General Information

Tardis3 cluster is a reinstallation of TARDIS Cluster using OpenHPC 2/CentOS 8.

Scheduler/Queues

The cluster scheduler is Slurm. See Slurm documentation page for details.
32 Dell R440 servers are available in the "c8" partition/queue with 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	?	no limit
c5	6	16	32	32	?	no limit
c4	16	12	24	32	?	no limit
c3	9	20	40	48	?	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

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

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
Quantum Espresso 6.7.0	/opt/ohpc/pub/apps/quantum-espresso/6.7.0	module load intel/2021.1.2.266 module load impi/2021.1.1 module load quantum-espresso/6.7.0
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

TARDIS3 Cluster

Contents