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BioHPC Lab:
User Guide

 


Workstations

There are several types of workstations available in the BioHPC Laboratory: interactive, remote (general, medium memory, large memory) and restricted. Interactive workstations can be used directly in Rhodes 625 the same way as any desktop computer (with a valid reservation, see below). They can be also accessed remotely via ssh or Remote Desktop. Remote workstations and restricted workstations can be only accessed remotely using ssh (graphical software can be used with remote X Windows or VNC, see access documentation). Remote workstations are more powerful than interactive with most of them having at least 2 quad core CPUs and are especially well suited for long and computationally intensive tasks. Restricted workstations include staff machines, hosted workstations and some regular workstations reserved for special collaboration or task. Detailed information about hardware configuration is available here.

Reservation

Only registered users may access workstations. To request an account please fill out and submit this Web form, you can also come during BioHPC Lab office hours and set up the account at this time. Workstations must be reserved in advance, reservations should be made via reservations web page. If you are already logged in, you may continue working even after your reservation has expired, but your session will be forcefully terminated and all processes killed when a different user with valid reservation attempts to log in. Thus, in such a case, it is advisable to re-visit the reservation page and extend your reservation if time slots are available. Please remember to remove any reservations you do not need to avoid blocking access for others and loosing your Lab Credit Account hours. 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. 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. "Time used" reflects the span for which you had the workstation reserved.

You can manage all your reservations from "My Reservations" web page. This page lists all your active reservations and provides tools for modifying them or cancelling. You can also add another Lab user to your reservation, in which case (s)he will be able to connect to your reserved workstation and work there, but won't be able to modify the reservation itself. You can also launch a VNC connection (see "Access") from this page.

You can also end the reservation programmatically by calling script /programs/bin/labutils/endres.pl with the reservation number as the parameter. This script must be executed on the reserved workstation.

Support and Training

Bioinformatics Facility staff will provide assistance with use of workstations and software. You can always ask for quick help from CBSU staff (our offices are Rhodes 616, 618-624), but training and other time consuming issues should be done during our Bio-computing Lab office hours. CBSU will run periodic workshops, and we welcome suggestions for workshop topics.

Genomic/Sequence Data Transfers

It is possible to use your BioHPC Lab account to receive sequencing data (or other type of data) from external facilities. For inbound data transfers you can request a temporary account for your external collaborator, you can grant access to your directory for this temporary account or we can move the data to appropriate user home directory, please contact us for more details. We have a standing agreement with Weill Cornell Genomics Resources Core Facility, you can ask them to transfer data to BioHPC Lab storage and they will know how to proceed. Data from Cornell Genomics Facility can be transferred directly as it is an internal Cornell unit.

Aspera SRA toolkit is installed on all computing servers. You can use it to download SRA data directly into the workstations. Please follow Apera SRA guidelines. The toolkit is installed in /opt/aspera, an example of use is

/opt/aspera/connect/bin/ascp -i /opt/aspera/connect/etc/asperaweb_id_dsa.openssh -k 1 -T -l200m anonftp@ftp.ncbi.nlm.nih.gov:/sra/sra-instant/reads/ByRun/sra/SRR/SRR304/SRR304976/SRR304976.sra /workdir

 

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