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BioHPC Cloud:
: User Guide

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Quick Start

  1. Get an account

    First, you need to get an account for BioHPC Cloud. BioHPC accounts are available to Cornell researchers and their collaborators, as well as researchers from upstate NY universities and companies. To request an account, please fill out and submit this Web form.

    Your user name will usually be the same as your Cornell NetID, but it is an entirely separate account and should have a different password. When your account is created, you will receive an e-mail with your username and instructions to set your password.

  2. If your lab has a hosted machine:

    • You will need your BioHPC account added to the lab group. This can be done by the group admin (usually the PI) on the My Groups submenu of the BioHPC webpage. Or, you can email us and request to be added to the group. It is helpful if you copy your PI on such a request.

      The lab group has a permanent reservation to the hosted machine, so once added to the group, you can skip to the next step.

    To use rental machines:

    • Create BioHPC Credit Account(s) or get added to an existing one.

      You need a credit account to reserve a server, you can set one up using the "My Credit Accounts" submenu. Click on "New Credit Account", name it and create. If you are a member of a group that already has a BioHPC credit account, you can ask the account owner to be added to it. You can also add other users to yours.

    • Buy or transfer Compute Units if needed.

      You need to purchase compute units unless you have been added to an existing credit account with purchased units. These units can be exchanged for reservation time (more or less depending on machine type; see our Pricing Page). You can buy units by clicking the "Purchase Compute Units" link in the "Action" column on "My Credit Accounts" page. Each Cornell PI is entitled to a free starting credit of 100 units (Contact us to request this credit). You can transfer units between lab credit accounts (bottom of "My Credit Accounts" page).

    • Reserve workstation(s) 

      Once you have a credit account with compute units available, you can go to the "Reservations" page (submenu under the "User:" tab). Your account will be charged by wall clock hours used (down to appropriate fraction of an hour). Only actually used hours are charged, if you cancel your reservation before it starts nothing is charged, if you cancel before it ends only the actual hours between start and cancel are charged. You can manage your reservations on the "My Reservations" page. You can also create and manage reservations on the command line with /programs/bin/labutils/biohpc_res. (Try biohpc_res --help for usage).

      NOTE: "time used" is defined as the wall clock time elapsed when your reservation is active - it has nothing to do with how much you actually used the CPU/RAM etc during this time. Amount of hours available on a credit account will depend on the machine type, conversion rates are listed on pricing page and on My Credit Accounts, the latter also shows how many hours you have available on each server type.

      When you are done computing, you can cancel your reservation on the webpage, or with the command biohpc_res cancel --current executed on the reserved machine. Cancelling the reservation ensures you are only charged for the time used.

  3. Transfer data, connect and compute

    You can connect to your workstation(s) and transfer data in many ways. A step by step summary is available in this document. Please refer to this document and our user guide for detailed instructions. Remember: you can always transfer data to/from your home directory without a reservation via one of our login machines:
    cbsulogin.biohpc.cornell.edu, cbsulogin2.biohpc.cornell.edu, or cbsulogin3.biohpc.cornell.edu.

    Overview of our storage is provided here, for more information on managing our networked storage (storage allocations, reserving extra storage) please refer to Lab storage guide. You can now also use Globus Online to transfer data to/from your home directory, Globus at BioHPC Cloud and Using Globus to Share Data for details.

  4. Support and Training

    Bioinformatics Facility staff will provide assistance with use of servers and software. You can always ask for quick help from Bioinformatics staff via e-mail (office hours. We offer many virtual workshops which you can register for at any time, and we welcome suggestions for workshop topics.


 

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