THECUBE Cluster
This is a private cluster.
Hardware
- Head node: thecube.cac.cornell.edu.
- access modes: ssh
- OpenHPC v1.3.8 with CentOS 7.6
- 32 compute nodes with Dual 8-core E5-2680 CPUs @ 2.7 GHz, 128 GB of RAM
- THECUBE Cluster Status: Ganglia.
- Submit HELP requests: help OR by sending an email to CAC support please include THECUBE in the subject area.
File Systems
Home Directories
- Path: ~
User home directories is located on a NFS export from the head node. Use your home directory (~) for archiving the data you wish to keep. Do NOT use this file system for computation as bandwidth to the compute nodes is very limited and will quickly be overwhelmed by file I/Os from large jobs.
Unless special arrangements are made, data in user's home directories are NOT backed up.
Scratch File System
LUSTRE file system runs Intel Lustre 2.7:
- Path: /scratch/<user name>
The scratch file system is a fast parallel file system. Use this file system for scratch space for your jobs. Copy the results you want to keep back to your home directory for safe keeping.
Scheduler/Queues
- The cluster scheduler is slurm. All nodes are configured to be in the "normal" partition with no time limits. See Slurm documentation page for details.
- Partitions (queues):
Name Description Time Limit normal all nodes no limit
Software
Working 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 2) prun/1.3 3) gnu8/8.3.0 4) openmpi3/3.1.4 5) ohpc
To show all available modules (as of Sept 30, 2013):
-bash-4.2$ module avail -------------------- /opt/ohpc/pub/moduledeps/gnu8-openmpi3 -------------------- boost/1.70.0 netcdf/4.6.3 pnetcdf/1.11.1 fftw/3.3.8 phdf5/1.10.5 py3-scipy/1.2.1 ------------------------ /opt/ohpc/pub/moduledeps/gnu8 ------------------------- R/3.5.3 mpich/3.3.1 openblas/0.3.5 py3-numpy/1.15.3 hdf5/1.10.5 mvapich2/2.3.1 openmpi3/3.1.4 (L) -------------------------- /opt/ohpc/pub/modulefiles --------------------------- autotools (L) intel/19.0.2.187 prun/1.3 (L) clustershell/1.8.1 julia/1.2.0 valgrind/3.15.0 cmake/3.14.3 octave/5.1.0 vim/8.1 gnu8/8.3.0 (L) ohpc (L) visit/3.0.1 gurobi/8.1.1 pmix/2.2.2 Where: L: Module is loaded
To load a module and verify:
-bash-4.2$ module load R/3.5.3 -bash-4.2$ module list Currently Loaded Modules: 1) autotools 3) gnu8/8.3.0 5) ohpc 7) R/3.5.3 2) prun/1.3 4) openmpi3/3.1.4 6) openblas/0.3.5
To unload a module and verify:
-bash-4.2$ module list Currently Loaded Modules: 1) autotools 2) prun/1.3 3) gnu8/8.3.0 4) openmpi3/3.1.4 5) ohpc
Managing Modules in Your Python Virtual Environment
Both python2 (2.7) and python3 (3.6) are 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.
- python2:
python -m virtualenv <your virtual environment directory>
- python3:
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 keras and tensorflow like this:
Software List
Software Path Notes Intel Compilers
(including MKL
but NOT impi compilers)/opt/ohpc/pub/compiler/intel/2019/
- module load intel/19.0.2.187
- IMPI compilers (mpiicc, etc) are not included
- IMPI runtimes are included.
gcc 8.3 /opt/ohpc/pub/compiler/gcc/8.3.0/
- module load gnu8/8.3.0 (Loaded by default)
Openmpi 3.1.4 /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4
- module load openmpi3/3.1.4 (Loaded by default)
Boost 1.70.0 /opt/ohpc/pub/libs/gnu8/openmpi3/boost/1.70.0
- module load boost/1.70.0
cmake 3.14.3 /opt/ohpc/pub/utils/cmake/3.14.3
- module load cmake/3.14.3
hdf5 1.10.5 /opt/ohpc/pub/libs/gnu8/hdf5/1.10.5
- module load hdf5/1.10.5
octave 5.1.0 /opt/ohpc/pub/apps/octave/5.1.0
- module load octave/5.1.0
netcdf 4.6.3 /opt/ohpc/pub/libs/gnu8/openmpi3/netcdf/4.6.3
- module load netcdf/4.6.3
fftw 3.3.8 /opt/ohpc/pub/libs/gnu8/openmpi3/fftw/3.3.8
- module load fftw/3.3.8
valgrind 3.15.0 /opt/ohpc/pub/utils/valgrind/3.15.0
- module load valgrind/3.15.0
visit 3.0.1 /opt/ohpc/pub/apps/visit/3.0.1
- module load visit/3.0.1
R 3.5.3 /opt/ohpc/pub/libs/gnu8/R/3.5.3
- module load R/3.5.3
openblas 0.3.5 /opt/ohpc/pub/libs/gnu8/openblas/0.3.5
- module load openblas/0.3.5
vim 8.1 /opt/ohpc/pub/apps/vim/8.1
- module load vim/8.1
julia 1.2.0 /opt/ohpc/pub/compiler/julia/1.2.0
- module load julia/1.2.0
gurobi 8.1.1 /opt/ohpc/pub/apps/gurobi/8.1.1
- module load gurobi/8.1.1
- Create a
~/gurobi.lic
file with the following line:
TOKENSERVER=infrastructure2.tc.cornell.edu
- To use gurobi in your python code:
module load gurobi/8.1.1
- Activate your python virtual environment.
python /opt/ohpc/pub/apps/gurobi/8.1.1/setup.py install
- Now you can import the
gurobipy
class in your python code
Help
- Cluster Status.
- Submit questions or requests at help or by sending email to: help@cac.cornell.edu. Please include THECUBE in the subject area.