System News and Updates
News, updates, outages, maintenance periods
June 2020
Updates
R/4.0.0 compiled with GNU8+OpenBLAS and Intel+MKL is available
Outage
06/09/20 - a persistent cooling problem in our campus datacenter forced us to power down the HPC until a permanent fix is in place.
May 2020
Updates
Documentation page moved to https://docs.hpc.cofc.edu
HPC@CofC highlighted on Campus IT's biannual newsletter
New JupyterHub kernels including Python[2.7/3.6/3.7], R, Julia, Matlab, Mathematica, GNUplot, and ArcGIS ... etc. Check them out at https://hpc.cofc.edu/jupyterhub
PGI compilers added
Outage
05/17/20 - a cooling problem in our campus datacenter forced us to power down most of the cluster for 18 hours. Everything has been restored to its normal state now. Please report any problems to hpc@cofc.edu
Maintenance
05/23/20 - the cluster will be inaccessible from 8AM-8PM due to a planned public network upgrade. The HPC will continue operating normally, but it won't be accessible during this period.
April 2020
Updates
JupyterHub installed. Please see the documentation here. Users are encouraged to use it instead of setting up SSH port forwarding themselves.
FastX3 upgraded to 3.0.46
March 2020
Updates
Singularity upgraded to version 3.4.1
FastX3 upgraded to 3.0.44
Jave JDK version updated to java/jdk-11.0.7. Use modules to load it.
February 2020
Updates
Split view of compute and storage servers in Ganglia
New 24-core compute node with 1 NVIDIA Quadro P4000 GPU and 2TB local storage deployed
MarvinSuite from ChemAxon available on the login node. Some features are not available in the free version, so you may need to get a license by creating an account at ChemAxon and request a free personal academic license.
Community version of Cambridge Crystallographic Data Centre's Mercury -- you would need your own license to access features only available in the commercial version such as CSD System, CSD Materials, CSD Discovery
Dec 2019 - Jan 2020
Updates
Newly installed software
chem/amber/18-gpu and chem/amber/18-cpu with AmberTools19
chem/xtb/6.2.2
math/matlab/r2019b
bio/ncbi-blast+/2.10.0
bio/mothur
See the example runs here
November 2019
Updates
Documentation on our remote desktop service (StarNet FastX) is added here. You can download the FastX desktop client or a web client.
Please run
module spiderto see newly installed and updated software
October 2019
Updates
A new remote desktop service (StarNet FastX) is available to get a full graphical Linux environment on the HPC. You can download the FastX client for your local computer here.
VisIT and ParaView visualizations are now available on the HPC to allow remote visualization of data on the HPC on your local computer. Documentation on these tools will be available soon.
The Spack package manger is made available to users to compile very complex software stacks in their own space. Please run '
module purge; module load spack' to set up the Spack environment.
Maintenance
10/04/19 - 10/20/19 : network access to the HPC may be blocked from certain locations during some traffic rerouting attempts to optimize the network's throughput
September 2019
Updates
A host of new bioinformatics packages are now installed on the cluster. You can access them using modules from a common area or install the Bioconda package from Anaconda to install them in your home directory. These packages are
bio/vcftools, bio/samtools, bio/ngstools, bio/minimap2, bio/hisat2, bio/bwa, bio/bowtie2, bio/bowtie, bio/bedtools, bio/angsd
For other newly installed software, please run
module spider. There should be accompanying example runs at CofC-HPC GitHub pageMore documentation including YouTube videos are in the works. Please check in later for links
August 2019
Updates
Standard version of AIMALL is installed to do atoms-in-molecules(AIM) analysis on molecular systems starting from quantum mechanical wavefunctions.
The host name of the login node (hpc.cofc.edu) has been aliased as 'openhpc.cofc.edu'
Documentation on using a Cendio Thinlinc client to get remote desktop access to the cluster is added here.
Maintenance
A maintenance period will be scheduled at the end of the month to enable database integration to our scheduler and make other changes.
July 2019
Updates
Jupyter Notebooks are now available. You can set up your own Anaconda environment to run Python2/3, R and other codes using a web Jupyter Notebook. Please see the Jupyter Notebooks page
Maintenance
Network access to the cluster will be intermittent Thursday, July 18, 2019 from 1:30PM to 4:00PM due to a planned firewall upgrade in the datacenter. All your calculations and services that are not dependent on external network access will proceed uninterrupted. Please report any problems to hpc@cofc.edu.
June 2019
Updates
The available software has been expanded substantially. Please check the Software List or enter
module spiderto see the current list.
Maintenance
05/20/19-07/03/19 - Support will be limited due to staff vacations. We will try to accommodate any requests sent to hpc@cofc.edu.
May 2019
Updates
R/3.4.2 and R/3.5.2 are added for the GNU7/8-openmpi3 and Intel-openmpi3 stacks
The available software has been expanded substantially. Please check the Software List or enter
module spiderto see the current list.
Outage
05/20/19 - a cooling problem in our campus datacenter forced us to power down the cluster for 10 hours. Everything has been restored to its normal state. Please report any problems to hpc@cofc.edu.
April 2019
Updates
04/25/19 - WebMO installation is up with interfaces to many computational chemistry software including Gaussian16, GAMESS, Orca, Psi4 and MOPAC
04/22/19 - the cluster is open to all campus users. Please feel free to Request an Account
04/05/19 - the cluster is open to a few users for testing. It'll be open to all other users in two weeks if it is deemed ready for production runs.
March 2019
Updates
03/07/19 - The HPC cluster is installed by Dell-EMC.
03/11/19 - Testing and benchmarking the cluster
03/26/19 - HPC software stack installation
04/02/19 - Configuration of user environments
04/05/19 - Cluster open to a few test users
04/22/19 - Cluster open to all users.
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