TARDIS3

General Information

  • Tardis3 cluster is a reinstallation of the Tardis cluster using OpenHPC 2/CentOS 8.
  • PIs are Craig Fennie and Nicole Benedek.
  • access is restricted.

Scheduler/Queues

  • The cluster scheduler is Slurm. See the Slurm documentation page for details. The Slurm Quick Start guide is a great place to get started.
  • 32 Dell R440 servers are available in the "c8" partition/queue with EDR infiniband and no time limits.
  • Older nodes from the Tardis cluster are also available.
  • Reminder: hyperthreading is enabled on the cluster; Slurm considers each physical core to consist of two logical CPUs.
  • Partitions (queues):
Name Node Count Physical Cores HT/Slurm CPUs RAM Infiniband Time Limit
c8 32 40 80 95 EDR (100 Gb/s) no limit
c7 16 20 40 64 IB no limit
c5 6 16 32 32 IB no limit
c4 16 12 24 32 IB no limit
c3 9 20 40 48 Ethernet no limit

Software

Python Virtual Environment

Use python virtual environment to install modules and configure python for running your python code.

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

  • 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

Software List

Software Path Notes
GNU Compilers 9.3.0 /opt/ohpc/pub/compiler/gcc/9.3.0 module load gnu9/9.3.0
*Intel Compilers 2021.1.2.266 (2021 Update 1) /opt/intel/oneapi/compiler/2021.1.2 module load intel/2021.1.2.266
*openmpi 4.0.4 */opt/ohpc/pub/mpi/openmpi4-gnu9 * /opt/ohpc/pub/mpi/openmpi4-intel module load openmpi4
abinit 9.4.0 /opt/ohpc/pub/apps/abinit/9.4.0 * module load intel/2021.1.2.266 * module load openmpi4/4.0.4 * module load abinit/9.4.0
fermisurfer 2.1.0 /opt/ohpc/pub/apps/fermisurfer/2.1.0 * module load intel/2021.1.2.266 * module load fermisurfer/2.1.0
phono3py 1.22.2 * phonopy 2.9.1 /opt/ohpc/pub/libs/intel/openmpi4/phono3py/1.22.2 * module load intel/2021.1.2.266 * module load openmpi4/4.0.4 * module load py3-phono3py/1.22.2
Octave 6.2.0 /opt/ohpc/pub/apps/octave/6.2.0 * module load intel * module load octave/6.2.0
Octave 6.2.0 /opt/ohpc/pub/apps/octave/6.2.0 * module load intel * module load octave/6.2.0
Vasp 6.2.0 /opt/ohpc/pub/apps/vasp/6.2.0-openmpi * module load intel/2021.1.2.266 * module load openmpi4/4.0.4 * module load vasp/6.2.0
xcrysden /opt/ohpc/pub/apps/xcrysden/1.6.2 * module load intel/2021.1.2.266 * module load xcrysden/1.6.2
xmgrace 5.1.25 /opt/ohpc/pub/apps/xmgrace/5.1.25 * module load intel * module load openmpi4/4.0.4 * module load xmgrace/5.1.25
WANNIER90 3.1.0 /opt/ohpc/pub/apps/wannier90/3.1.0 * module load intel/2021.1.2.266 * module load openmpi4/4.0.4 * module load wannier90/3.1.0