Difference between revisions of "TARDIS3 Cluster"

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::{| border="1" cellspacing="0" cellpadding="10"
 
::{| border="1" cellspacing="0" cellpadding="10"
 
! Name
 
! Name
! Description
+
! Physical Cores
 +
! HT/Slurm CPUs
 +
! RAM
 +
! Infiniband
 
! Time Limit
 
! Time Limit
 
|-
 
|-
 
| c8
 
| c8
| Newest Dell R440 Servers
+
| 40
 +
| 80
 +
| 95
 +
| EDR (100 Gb/s)
 
| no limit
 
| 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.
 +
 +
<pre>
 +
python3 -m venv <your virtual environment directory>
 +
</pre>
 +
 +
=== Activate Virtual Environment ===
 +
 +
You need to '''activate''' a virtual environment before using it:
 +
 +
<pre>source <your virtual environment directory>/bin/activate</pre>
 +
 +
=== 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 <code>pip</code> first:
 +
<pre>pip install --upgrade pip</pre>
 +
 +
* Install the module:
 +
<pre>pip install <module name></pre>
 +
 +
* List installed python modules in the environment:
 +
<pre>pip list modules</pre>
 +
 +
* Examples: Install <code>tensorflow</code> and <code>keras</code> like this:
 +
 +
<pre>
 +
-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
 +
</pre>
  
 
== Software List ==
 
== Software List ==
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! Notes
 
! Notes
 
|-
 
|-
| *GNU Compilers 9.3.0  
+
| GNU Compilers 9.3.0  
 
| /opt/ohpc/pub/compiler/gcc/9.3.0  
 
| /opt/ohpc/pub/compiler/gcc/9.3.0  
 
| module load gnu9/9.3.0
 
| module load gnu9/9.3.0
 
|-
 
|-
| Intel Compilers 2021.1.2.266 (2021 Update 1)
+
| *Intel Compilers 2021.1.2.266 (2021 Update 1)
 
| /opt/intel/oneapi/compiler/2021.1.2
 
| /opt/intel/oneapi/compiler/2021.1.2
 
| module load intel/2021.1.2.266
 
| module load intel/2021.1.2.266
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* /opt/ohpc/pub/mpi/openmpi4-intel
 
* /opt/ohpc/pub/mpi/openmpi4-intel
 
| module load openmpi4
 
| 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
 
| Quantum Espresso 6.7.0
Line 42: Line 158:
 
|  
 
|  
 
* module load intel/2021.1.2.266
 
* 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 openmpi4/4.0.4
* module load quantum-espresso/6.7.0
+
* 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
 
|}
 
|}

Latest revision as of 15:24, 27 August 2021

General Information

Tardis3 cluster is a reinstallation of TARDIS Cluster using OpenHPC 2/CentOS 8. TARDIS Cluster nodes will eventually be migrated to this new cluster.

Scheduler/Queues

  • The cluster scheduler is Slurm. Currently 32 new Dell R440 servers are configured to be in the "c8" partition/queue with no time limits. c1 to c7 queues will be added as the nodes are migrated from the TARDIS Cluster. See Slurm documentation page for details.
  • Remember, hyperthreading is enabled on the cluster, so Slurm considers each physical core to consist of two logical CPUs.
  • Partitions (queues):
Name Physical Cores HT/Slurm CPUs RAM Infiniband Time Limit
c8 40 80 95 EDR (100 Gb/s) 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