Difference between revisions of "TARDIS3 Cluster"

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== General Information ==
 
== 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.
+
:* Tardis3 cluster is a reinstallation of [[TARDIS Cluster]] using OpenHPC 2/CentOS 8.
 +
:* PIs are Craig Fennie and Nicole Benedek.
 +
:* access is restricted.
  
 
= Scheduler/Queues =
 
= 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 | Slurm documentation page ]] for details.
+
:* The cluster scheduler is Slurm. See [[ slurm | Slurm documentation page ]] for details.
−
:* Remember, hyperthreading is enabled on the cluster, so Slurm considers each physical core to consist of two logical CPUs.
+
:* '''[[Slurm Quick Start | 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):
 
:* Partitions (queues):
 
::{| border="1" cellspacing="0" cellpadding="10"
 
::{| border="1" cellspacing="0" cellpadding="10"
 
! Name
 
! Name
 +
! Node Count
 
! Physical Cores
 
! Physical Cores
 
! HT/Slurm CPUs
 
! HT/Slurm CPUs
Line 17: Line 23:
 
|-
 
|-
 
| c8
 
| c8
 +
| 32
 
| 40
 
| 40
 
| 80
 
| 80
Line 22: Line 29:
 
| EDR (100 Gb/s)
 
| EDR (100 Gb/s)
 
| no limit
 
| 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.
 +
 +
<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 ==
Line 30: Line 152:
 
! 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
Line 57: Line 179:
 
* module load fermisurfer/2.1.0
 
* module load fermisurfer/2.1.0
 
|-
 
|-
−
| phonopy 1.22.2
+
|  
 +
* phono3py 1.22.2
 +
* phonopy 2.9.1
 
| /opt/ohpc/pub/libs/intel/openmpi4/phono3py/1.22.2
 
| /opt/ohpc/pub/libs/intel/openmpi4/phono3py/1.22.2
 
|  
 
|  
Line 63: Line 187:
 
* module load openmpi4/4.0.4
 
* module load openmpi4/4.0.4
 
* module load py3-phono3py/1.22.2
 
* 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
 
| /opt/ohpc/pub/apps/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 intel/2021.1.2.266
 
* module load openmpi4/4.0.4
 
* module load openmpi4/4.0.4
−
* module load quantum-espresso/6.7.0
+
* module load vasp/6.2.0
 
|-
 
|-
−
| Vasp 5.4.1 (with WANNIER90)
+
| xcrysden
−
| /opt/ohpc/pub/apps/vasp/5.4.1
+
| /opt/ohpc/pub/apps/xcrysden/1.6.2
 
|  
 
|  
 
* module load intel/2021.1.2.266
 
* 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 vasp/5.4.1
+
* module load xmgrace/5.1.25
 
|-
 
|-
 
| WANNIER90 3.1.0
 
| WANNIER90 3.1.0

Latest revision as of 15:53, 17 March 2023

General Information

  • Tardis3 cluster is a reinstallation of 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 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
  • 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
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