Biowulf High Performance Computing at the NIH
Locally Mounting HPC System Directories

The HPC System Directories, which include /home, /data, and /scratch, can be mounted to your local workstation if you are on the NIH network or VPN, allowing you to easily drag and drop files between the two places. Note that this is most suitable for transferring small file. Users transferring large amounts of data to and from the HPC systems should continue to use scp/sftp/globus.

Mounting your HPC directories to your local system is particularly userful for viewing HTML reports generated in the course of your analyses on the HPC systems. For these cases, you should be able to navigate to and select the desired html file to open them in your local system's web browser.

Windows: Mapped Network Drive

  1. On your desktop machine, open the 'Computer' tab and open the Tools → Map Network Drive tab.

    My Computer folder

  2. Enter the directory you want to mount as follows:

    • /home/[user]: \\helixdrive.nih.gov\[user]
    • /data/[user]: \\helixdrive.nih.gov\data
    • /scratch: \\helixdrive.nih.gov\scratch
    • Shared group area (e.g. /data/PQRlab: \\helixdrive.nih.gov\name_of_shared_area

    Make sure to replace [user] with your NIH login!!!

    Map Network Drive window

    Because the NIH HPC systems are authenticated using NIH Login, you should not have to enter your user or password. Click the 'Finish' button.

  3. You have successfully mapped your HPC directory to your desktop machine! You should see a network icon in the My Computer folder. You can create a shortcut to this drive on your desktop.

    /home icon

  4. Please note that the disk usage information is not correct for your /home directory, but it is correct for your /data directory.

    /data icon

Windows: Add Network Location

This method is ALWAYS ACCESSIBLE unless there are network issues or you get a new machine.

  1. On your desktop machine, right-click the 'Computer' tab and click the 'Add Network Location' menu item to start the wizard. Click 'Next' when the following window pops up

    add network location

  2. Click 'Next' in this window

    where to create

  3. Enter the shared drive you want to mount as follows:

    • /home/[user]: \\helixdrive.nih.gov\[user]
    • /data/[user]: \\helixdrive.nih.gov\data
    • /scratch: \\helixdrive.nih.gov\scratch
    • Shared group area (e.g. /data/PQRlab: \\helixdrive.nih.gov\name_of_shared_area

    Make sure to replace [user] with your NIH login!!!

    specify location

    Click the 'Next' button.

  4. You can name the location, although, the default name is fine.

    name location image

  5. Completing the wizard

    completing the wizard

    Click the 'Finish' button

    /data icon

    To see larger image, right-click &arr; View Image

Macs: Mapped Network Drive

Note:

Mac users should consider creating (or editing) the following file on their system if they would like like to use mapped network drives:

/etc/sysctl.conf

include this line in the file (it may be the only contents of the file):

net.inet.tcp.delayed_ack=0

After the file is created/appended, reboot your Mac. This will profoundly increase file-transfer performance. Without this alteration, performance may be bad enough to render Helixdrive shares unusable. If you are unable or unwilling to set this file, you'll likely want to use sftp or scp rather than Helixdrive.

  1. From the main Mac menu, click on Go → Connect to server.
  2. For 'Server address', enter the HPC directory you want to mount:
    • /home/[user]: smb://helixdrive.nih.gov/user
    • /data/[user]: smb://helixdrive.nih.gov/data
    • /scratch: smb://helixdrive.nih.gov/scratch
    • Shared group area (e.g./data/PQRlab): smb://helixdrive.nih.gov/name_of_shared_area
    (Replace 'user' by your NIH login username.)

    server connection display

  3. Click 'Connect' and in the subsequent window, enter your NIH Login user and password. NIH AD usernames and passwords are used to connect to all Helix & Biowulf services.

    login/password

  4. The requested area should now be mounted as a shared drive. In your Finder window, you will see 'helixdrive.nih.gov' listed under 'Shared', and can drag and drop files to your HPC directories.

    folder display

Linux: Mapped Network Drive

Since your uid/gid is likely to be different on your desktop than on biowulf you may also need to include the uid and gid options. For example, if you local uid and gid are 3245, you would add uid=3245,gid=3245 to the mount option string.

You will need to have the cifs-utils package installed in order for this to work.

Typical mount commands for accessing a CIFS file system:

To mount your Biowulf /home/[user]:

mount -t cifs -o rw,vers=2.0,nosetuids,sec=ntlmsspi,user=jdoe,domain=NIH.gov //helixdrive.nih.gov/[user] /mnt/bw-home

To mount your Biowulf /data/[user]:

mount -t cifs -o rw,vers=2.0,nosetuids,sec=ntlmsspi,user=jdoe,domain=NIH.gov //helixdrive.nih.gov/data /mnt/bw-data

To mount Biowulf /scratch:

mount -t cifs -o rw,vers=2.0,nosetuids,sec=ntlmsspi,user=jdoe,domain=NIH.gov //helixdrive.nih.gov/scratch /mnt/bw-scratch

To mount a shared group area: (e.g. /data/PQRlab)

mount -t cifs -o rw,vers=2.0,nosetuids,sec=ntlmsspi,user=jdoe,domain=NIH.gov //helixdrive.nih.gov/PQRlab /mnt/bw_PQRlab

Note that the path of the local directory used as mount points may have to be adapted to your situation and jdoe has to be replaced with your Biowulf username.