Difference between revisions of "WALLE Cluster"

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Line 196: Line 196:
| /opt/ohpc/pub/compiler/julia/1.6.1
| /opt/ohpc/pub/compiler/julia/1.6.1
| module load julia/1.6.1
| module load julia/1.6.1
| JDFTx 1.6.0
| /opt/ohpc/pub/apps/jdftx/1.6.0
| module load jdftx/1.6.0
| CUDA 11.3
| CUDA 11.3

Revision as of 15:07, 14 October 2021

General Information

  • Walle is a private virtual cluster in Red Cloud with restricted access to the following groups: ek436_0001. Please see Virtual Cluster in Red Cloud page for more usage information.
  • Head node: walle.cac.cornell.edu (access via ssh)
    • OpenHPC deployment running CentOS 8
    • Cluster scheduler: slurm
  • compute nodes - on demand via slurm
  • data on the walle cluster storage is NOT backed up
  • Please send any questions and report problems to: cac-help@cornell.edu

Compute Nodes

Slurm will create the required Red Cloud instance to run the jobs submitted to the partition. If no partition is specified in the sbatch or srun command, the c2 partition is the default.

Slurm Partitions
Slurm Partition Red Cloud Instance Flavor CPU RAM (GB) GPU
c2 c2.m16 2 16 None
c20 c20.m160 20 160 None
c28 c.28.m224 28 224 None
t1 c4.t1.m20 4 20 Nvidia T4
g1 c14.g1.m60 14 60 Nvidia V100


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)    libfabric/1.10.1 (L)    pmix/3.1.4
   cmake/3.16.2        ohpc             (L)    prun/2.0   (L)
   gnu9/9.3.0   (L)    os                      ucx/1.8.0  (L)

   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 

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 / MKL 2021.2.0.610 (2021 Update 2) /opt/intel/oneapi/compiler/2021.2.0 module load intel/2021.2.0.610
*openmpi 4.0.5
  • /opt/ohpc/pub/mpi/openmpi4-gnu9
  • /opt/ohpc/pub/mpi/openmpi4-intel
module load openmpi4
Intel MPI 2021.2.0 /opt/intel/oneapi/mpi/2021.2.0 module load impi/2021.2.0
Julia 1.6.1 /opt/ohpc/pub/compiler/julia/1.6.1 module load julia/1.6.1
JDFTx 1.6.0 /opt/ohpc/pub/apps/jdftx/1.6.0 module load jdftx/1.6.0
CUDA 11.3 /usr/local/cuda-11.3 module load cuda/11.3
petsc / petsc4py 3.15.0
  • /opt/ohpc/pub/libs/gnu9/openmpi4/petsc/3.15.0
  • /opt/ohpc/pub/libs/intel/impi/petsc/3.15.0
module load petsc/3.15.0
slepc / slepc4py 3.15.0
  • /opt/ohpc/pub/libs/gnu9/openmpi4/slepc/3.15.0
  • /opt/ohpc/pub/libs/intel/impi/slepc/3.15.0
module load slepc/3.15.0
Python3 Modules

(pytorch with CUDA support, numpy, scipy, matplotlib, pandas tensorflow, keras, sklearn, umap)

/opt/ohpc/pub/utils/py3-libs/ module load py3-libs