Marx1

General Information

  • Marx1 is a private virtual cluster in Red Cloud with restricted access to the following groups: mtm83_0001. Please see Virtual Cluster in Red Cloud page for more usage information.
  • Head node: marx1.cac.cornell.edu (access via ssh)
  • compute nodes - on demand via slurm
  • data on the Marx1 cluster storage is NOT backed up
  • Please send any questions and report problems to: cac-help@cornell.edu

Globus Access

Software

Work with Environment Modules

Set up the working environment for each package using the module command. The module command will activate dependent modules if there are any.

To show currently loaded modules: (These modules are loaded by default system configurations)

-bash-4.2$ module list

Currently Loaded Modules:
  1) autotools   3) gnu9/9.3.0   5) libfabric/1.10.1   7) ohpc
  2) prun/2.0    4) ucx/1.8.0    6) openmpi4/4.0.4

To show all available modules:

-bash-4.2$ module avail

-------------------- /opt/ohpc/pub/moduledeps/gnu9-openmpi4 --------------------
adios/1.13.1        netcdf-fortran/4.5.2    py3-mpi4py/3.0.3
boost/1.73.0        netcdf/4.7.3            py3-scipy/1.5.1
fftw/3.3.8          opencoarrays/2.8.0      scalapack/2.1.0
hypre/2.18.1        petsc/3.13.1            slepc/3.13.2
mfem/4.1            phdf5/1.10.6            superlu_dist/6.1.1
mumps/5.2.1         pnetcdf/1.12.1          trilinos/13.0.0
netcdf-cxx/4.3.1    ptscotch/6.0.6

------------------------ /opt/ohpc/pub/moduledeps/gnu9 -------------------------
gsl/2.6        mpich/3.3.2-ofi    openmpi4/4.0.4   (L)
hdf5/1.10.6    mvapich2/2.3.2     py3-numpy/1.19.0
metis/5.1.0    openblas/0.3.7     superlu/5.2.1

-------------------------- /opt/ohpc/pub/modulefiles ---------------------------
autotools    (L)    gsutil/4.6.2            os            prun/2.0  (L)
cmake/3.16.2        libfabric/1.10.1 (L)    perl5-libs    ucx/1.8.0 (L)
gnu9/9.3.0   (L)    ohpc             (L)    pmix/3.1.4

Where:
    L:  Module is loaded

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching
any of the "keys".

To load a module and verify:

-bash-4.2$ module load cmake
-bash-4.2$ module list

Currently Loaded Modules:
1) autotools   3) gnu9/9.3.0   5) libfabric/1.10.1   7) ohpc
2) prun/2.0    4) ucx/1.8.0    6) openmpi4/4.0.4     8) cmake/3.16.2

Manage Modules in Your Python Virtual Environment

python 3.6.8 is installed. Users can manage their own python environment (including installing needed modules) using virtual environments. Please see the documentation on virtual environments on python.org for details.

Create Virtual Environment

You can create as many virtual environments, each in their own directory, as needed.

python3 -m venv <your virtual environment directory>

Activate Virtual Environment

You need to activate a virtual environment before using it:

source <your virtual environment directory>/bin/activate

Install Python Modules Using pip

After activating your virtual environment, you can now install python modules for the activated environment:

  • It's always a good idea to update pip first:

    pip install --upgrade pip

  • Install the module:

    pip install <module name>

  • List installed python modules in the environment:

    pip list modules

  • Examples: Install tensorflow and keras like this:

    -bash-4.2$ python3 -m venv tensorflow
-bash-4.2$ source tensorflow/bin/activate
(tensorflow) -bash-4.2$ pip install --upgrade pip
Collecting pip
    Using cached https://files.pythonhosted.org/packages/30/db/9e38760b32e3e7f40cce46dd5fb107b8c73840df38f0046d8e6514e675a1/pip-19.2.3-py2.py3-none-any.whl
Installing collected packages: pip
    Found existing installation: pip 18.1
        Uninstalling pip-18.1:
            Successfully uninstalled pip-18.1
Successfully installed pip-19.2.3
(tensorflow) -bash-4.2$ pip install tensorflow keras
Collecting tensorflow
    Using cached https://files.pythonhosted.org/packages/de/f0/96fb2e0412ae9692dbf400e5b04432885f677ad6241c088ccc5fe7724d69/tensorflow-1.14.0-cp36-cp36m-manylinux1_x86_64.whl
:
:
:
Successfully installed absl-py-0.8.0 astor-0.8.0 gast-0.2.2 google-pasta-0.1.7 grpcio-1.23.0 h5py-2.9.0 keras-2.2.5 keras-applications-1.0.8 keras-preprocessing-1.1.0 markdown-3.1.1 numpy-1.17.1 protobuf-3.9.1 pyyaml-5.1.2 scipy-1.3.1 six-1.12.0 tensorboard-1.14.0 tensorflow-1.14.0 tensorflow-estimator-1.14.0 termcolor-1.1.0 werkzeug-0.15.5 wheel-0.33.6 wrapt-1.11.2
(tensorflow) -bash-4.2$ pip list modules
Package              Version
-------------------- -------
absl-py              0.8.0  
astor                0.8.0  
gast                 0.2.2  
google-pasta         0.1.7  
grpcio               1.23.0 
h5py                 2.9.0  
Keras                2.2.5  
Keras-Applications   1.0.8  
Keras-Preprocessing  1.1.0  
Markdown             3.1.1  
numpy                1.17.1 
pip                  19.2.3 
protobuf             3.9.1  
PyYAML               5.1.2  
scipy                1.3.1  
setuptools           40.6.2 
six                  1.12.0 
tensorboard          1.14.0 
tensorflow           1.14.0 
tensorflow-estimator 1.14.0 
termcolor            1.1.0  
Werkzeug             0.15.5 
wheel                0.33.6 
wrapt                1.11.2