NSG FAQ

Q: What is NSG?
A: NSG is a Science Gateway which allows computational neuroscientists to run pre-installed neuronal simulation software on high performance computing (supercomputer clusters) resources.

Q: What is the difference between NSGportal and NSG-R?
NSGportal is a simple online portal that the user can login to submit their simulation code and retrieve results. The same functionality if accessed programmatically using RESTful services is called NSG-R. Please note that the underlying infrastructure is different for both access points.If you run/save output through the web portal, you will not be able to access the same data using NSG-R and vice versa.

Q: What is the cost to use NSG?
A: Free!(for all academic users). Industry and for-profit organizations please contact us for usage restrictions.

Q: Who may use NSG?
A: Anyone! Academic neuroscience researchers, Industry researchers, educators or students.

Q: How do I get an account for NSG?
A: Please go to the NSG registration to fill out the form. Once approved you will have an account to access both NSGportal and NSG-R services. We recommend users to choose the best access mechanism according to their comfort level and needs.

Q: What software applications are available through the NSG?
A: The list of software applications are listed here Users can also run model code written in Python. Commonly used python modules are made available. Analysis tools such as R, Octave are also available through our backend HPC resources.We are always interested to know what other neuronal simulation or analysis tools users might be interested in. Please nsghelp@sdsc.edu

Q: I need you to install a software, what is the procedure?
A: Please contact us at nsghelp@sdsc.edu for any new software or features request.

Q: Is there an illustrated document showing how to: request an account, submit a job, find models to run, retrieve output data, etc.?
A: Our user guide has step-by-step instructions on basic usage -- user guide You can also find our NSG-R usage instructions here

Q: How should I upload my input file?
A: NSG supports only zipped file format. Please compress your directory and upload the input file. The zip file should have only one directory (containing the model code) in the top level. In unix or mac, once you have a directory with your model, use tar and gzip to create a compressed tar file:
cd <model directory>
cd ..
zip -r input <model directory>

Q: What is the largest number of nodes and cores I can request?
A: It depends on the resource you choose to run on. On Comet, each job can run on a maximum of 72 nodes with 24 cores each. On Stampede, we allow a maximum of 256 nodes with 16 cores each. But as usage requirements grow, we will increase these limits

Q: What is the longest time I may request?
A: 48 hours (but based on users' requirements we will increase this time limit)

Q: How do I request help?
A: Email nsghelp@sdsc.edu

Q: I am an user from the United States and have my own allocation on NSF's XSEDE high performance resources. Can I still use neuronal simulation codes via NSG and charge to my own allocation?
A: Yes. Please email nsghelp@sdsc.edu to discuss this and use this feature.

Q: How do I cite usage of NSG in my publications?
A: See How to cite

Q: I need to do parameter sweep study on my model. How can I do it on NSG?
A: Bundled job submission is available for Brian. Please create a file called jobs-list and write your executable command line options, one per line Eg.
jobs-list:
python one.py 1 2
python one.py 4 5
python one.py 5 7
(if you have question, please email nsghelp@sdsc.edu)

Q: Is bundled job submission only available for Brian?
A: Yes currently it is only available for Brian. We are looking into providing bundled job submission for other neuronal simulation tools also. If you have request for this, please email nsghelp@sdsc.edu

Q: I am teaching a computational neuroscience course (or workshop). Can my students use NSG for the class (or workshop)?
A: Yes. Please email nsghelp@sdsc.edu well ahead of the start date of the class.