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FAQs

Topics:

    Q: I am a Mount Sinai employee and I lost my password. I need to reset it.
    Q: I am an external collaborator on Minerva and I lost my password. I need to reset it.
    Q: I lost my token, replaced or lost my cell phone! What do I do?
    Q: My account is locked. What do I do?
    Q: Can I set up my own module system?
    Q: The module I need is only available on Manda, or Mothra, but not both.
    Q: The package I need isn’t available! Will you install and maintain it?
    Q: When I load a module, it gives me an error. What do I do?
    Q: I get errors using java when I submit a job, but not when testing locally.
    Q: The documentation on the web site is not organized well, I can’t figure out what I need to know!
    Q: I don’t like web- or e-mail-only communication. What can I do?
    Q: The allocations process is cumbersome - it takes too long to get my work up and running. Can you help?
    Q: How to submit job to himem node (1TB of RAM)?


    Q: I am a Mount Sinai employee and I lost my password. I need to reset it.
    A: The password you use to log into Minerva is your Mount Sinai password. We do not reset passwords. If you have forgotten your Sinai password, reset it here.
    Note that employees from SLR, BI, and NYEE cannot use this link — they must call their respective IT Help Desks.


    Q: I am an external collaborator on Minerva and I lost my password. I need to reset it.
    A: If you are an external collaborator, you will need to email us at hpchelp@hpc.mssm.edu to reset your password.


    Q: I lost my token, replaced or lost my cell phone! What do I do?
    A: If you’ve lost your token, make sure to send in a ticket to us so that we remove it from the system. Once we do this, you can easily register a new token the same way you did the first time around. You can obtain a virtual token for your electronic devices, or stop by Icahn 3rd Floor, Room 70, Desk 31 to pick up a new physical token. If no one is at the desk, please see any of the HPC staff sitting in the same area, who should also have a token. If you are an external collaborator who has lost a yubikey, please write to us and we will send a new one.


    Q: My account is locked. What do I do?
    A: The most common reason for failure to log in is a locked two-factor authentication token. This usually happens after successive failed attempts to use the token. Please remember that you can only use a two-factor token output one time. If your password does not work, you will need to wait 30 seconds for the next two-factor token output. We can check if your token is locked, and unlock them. Just send us a message to hpchelp@hpc.mssm.edu.


    Q: Can I set up my own module system?
    A: Yes! Many of our more advanced users maintain their own packages while in active development, or if they are frequently making changes. Please reference our MODULES documentation, which can be found on this website, for information about setting up your own modules.


    Q: The module I need is only available on Manda, or Mothra, but not both.
    A: The scientific computing team maintains 3 packages repositories. In most cases, the software is installed in the “common” repository, which is available to all nodes in the cluster. Occasionally, performance considerations require us to maintain separate versions for each architecture on the machine, leading to a split in the versioning between the “manda” and “mothra” modules. Additionally, as we have expanded Minerva, legacy packages get left behind when not in active use. The solution is simple: just send us a ticket at hpchelp@hpc.mssm.edu, and we’ll fix the issue.


    Q: The package I need isn’t available! Will you install and maintain it?
    A: Probably. We do our best to meet the module needs of all of our users, and the vast majority of packages will be supported if they are useful to more than just an individual user, and have achieved a certain level of maturity. For example, a perl script you wrote yesterday for your own downstream analysis will not be supported, but any community software will be. This is true of top-level packages, as well as R or python packages, for example.


    Q: When I load a module, it gives me an error. What do I do?
    A: Most of the time this happens it is because of conflicts with already loaded modules. For example, most of the packages we build depend on gcc 4.8.2, our default compiler. If you’ve loaded another compiler toolchain for your own work, and then load a package that depends on a conflicting compiler toolchain, the module system will complain to you. Starting fresh by issuing a “module purge” command will typically fix any problems you have. If you continue to see errors, or need two conflicting packages to be loaded simultaneously, just send in a ticket and we’ll get it sorted out.


    Q: I get errors using java when I submit a job, but not when testing locally.
    A: Nodes have their own java versions which are local to the operating system installed on the node. Users should always load java using the modulefile system, which will ensure uniform behavior across the entire cluster. The java packages on Minerva are in the “common” module repository.


    Q: The documentation on the web site is not organized well - I can’t figure out what I need to know!
    A: We are aware that our online documentation is currently lacking, and we are moving improvements to documentation to the top of our to-do list based on recent feedback from users.


    Q: I don’t like web- or e-mail-only communication. What can I do?
    A: The HPC staff is always available to talk 1-on-1. You can come talk to us in person on the 3rd floor of Icahn, or send a message to arrange a meeting. We also provide help sessions twice a month which are announced in the weekly Friday emails to all Minerva users.


    Q: The allocations process is cumbersome - it takes too long to get my work up and running. Can you help?
    A: We’re working on a brand new allocations process for the next cycle which should significant streamline and simplify the procedure for obtaining an allocation.


    Q: How to submit job to himem node (1TB of RAM)?
    A: You can submit job to any queue, except private and ask for himem resource "bsub -q low -R "himem" ...."

    FAQs updated 2/14/2017 with correct staff email

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