SHARCNET runs a competition for dedicated programming support, details can be found in the web portal here.
This page serves to tie together documentation for all of the projects. This may include documentation concerning the design and implementation of the programs, build and usage instructions, milestones accomplished, future work, etc.
- Computing the Stability of Three-Dimensional Shear Flows
- Toward Exascale Simulations of 3D Radiative Transfer for Cloudy Atmospheres
- Individual-based Model of Forest Dynamics to Study Global Ecological Change
- Parallelizing the Computation of Relationships Extracted from Textual Information
- Indirect Geneology Matching from Varied Sources
- Genome-wide Prediction of Mutant Single Nucleotide Polymorphisms based on Shannon Information Theory
- Quantifying the Importance of Horizontal Gene Transfer for Bacterial Genome Evolution
The code for (most) dedicated programming projects is stored in the SHARCNET git repository. What follows is some details regarding using git with these repositories. Please refer to our git page for general information on using git.
If you are seeing error messages like error: server certificate verification failed ... while performing a clone, push, fetch, or pull, your system cannot verify the authenticity of www.sharcnet.ca. This is caused by either not connecting directly to www.sharcnet.ca (as when using ssh port tunneling as described below) or by your SSL stack having dropped support for the deprecated MD5 signatures (as with GnuTLS for SSL under Debian).
In either case, you will have to turn off git's SSL verification by setting the environment variable GIT_SSL_NO_VERIFY=1 or running the command
git config http.sslVerify false
inside your repository (the former must be used for cloning as the repository won't exist yet).
Our current certificate expires on March 10, 2012. If you have disabled SSL verification due to the MD5 issue, you should re-enable it at this point as we will have purchased a new certificate without this issue.
If you are periodically seeing error messages like Cannot obtain needed blob ... while performing a clone, push, fetch, or pull, an intermediate network is occasionally dropping your connections. This has been a known problem on at least the Western campus.
A solution is to use SSH to create a tunnel across the intermediate network to the SHARCNET network.
ssh -N -L <port>:www.sharcnet.ca:443 <user>@<cluster>
where <port> is a free port (such as 4000), <user> is your SHARCNET user name, and <cluster> is any of the SHARCNET clusters. While this ssh session is running, connections to localhost:<port> will be forwarded www.sharcnet.ca:443 via <cluster>. For example
GIT_SSL_NO_VERIFY=1 git clone https://localhost:<port>/<project>
will check out <project> over the tunnel.
The GIT_SSL_NO_VERIFY environment variable is required as SSL verification will otherwise fail due to the port forwarding. Once you have checked out the project, you can permanently disable SSL verification by running
git config http.sslVerify false
in the project directory.
Note that every time you access the SHARCNET git server (i.e., do a clone, push, fetch, or pull), you need to have the ssh tunnel running. If you try and access the remote without the ssh tunnel running, you will get an error: couldn't connect to host while accessing ... message.