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lab-protocols

A collection of protocols for the lab

Function of lab servers

The lab servers serve three functions:

  1. Allow users to transfer data from the shared computers in the Carver Center for Genomics (CCG) and Carver Center for Imaging (CCI).
  2. Allow members of the lab to collaborate easily by sharing data.
  3. Store all raw data safely. If you have a piece of raw data that is only stored on your personal computer, it is wrong!

Note that we store semi-processed data and analysis codes and results using project GitHub repository.

We have two storage servers available. LSS is used for remote computing on the Argon cluster. All other data transfer and storage uses RDSS.

Request access to the lab servers

Once you join the lab, ask the Biology IT group to add you to our security group, cc Bin on your email. It may take a day or two for the security group to be updated so you can access the lab servers. If in doubt, ask Bin.

The lab servers can be accessed by several means:

Map RDSS as a folder (drive)

RDSS is used for everything except for next generation sequencing data storage, analysis or other computation that requires access to the high performance computing cluster (Argon)

Note: on CCG computers, look for a folder on the desktop under the name “He”, and there should be a shortcut inside that allows you to map the drive. If not, right click on the “Computer” icon and choose “Map Network Drive”. Put in the address and credentials as shown below

Table 1 RDSS mounting as a folder

OS Menu item Address
Mac Finder -> Connect to server… smb://IOWA;HawkID@iowa.uiowa.edu/shared/researchdata/rdss_bhe2
Linux File manager -> Ctrl+L smb://IOWA;HawkID@iowa.uiowa.edu/shared/researchdata/rdss_bhe2
Windows Instructions \\iowa.uiowa.edu\shared\researchdata\rdss_bhe2

This approach allows you to interact with the lab server as if it were an additional folder on your personal computer. Once it’s connected, you will see the following folder structure:

.
├── Core
├── Project
└── User

For work related to a specific project, use of the Project folder is preferred. For things that don’t fall under a single project, use the folder under your name in the User folder.

Command line mounting

Note: If you use one of the lab provided linux desktops, once you log in, use the command line to navigate to /mnt/nfs/lss_grelab for LSS and to /mnt/cifs/rdss/rdss_bhe2 for RDSS, and you would have full access to the server space.

If you are using your personal computer running Linux / Mac OS, use the following command to mount LSS

# LSS
mount -t cifs -o username=HawkID,sec=ntlm,domain=iowa,uid=$(id -u $(whoami)),gid=$(id -g $(whoami)) //lc-rs-storage17.hpc.uiowa.edu/grelab /mnt/cifs/lss_grelab

# RDSS
mount -t cifs -o username=HawkID,domain=iowa,uid=$(id -u $(whoami)),gid=$(id -g $(whoami)) //rdss.iowa.uiowa.edu/rdss_bhe2 /mnt/cifs/rdss_bhe2 
# the additional uid and gid options are required so that the cifs client knows that these are the uid and gid for the user that matches the uid and gid on the server, which can be different.

Access LSS on HPC

LSS is mounted automatically under /Shared/grelab

FTP

To download or upload files onto LSS server, use the following instructions:

data.hpc.uiowa.edu with HawkID and password. The LSS share will be automounted under /Shared/grelab

Download a FTP client such as FileZilla, and point to data.hpc.uiowa.edu, login with your HawkID credentials.

Map LSS as a folder

Note that LSS is meant to be accessed through the HPC clusters. If you need to download or upload files, FTP is recommended over mapping as a folder.

Table 2 LSS mounting

OS Menu item Address
Mac Finder -> Connect to server… smb://IOWA;HawkID@lc-rs-storage17.hpc.uiowa.edu/grelab
Windows Instructions \\lc-rs-storage17.hpc.uiowa.edu\grelab
Linux1 File manager -> Ctrl+l smb://IOWA;HawkID@lc-rs-storage17.hpc.uiowa.edu/grelab

FAQ

  1. What’s the difference between RDSS and LSS?

    These two storage servers are both provided and managed by the Information Technology Services. RDSS, standing for Research Data Storage Service, is managed by the ITS Enterprise Services. It provides 5TB for free, with 24/7 tech support. It is not accessible, however, on the High Performance Computing clusters. LSS, or Large Storage Service, is offered and managed by the HPC Sysadmins. All UI3 associated labs get 5 TB of LSS storage. Its technical support is business hours only. It is available on the HPC system.

    Below is a chart of comparison, also see here

    Table 3 Comparison of RDSS and LSSS

      RDSS LSS
    Website https://its.uiowa.edu/rdss https://its.uiowa.edu/lss
    Space 5 TB 5 TB
    Use Desktop file sharing Desktop file sharing & HPC
    Backups Yes Optional
    Snapshops Daily HPC: Hourly, Daily, Monthly; Non-HPC: daily
    Backup retention 30 days 30-90 days
    Email, general its-etm@uiowa.edu hpc-sysadmins@iowa.uiowa.edu
    Contact person Ryan West at ITS-ETM John Sexton at john-sexton@uiowa.edu
    Request permission change RDSS Security change form email hpc-sysadmins@iowa.uiowa.edu

  2. In Linux/Mac OS, is the “map as a folder” the same as “command line mount”? Where are they in the file system?

    The main difference between the two is that the former method uses GVfs (GNOME Virtual file system) as part of the GNU library while the latter uses the mount function in the kernel. When “connect to server” in the GUI is used, the mount point in recent Linux versions (circa 2018, tested in Fedora+MATE and Ubuntu 16.04) is /run/user/$UID/gvfs/. When mount command is used, the user specifies the mount position. Since these are simply different “portal” for the same windows share, they should be synced.