Installing SuSMoST
Installing SuSMoST from complete archive
The simplest way to start with SuSMoST is to download and install complete SuSMoST archive for your Linux from Downloads page.
For example is you have Debian Testing distribution run the following command in the shell:
$ mkdir susmost
$ cd susmost
$ wget http://susmost.com/_downloads/3f65cc15bf7fa1481a3d78b4228f479c/susmost-debian_testing-openmpi3.1.3.tgz
$ tar -xf susmost-debian_testing-openmpi3.1.3.tgz
These commands will create a working folder susmost
, download an archive with complete SuSMoST for Debian Testing and extract it into the folder. The working folder will contain subfolders with untility scripts (utils
), energy calculators (calculators
), adsoption complexes (acs
) and models (models
). Also Python Wheels of susmost
and susmost.mc
packages will be there. You can observe the folder content with the follwing command:
$ ls -lAh
Its typical output should look like this:
total 22M
drwxr-xr-x 2 pvst lp 4.0K Oct 16 13:04 acs
drwxr-xr-x 2 pvst lp 4.0K Oct 16 13:04 calculators
drwxr-xr-x 7 pvst lp 4.0K Oct 16 13:04 models
-rwxr-xr-x 1 pvst lp 791 Oct 16 13:04 setupve.sh
-rw-r--r-- 1 pvst lp 6.5M Oct 16 12:58 SuSMoST-0.4-cp37-cp37m-linux_x86_64.whl
-rw-r--r-- 1 pvst lp 14M Oct 16 13:05 susmost-debian_testing-openmpi3.1.3.tgz
-rw-r--r-- 1 pvst lp 1.8M Oct 16 12:58 SuSMoST_Monte_Carlo-0.4-cp37-cp37m-linux_x86_64.whl
drwxr-xr-x 2 pvst lp 4.0K Oct 16 13:04 utils
To start working with SuSMoST, you should install its Python packages susmost
and susmost.mc
from corresponding wheels SuSMoST-0.4-cp37-cp37m-linux_x86_64.whl
and SuSMoST_Monte_Carlo-0.4-cp37-cp37m-linux_x86_64.whl
. The setupve.sh
script is intended to help you with this. In modern Debian or Ubuntu distributions just run it with the following command:
$ ./setupve.sh
In CentOS, Red Hat or Fedora you should preliminarly add a path to the corresponding OpenMPI binary files to the PATH environment variable:
$ export PATH=$PATH:/lib64/openmpi/bin
To ensure that your OpenMPI installation is available and of a correct version, run the following command:
$ mpiexec --version
It should show you something like this:
mpiexec (OpenRTE) 3.1.3
Report bugs to http://www.open-mpi.org/community/help/
By default setupve.sh
uses python3
command to create new virtual environment. If python3
interpreter is of an incompatible version, then the script tries to use python3.7
and python3.6
commands. But you can excplicitly specify the command to be used as a Python interpreter by setting SUSMOST_PYTHON
environment variable:
$ SUSMOST_PYTHON=python3.7 ./setupve.sh
You can check Python version with the following command:
$ python3 -V
The setupve.sh
script creates Python virtual environment in the ve
subfolder of the current folder and installs SuSMoST packages along with its dependencies in this environment. To use the virtual environment either activate it with the following command:
$ source ve/bin/activate
or explicitly call the corresponding Python binaries:
$ ve/bin/ipython
If you are not willing to use Python Virtual Environments you can install SuSMoST packages on your own with pip
.
Warning
If you need to use old versions before v.1.0 you should manually install spglib version 1.14.1:
pip install spglib==1.14.1.post0
Installing susmost
package (minimal requirement) with PIP
Download SuSMoST package: Downloads.
Install it with pip
command:
$ pip install susmost
Check installation with command:
$ python -c 'import susmost; print (susmost)'
Download a transfer-matrix tutorial file tm_langmuir_int.py
and try to follow the Tutorial - Transfer-matrix simulation Langmuir adsorption model with interaction.
Installing susmost.mc
package (Monte Carlo addon) with PIP
Make sure that you have Open MPI installed and available. Check MPI version available on your computer with the following command:
$ mpiexec --version
It should show you something like this:
mpiexec (OpenRTE) 2.1.1
Report bugs to http://www.open-mpi.org/community/help/
For successfull installation of both mpicc
command as well as mpiexec
should work in the current shell. It may be necessary to add bin
directory of the appropriate Open MPI installation into the environment variable PATH
. For example:
$ export PATH=$PATH:/usr/lib64/openmpi/bin
Download SuSMoST Monte Carlo package: Downloads
Install it with pip
command:
$ pip install susmost-monte-carlo
Download a Monte Carlo test file test_mc_binary_gas.py
and try to run it.
To start a Monte Carlo test use the following command:
$ mpiexec -np 1 python3 test_mc_binary_gas.py
Here -np 1
is an option that specifies number of MPI processes to be started.
Note
Number of MPI processes must be equal to number of parallel tempering replicas used by Monte Carlo simulation code.