd build
make install install_python
cd ..

Example

The file example_install.sh contains an example install of dismod_at . The section get_started contains a list of examples and tests of using dismod_at . These tests are run as part of the make check command above.