Frequently Asked Questions

The following provides guidance on frequently asked questions for the various areas of Scientific Computing.

Total number of nodes: 548
Total number of cores: 13,120
Total number of storage space: 20 PB

Details about the nodes:

Manda:

  • 120 nodes with 64 cores AMD Interlagos and 256 GB RAM each
  • 4 GPGPU nodes with 64 core AMD Interlagos and 256 GB RAM each

Mothra:

  • 209 nodes with 12 cores Intel Ivy Bridge and 64 GB RAM each
  • 8 GPGPU nodes with 24 cores Intel Ivy Bridge and 256 GB RAM each

BODE:

  • 207 nodes with 12 cores Intel Haswell and 64 GB RAM each

Can I Work With Minerva?

Members of the ISMMS faculty, their students, and any outside collaborators who have the sponsorship of a faculty member are welcome to use Minerva.

What types of projects does Minerva handle?

Minerva is designed to handle a variety of computationally intensive scientific workflows. The variety spans the range of the data-intensive, data-parallel types of projects that are prevalent in computational biology to the more numerical intensive, computationally parallel aspects of computational chemistry.

What are the benefits of working with Minerva?

The supercomputer provides massive computation and high-bandwidth, low-latency interconnections and storage, as well as 256GB of memory per node, all of which enables researchers to run faster and more complex projects. Minerva is also an easy-to-use platform for running your job, and it is optimized for the type of scientific computing jobs that are performed at ISMMS.

What is the process of using Minerva for a project?

To request a user account, log onto http://hpc.mssm.edu from the internal ISMMS network, and click on “Request New Account.” Once you have an account, you will be able to submit jobs. If you need additional assistance with creating a new account, visit www.hpc.mssm.edu and/or email hpchelp@hpc.mssm.edu.

What kind of technical help is available?

Within our division of Scientific Computing, Minerva has a team of computational scientists who are familiar with both science and computer methods, and system administrators who have practical experience in the use and configuration of super- and high-performance computer installations. Both groups are available to researchers on a consulting and collaboration basis. For assistance, please contact hpchelp@hpc.mssm.edu.

What is the charge back policy for Minerva?

The chargeback policy for Minerva for parallelization of code is $95/hour.

When can I access data warehouse for online query?
The Data Warehouse is available Monday-Friday for on-line querying except when it is being updated. Our nightly update process kicks off at 6:45 PM, and runs all night (on average we load over 800,000 facts per night!). The update process finishes at variable times, depending on load volume and other factors. It generally completes between 6-9 AM. The Cohort Query Tool status (displayed on the logon screen) changes to “Available” as soon as the update process completes, and it remains available until 6:45 PM.

What if I encountered any issue with data warehouse online query tool?
The support for Cohort Query Tool (CQT) and Resident Tracking Application (RT) is available Monday through Friday from 9 AM to 5 PM. Please report any issue to #MSDW_GROUP@mountsinai.org.

Where can I find data warehouse reports?
You will need to be granted access to the data warehouse before being able to view reports.  Reports are viewed with special software packages that can be accessed through your web browser.  Follow the links and instructions on this website to obtain access.

How current are the warehouse reports?
We have a batch cycle that refreshes the warehouse every evening.  Reports have access to all data loaded up to 7 PM on the previous day.

How far back in time does the data in the warehouse go?
The historical data goes back as far as January 1, 2003 in the data warehouse.  

Can anyone look at these reports?
You must fill in the forms and be authorized to view warehouse reports.  Most users will have access to de-identified data which cannot be traced to an individual person.  Users with sufficient authorizations may be granted access to identifiable data.

Can the reports be specialized for my individual needs?
Yes they can.  The warehouse tools allow you to create your own reports.   We strongly recommend that you receive training for the tool that you will be using.

Do I need to install any software to see the reports?
No, the tools and reports are web-based and can be accessed through your browser.

What tools do you use to build the reports?
There are two tools that we offer: (1) a vendor (SAP) Business Intelligence package called Business Objects and (2) a tool developed at Mt Sinai called Cohort. Refer to the Tools and Training links for more information.  

How much data is in the data warehouse?
There are currently about 600 million records in the data warehouse.

What kinds of reports are available?
Many reports are available and you can also create your own. There are currently 17 source systems that are feeding the warehouse.  The source systems represent many functional areas at Mount Sinai.  Refer to the home page for information about what data is available. You will have access to all this data.

What are the reports used for?
There are different types of users who will use data warehouse reports for different purposes. Examples are: clinical research, trend analysis, business forecasting, predicting, and identifying inefficiencies in the way health care is delivered at Mount Sinai.

What is the chargeback policy for MSDW?

For Data Warehouse programming (custom reports, data marts, data extracts, data re-identification, new data sources, or other programming) there is a charge of $95/hour. Requestors must provide an account# to be charged via funds transfer. Please plan funding for Data Warehouse services in your grant applications or departmental budgets. For help in estimating costs, please use our Report Request Form  to describe the data requirements for the research you will be proposing (be sure to specify that the request is for estimation only).

How do I request a new user account in eRAP?

The "Apply for a New User ID" form should be filled out by anyone wishing to get access to eRAP for the first time and never had eRAP user ID before. When selecting this option, you will be asked to provide the eRAP application and project you are applying for access to.

If you are a Mount Sinai employee, you will pick “Use my Mount Sinai Health System network login.” If you are not a Mount Sinai employee,you will pick “proceed without login”.  Once the authentication is selected, a form will need to be filled out with user information for the account.

Note: If you opted to use your Mount Sinai Health network login, a large portion of next form will be filled in and your life number will be included. Your email address will be your Mount Sinai email – it would be best not to change that email.  If you do, please be sure to check the new email for verification.  Your account MUST be verified as part of the new user account process.

Note: Please use an email account you check – you will be sent an email verification notification. 

After you click submit, your request will be processed and a new account will be created.

Q. I forgot my password, what do I do?

If you have forgotten your password and are using your login from your MSSM network – you will need to reset your network password by going to https://chief.mssm.edu/ 

If you are using a non-mssm login, you will need to use the following process:

Click on “Forgot Password?”

Enter your Login in the first textbox, enter your e-mail address in the second textbox, and then enter the “Text on the Image” (Captcha) in the third textbox. When you’re done, click on “Submit” and the system will e-mail your password to you.

NOTE: When you get the reset password notification email: Be sure you type out the new password – DO NOT CUT AND PASTE.  If you do, you will end up locking your account.  If your account becomes locked, you will need to submit a ticket asking for it to be unlocked.  What type of ticket do I open?

Q. How do I open an eRAP Ticket?

When you arrive at the support page start by selecting a support topic from a list of topics.

Once a topic is selected, additional fields will appear to collect the information pertinent to your support request.  IMPORTANT NOTE: The more fields you fill out, and the more information you provide about why you are opening a ticket, the faster your eRAP Ticket can be resolved.

What is the chargeback policy for eRAP?

For eRAP programming (custom database, custom reports, change requests or other programming) there is a charge of $95/hour. Requestors must provide an account # to be charged via funds transfer. Please plan funding for eRAP services in your grant applications or departmental budgets. For new projects and help in estimating costs for significant changes to existing databases, please request the User Service Request Form.