Gurobi: Difference between revisions

===Academic Usage Agreement=== <!--T:4-->

  My Compute Canada username is "_______" and I am a member of the academic institution "_____________________".  This message confirms that I will only use the Compute Canada Gurobi license provided on Compute Canada systems for the purpose of non-commercial research project(s) to be published in publicly available article(s).

You do NOT need to create a <code>~/.licenses/gurobi.lic</code> file.  The required settings to use the Compute Canada Gurobi license are configured by default when you load a gurobi module on any cluster.  To verify your username has been added to the Compute Canada Gurobi license and is working properly run the following command.  If it returns "Fail" then open a ticket to request help.

  $ gurobi_cl 1> /dev/null && echo Success || echo Fail

  <!--T:42-->

  [gra800:~] gurobi_cl --help

   

  [gra-login2:~] salloc --time=1:00:0 --cpus-per-task=8 --mem=1G --account=def-xyz

  gurobi> help()

where

     * https://www.gurobi.com/documentation/8.1/refman/recording_api_calls.html

  **** https://www.gurobi.com/documentation/8.1/refman/attributes.html

You can record API calls and repeat them with command

[gra800:~] gurobi_cl recording000.grbr

Reference: https://www.gurobi.com/documentation/8.1/refman/recording_api_calls.html

This is an example job script for an optimization model written in the [https://www.gurobi.com/documentation/8.1/refman/lp_format.html LP format].

{{File

#SBATCH --mem-per-cpu=1000M  # memory per CPU (in MB)

# use a version >= 9.0.3  

module load StdEnv/2020

module load gurobi/9.1.0

# Create environment file in current directory setting the number of threads:

echo "Threads ${SLURM_CPUS_ON_NODE:-1}" > gurobi.env

gurobi_cl ${GUROBI_HOME}/examples/data/coins.lp

}}

This is an example jobscript for a model using [https://www.gurobi.com/documentation/8.1/refman/py_python_api_overview.html#sec:Python Gurobi-Python].

{{File

#SBATCH --mem-per-cpu=1000M  # memory per CPU (in MB)

# use a version <= 9.0.2  

module load StdEnv/2016.4    # or StdEnv/2018.3

module load gurobi/9.0.2

# Create environment file in current directory setting the number of threads:

echo "Threads ${SLURM_CPUS_ON_NODE:-1}" > gurobi.env

gurobi.sh  ${GUROBI_HOME}/examples/python/facility.py

}}

Gurobi brings it's own version of Python but that one does not contain any 3rd-party Python packages except Gurobi.  In order to use Gurobi together with popular Python  

packages like NumPy, Matplotlib, Pandas and others, we need to create a [[Python#Creating_and_using_a_virtual_environment|virtual Python environment]] in which we can install both <code>gurobipy</code> and e.g. <code>pandas</code>.

Before we start, we need to decide which combination of versions for Gurobi and Python to use.

<translate>

We see that <code>gurobi/8.1.1</code> brings it's own installation of <code>python2.7/</code> and Python packages for Python 2.7, 3.5, 3.6 and 3.7 (<code>pythonX.Y_utf32/</code>),

while <code>gurobi/9.0.1</code> by default uses <code>python3.7/</code> and brings Python packages for Python 2.7, 3.5, 3.6, 3.7 and 3.8 (<code>pythonX.Y_utf32/</code>).

In this example we want to create a Python environment based on <code>python/3.7</code> in which we want to use <code>gurobi/9.0.1</code> and install the Pandas package.

These steps need to be done only once per system.  

The first step is to load the modules to [[Python#Creating_and_using_a_virtual_environment|create the virtual environment]] and activate it.

{{Commands|prompt=[name@server ~] $

| module load gurobi/9.0.1 python/3.7

}}

Now that the environment has been activated we can install the Python packages we want to use, in this case <code>pandas</code>.

{{Commands|prompt=(env_gurobi) [name@server ~] $

| pip install --no-index  pandas

}}

The third step is to install gurobipy into the environment:

{{Commands|prompt=(env_gurobi) [name@server ~] $

| cd $EBROOTGUROBI

}}

Python scripts can now import both Pandas and Gurobi:

import pandas as pd

  import numpy as np

  # [...]

Once created we can activate Gurobi and the environment with:

module load gurobi/9.0.1

  source ~/env_gurobi/bin/activate

  python  my_gurobi_script.py

Note that we now use <code>python</code> instead of <code>gurobi.sh</code>!

And this is an example job script that we can use:

</translate>

<translate>

Please see [https://support.gurobi.com/hc/en-us/articles/360013195592-How-do-I-cite-Gurobi-software-for-an-academic-publication- How do I cite Gurobi software for an academic publication?]

</translate>