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AlTar(2.0) Installation Guide (Mac)

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Lijun Zhu edited this page Mar 15, 2019 · 3 revisions

AlTar(2.0) Installation Guide (Mac)

1   Prerequisites

1.1   Install Macports

Please follow the instructions from https://www.macports.org/install.php.

The detailed steps are as follows:

  • Install Xcode command line tools. Open a Terminal, and run the following command:

    $ sudo xcode-select --install

    You may receive a warning "Xcode does not appear to be installed" when installing packages: you may neglect these warnings. Alternatively, you can install a full version of Xcode from App Store and activate it by:

    $ sudo xcodebuild -license

  • Download the Macports pkg installer according to your MacOS version from https://www.macports.org/install.php. (To find out your MacOS version, click the Apple logo at the top left corner of the screen and then click "About This Mac".) The download links for current version of Macports are provided below

    Click the downloaded .pkg file from browser or Finder to install Macports. The default installation location of Macports is /opt/local. To check whether Macports is installed properly, you may run:

    $ which port
/opt/local/bin/port

If nothing is shown, you may need to set up the right path to Macports by

$ export PATH=/opt/local/bin:$PATH

and run which port command again.

  • Update Macports repo

    $ sudo port -v selfupdate

  • Some useful port commands

    ### search a package name, e.g. gcc7
$ sudo port search gcc7
### install a package
$ sudo port install gcc7
### uninstall a package
$ sudo port uninstall gcc7
### select the default/active package from available versions (e.g., gcc)
$ sudo port select --list gcc
Available versions for gcc:
        mp-gcc7
        none (active)
$ sudo port select --set gcc mp-gcc7 #to use gcc7 as the default gcc/g++ compiler
$ sudo port select --set gcc none #to use the mac clang as the default gcc/g++ compiler
### list installed packages
$ sudo port installed
### update Macports (run periodically)
$ sudo port -v selfupdate
$ sudo port upgrade outdated

1.2   Install required Macports packages

The required packages for pyre/altar are listed as follows:

gmake
git +bash_completion
python37 +readline
gcc7
openmpi-gcc7 +fortran +threads
gsl +gcc7
openblas +gcc7
hdf5 +cxx +gcc7 +openmpi
fftw-3-single
postgresql10
gdal +gcc7 +hdf5 +openmpi +sqlite3 +spatialite

(Update 2019/03: python >= 3.7 is required.)

download link:

ports.requested

$ curl -L https://raw.githubusercontent.com/lijun99/altar-install/master/mac/ports.requested -o ports.requested

You may install the packages in a batch mode by

$ sudo port -Nu install $(cat ports.requested)

The whole process may take a long time (30mins to an hour). (You may proceed to the following steps while waiting.)

Some post-installation configurations include,

  • select default compilers

    $ sudo port select --set python3 python37
$ sudo port select --set gcc mp-gcc7
$ sudo port select --set mpi openmpi-gcc7-fortran

  • To use bash_completion, add the following lines at the end of your .bash_profile (create one if not exist):

    if [ -f /opt/local/etc/profile.d/bash_completion.sh ]; then
    . /opt/local/etc/profile.d/bash_completion.sh
fi

  • install other common python packages, e.g.,

    $ sudo port install py37-scipy

2   Download config/pyre/altar

Choose a directory where you plan to put all files, e.g., ${HOME}/tools

$ mkdir ${HOME}/tools
$ cd ${HOME}/tools

Download the config/pyre/altar from their github repositories:

$ git clone https://github.com/aivazis/config.git
$ git clone https://github.com/pyre/pyre.git
$ git clone https://github.com/AlTarFramework/altar.git

You shall see three directories config, pyre, altar under ${HOME}/tools.

For developers: the instructions on how to sync with github repos will be provided elsewhere.

3   Install pyre

A detailed guide is available at http://pyre.orthologue.com/install.

3.1   Setup mm environment

mm is software building tool similar to make, scons. To setup mm, download a script file mm.rc and put it under, e.g., ${HOME}/tools/ directory:

content:

${HOME}/tools/mm.rc
download link:

mm.rc

curl -L https://raw.githubusercontent.com/lijun99/altar-install/master/mac/mm.rc -o ${HOME}/tools/mm.rc

To load the mm environment, use the following command in a Terminal

$ . ${HOME}/tools/mm.rc
### or #####
$ source ${HOME}/tools/mm.rc

3.2   Create mm config file for pyre

Create a config.def file under ${HOME}/tools/pyre/.mm directory.

content:

${HOME}/tools/pyre/.mm/config.def
download link:

config.def

$ curl -L https://raw.githubusercontent.com/lijun99/altar-install/master/mac/config.def -o ${HOME}/tools/pyre/.mm/config.def

The config.def contains information (versions, paths) to required packages. Please modify this file manually if you have a different version of packages, and/or have them installed in a different directory (this will be the important step for Linux and other systems).

3.3   Compile pyre

Currently there is a bug in compile process: before Michael fixes this, please run

$ mkdir -p ${HOME}/tools/pyre/products/modules

at first.

To compiler pyre, simply go to pyre directory and run mm

$ cd ${HOME}/tools/pyre
$ mm

You may experience a ConnectionRefusedError: [Errno 61] Connection refused error in the end. This is due to that ssh-server is not enabled in your Mac (System Preferences->Sharing->Remote Login). You may safely neglect this.

If you get an error message about the tests not running correctly, you might need to change your LANG environment variable so that it reads the UTF-8 characters that Michael uses in his code:

setenv LANG en_US.utf-8  (for csh/tcsh)

3.4   Install pyre to tools directory

The compiled pyre package, including python packages, shared libraries, by default, is under ${HOME}/tools/pyre/products directory. It is preferred to install pyre to another directory (e.g., ${HOME}/tools) to keep a stable working version

$ cd ${HOME}/tools
$ rsync -r ${HOME}/tools/pyre/products/* .

To set up environmental variables (different paths) for pyre, create a ${HOME}/tools/altar.rc script file as follows (we name it after altar already because altar is going to be installed in ${HOME}/tools as well and one script is enough to load both pyre and altar)

content:

${HOME}/tools/altar.rc
download link:

altar.rc

$ curl -L https://raw.githubusercontent.com/lijun99/altar-install/master/mac/altar.rc -o ${HOME}/tools/altar.rc

To load pyre (which is required for compiling altar), use the command:

$ . ${HOME}/tools/altar.rc

3.5   Simple test

To test pyre is properly installed, you may try (from any directory):

$ python3
>>> import pyre
>>> pyre.version()
(1, 0, 'bb78330f')

4   Install altar(2.0)

4.1   Prepare the mm config file

Create a file ${HOME}/tools/altar/.mm/config.mm.

content:

${HOME}/tools/altar/.mm/config.mm
download link:

config.m

$ mkdir ${HOME}/tools/altar/.mm
$ curl -L https://raw.githubusercontent.com/lijun99/altar-install/master/mac/config.mm -o ${HOME}/tools/altar/.mm/config.mm

4.2   Compile altar

Go to altar directory and run make

$ cd ${HOME}/tools/altar
$ make

4.3   Install altar to tools directory

The compiled altar package is located, by default, at ${HOME}/tools/altar/builds. Again, we recommend to install these files to ${HOME}/tools/ as well

$ rsync -r ${HOME}/tools/altar/builds/* ${HOME}/tools

4.4   A simple test

The ${HOME}/tools/altar.rc script sets up environmental variables for both pyre and alter. Once it is sourced, you may access them from any working directory.

We use the Gaussian model as a test:

$ mkdir ${HOME}/test
$ cp ${HOME}/tools/altar/models/gaussian/examples/gaussian.pfg ${HOME}/test
$ cd ${HOME}/test
$ gaussian

If you see the altar running with annealing process reports, congratulations! If not, please ask for help!

5   Set up environments for future runs

To run pyre/altar in the future, it will be convenient to add the following lines to ${HOME}/.bash_profile file so that the environmental variables are automatically set once you log in or open a Terminal

## ~/.bash_profile
export PATH=/opt/local/bin:$PATH
. ${HOME}/tools/altar.rc
. ${HOME}/tools/mm.rc
if [ -f /opt/local/etc/profile.d/bash_completion.sh ]; then
    . /opt/local/etc/profile.d/bash_completion.sh
fi
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