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--- software:gurobi:caviness [2020-04-13 17:30] – [Serial or Threaded Python] anita
+++ software:gurobi:caviness [2022-05-05 11:49] – anita
@@ Line 1: / Line 1: @@
-====== Gurobi on Caviness ======
-<code bash>
-[traine@login00 ~]$ vpkg_versions gurobi
-Available versions in package (* = default version):
-[/opt/shared/valet/2.1/etc/gurobi.vpkg_yaml]
-gurobi  The most powerful mathematical optimization solver out there
-* 9.0.1 release 9.0.1 for Linux
-</code>
-===== Serial or Threaded Python Environment =====
-==== Adding Gurobi to a Anaconda Environment ===
-Based on the instructions on Gurobi's site for installing the Anaconda Python distribution (https://www.gurobi.com/documentation/9.0/quickstart_linux/ins_the_anaconda_python_di.html#section:Anaconda). The following steps can be adapted from those instructions to create an Anaconda Python environment for running Gurobi.
-The workgroup ''it_css'' will be used in this example. The anaconda environment will be created in the home directory of user ''traine''. The workgroup (''$WORKGROUP'') and home directory (''$HOME'') should be changed to reflect your workgroup and home directory. If Gurobi is going to be used by multiple people in a workgroup, then it might be worth installing the Gurobi anaconda environment in a workgroup directory (''$WORKDIR''), instead of installing in each person's home directory. Installing it in a workgroup directory will allow everyone within a workgroup to share that Gurobi anaconda environment, and not have to create their own. See [[abstract:caviness:install_software:workgroup-sw|workgroup software installs on Caviness]] for more details.
-<code bash>
-[traine@login00 ~]$ workgroup -g it_css
-[(it_css:traine)@login00 ~]$ vpkg_require gurobi
-Adding package `gurobi/9.0.1` to your environment
-[(it_css:traine)@login00 ~]$ vpkg_require anaconda/5.2.0:python3
-Adding package `anaconda/5.2.0:python3` to your environment
-[(it_css:traine)@login00 ~]$ conda config --add channels http://conda.anaconda.org/gurobi
-[(it_css:traine)@login00 ~]$ conda create -p ~/gurobiproject
-Solving environment: done
-==> WARNING: A newer version of conda exists. <==
-  current version: 4.5.11
-  latest version: 4.8.3
-Please update conda by running
-    $ conda update -n base -c defaults conda
-## Package Plan ##
-  environment location: /home/1201/gurobiproject
-Proceed ([y]/n)? y
-Preparing transaction: done
-Verifying transaction: done
-Executing transaction: done
-#
-# To activate this environment, use:
-# > source activate /home/1201/gurobiproject
-#
-# To deactivate an active environment, use:
-# > source deactivate
-#
-[(it_css:traine)@login00 ~]$ source activate $HOME/gurobiproject
-(/home/1201/gurobiproject)[(it_css:traine)@login00 ~]$ conda install gurobi scipy pandas joblib
-Solving environment: done
-==> WARNING: A newer version of conda exists. <==
-  current version: 4.5.11
-  latest version: 4.8.3
-Please update conda by running
-    $ conda update -n base -c defaults conda
-## Package Plan ##
-  environment location: /home/2179/gurobiproject
-  added / updated specs:
-    - gurobi
-    - joblib
-    - pandas
-    - scipy
-The following NEW packages will be INSTALLED:
-    _libgcc_mutex:    0.1-main
-    blas:             1.0-mkl
-    ca-certificates:  2020.1.1-0
-    certifi:          2019.11.28-py37_1
-    gurobi:           9.0.1-py37_0             gurobi
-    intel-openmp:     2020.0-166
-    joblib:           0.14.1-py_0
-    ld_impl_linux-64: 2.33.1-h53a641e_7
-    libedit:          3.1.20181209-hc058e9b_0
-    libffi:           3.2.1-hd88cf55_4
-    libgcc-ng:        9.1.0-hdf63c60_0
-    libgfortran-ng:   7.3.0-hdf63c60_0
-    libstdcxx-ng:     9.1.0-hdf63c60_0
-    mkl:              2020.0-166
-    mkl-service:      2.3.0-py37he904b0f_0
-    mkl_fft:          1.0.15-py37ha843d7b_0
-    mkl_random:       1.1.0-py37hd6b4f25_0
-    ncurses:          6.2-he6710b0_0
-    numpy:            1.18.1-py37h4f9e942_0
-    numpy-base:       1.18.1-py37hde5b4d6_1
-    openssl:          1.1.1e-h7b6447c_0
-    pandas:           1.0.3-py37h0573a6f_0
-    pip:              20.0.2-py37_1
-    python:           3.7.7-hcf32534_0_cpython
-    python-dateutil:  2.8.1-py_0
-    pytz:             2019.3-py_0
-    readline:         8.0-h7b6447c_0
-    scipy:            1.4.1-py37h0b6359f_0
-    setuptools:       46.1.3-py37_0
-    six:              1.14.0-py37_0
-    sqlite:           3.31.1-h7b6447c_0
-    tk:               8.6.8-hbc83047_0
-    wheel:            0.34.2-py37_0
-    xz:               5.2.4-h14c3975_4
-    zlib:             1.2.11-h7b6447c_3
-Proceed ([y]/n)? y
-Preparing transaction: done
-Verifying transaction: done
-Executing transaction: done
-[(it_css:traine)@login00 ~]$ source deactivate
-</code>
-==== Running a Gurobi Serial or Threaded Job ====
-The below steps are based on copying a template job script and modifying ''serial.qs'' or ''threads.qs'' script to load run your Gurobi Anaconda environment.
-<note tip>It is a good idea to periodically check in ''/opt/templates/slurm/'' for updated or new [[technical:slurm:templates:start|templates]] to use as job scripts to run generic or specific applications, designed to provide the best performance on Caviness.</note>
-To start, use VALET to load Gurobi and Anaconda. Once those two packages are loaded, the Gurobi Anaconda environment will need to be activated. After the Gurobi Anaconda environment is activated, then the python script that uses Gurobi can be called and ran. After the python script has completed, then the Gurobi Anaconda environment will be need to be deactivated.
-=== Example serial.qs script ===
-<code bash>
-#
-# Do general job environment setup:
-#
-. /opt/shared/slurm/templates/libexec/common.sh
-#
-# [EDIT] Add your script statements hereafter, or execute a script or program
-#        using the srun command.
-#
-vpkg_require gurobi
-vpkg_require anaconda/5.2.0:python3
-source activate ~${USER}/gurobiproject #Directory where the Gurobi Anaconda Environment was installed
-python serial_test.py
-source deactivate
-</code>
-=== Example threads.qs script ===
-<code bash>
-#
-# Do standard OpenMP environment setup:
-#
-. /opt/shared/slurm/templates/libexec/openmp.sh
-#
-# [EDIT] Execute your OpenMP/threaded program using the srun command:
-#
-vpkg_require gurobi
-vpkg_require anaconda/5.2.0:python3
-source activate ~${USER}/gurobiproject #Directory where the Gurobi Anaconda Environment was installed
-python sample_parallel.py
-source deactivate
-</code>
-===== MPI =====