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AlTar(2.0) Installation Guide (Linux)

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lijun99 edited this page Sep 14, 2018 · 7 revisions

AlTar(2.0) Installation Guide (Linux)

1   Prerequisites

1.1   List of required libraries

To compile altar/pyre, the following software or libraries are required

python3  >= 3.6 (**must**)
gcc >= gcc6 (**must**)
gsl
hdf5
postgresql
openmpi

openblas (recommended)
cuda (optional)

It is recommended that you download the source code and compile these packages by your own. (Most systems come with older versions of python3/gcc; they won't be able to catch the pace of pyre or Michael.)

1.2   Use SPACK to install required packages

Spack

1.3   Use EasyBuild to install required packages

Some recommended compiling options are listed here

python3: --enable-shared
openmpi: --enable-shared --enable-mpi-cxx --with-cuda=${CUDA_PATH}
hdf5: --enable-shared --enable-cxx

2   Download config/pyre/altar

Choose a directory where you plan to put all files, e.g., ${HOME}/tools, and define it as ALTAR_SRC_DIR (the following guide assumes bash, please switch to bash if you are using other shells)

$ 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,

#### bash #####
$ alias mm='python3 ${HOME}/tools/config/make/mm.py'
#### csh/tcsh #####
$ alias mm 'python3 ${HOME}/tools/config/make/mm.py'

3.2   Create mm config file for pyre

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

APPS_DIR = /home/geomod/apps/rhel7

GSL_DIR = $(APPS_DIR)/gsl
GSL_INCDIR = $(GSL_DIR)/include
GSL_LIBDIR = $(GSL_DIR)/lib

HDF5_DIR = $(APPS_DIR)/hdf5
HDF5_INCDIR = $(HDF5_DIR)/include
HDF5_LIBDIR = $(HDF5_DIR)/lib

LIBPQ_DIR = $(APPS_DIR)/postgresql
LIBPQ_INCDIR = $(LIBPQ_DIR)/include
LIBPQ_LIBDIR = $(LIBPQ_DIR)/lib

MPI_DIR = $(APPS_DIR)/openmpi
MPI_EXECUTIVE = mpirun
MPI_INCDIR = $(MPI_DIR)/include
MPI_LIBDIR = $(MPI_DIR)/lib
MPI_VERSION = openmpi

PYTHON = python3.6m
PYTHON_DIR = $(APPS_DIR)/python3
PYTHON_INCDIR = $(PYTHON_DIR)/include/$(PYTHON)
PYTHON_LIB = $(PYTHON)
PYTHON_LIBDIR = $(PYTHON_DIR)/lib
PYTHON_PYCFLAGS = -b

CUDA_DIR = /usr/local/cuda
CUDA_INCDIR = $(CUDA_DIR)/include
CUDA_LIBDIR = $(CUDA_DIR)/lib64

Please modify this file manually if you have a different version of packages, and/or have them installed in a different directory.

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

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 environment 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

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 (please change APPS_DIR and pyre.dir if neccesary):

APPS_DIR = /home/geomod/apps/rhel7
gsl.dir = ${APPS_DIR}/gsl
hdf5.dir = ${APPS_DIR}/hdf5
mpi.dir = ${APPS_DIR}/openmpi
openblas.dir = ${APPS_DIR}/openblas
pyre.dir = ${HOME}/tools
python.dir = ${APPS_DIR}/python3
python.version = 3.6
# end of file

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 environment 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 environment for future runs

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

## ~/.bashrc
. ${HOME}/tools/altar.rc
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