General Topics

MARCC is a resource for JHU and University of Maryland researchers who require access to advanced computing resources and expertise of research collaborators in the analysis and management of big data sets.
After your PI is granted an allocation, users can request accounts that must be approved by the Pi via email:
Please fill out the Request an Account form.
HOME Directory: 20 GBytes (/home/userid)
Lustre: 1 TByte per group (/scratch/users/userid and /scratch/groups/groupid)
data: 1 TByte per group
Storage can be increased up to 10TB per request from the PI
Type the command “groups”.
HOME directories and “data”
ssh gateway2.marcc.jhu.edu -l userid
A two-factor authentication code is needed and a robust password

This research project (or part of this research project) was conducted using computational resources (and/or scientific computing services) at the Maryland Advanced Research Computing Center (MARCC).”

Please feel free to edit it and/or include more details.

ALLOCATIONS

Any faculty member at Johns Hopkins University can request an allocation. All requests will be approved by the Dean’s office
Please fill out and Allocation Request form.

The Deans of the schools will make decisions on how to allocate resources.

To find out the group utilization the PI should use the command sbalance. It will give information about utilization by all members of the group.

SLURM

For a summary of available partitions and their status, use the command sinfo -s
Use the “interact” command and “interact -usage" for options.

Users who need to run jobs immediately may be able to find out if resources are available. Use the command:
sinfo -s

A/I/O/T = Allocated/Idle/Out/Total

HELP

An email will be sent out to all users. Also, please check the website, HOME page.

Data Transfer

DTNs are a set of dedicated nodes for file transfer. These servers are GlobusConnect end point and should be used to transfer large amounts of data.

  1. ssh dtn2.marcc.jhu.edu (with your username and passwd)
  2. scp largefile.ext userid@your-destination
    Note that the speed is limited by the connectivity at your destination
  3. From your machine to MARCC: scp largefile.ext userid@dtn2.marcc.jhu.edu:~/
  4. Use the Globus connect end point
    1. Request a GlobusConnect account
    2. Login into your globus connect account
    3. Select the end points (MARCC)
    4. Authenticate to your end points
    5. Select the file(s) to transfer
    6. Start the file transfer
  1. ssh dtn2.marcc.jhu.edu (with your username, TFA and passwd)
  2. module load aspera
  3. ascp-marcc is an alias to “ascp -T -l8G -i /cm/shared/apps/aspera-cli/3.7.2.354/etc/asperaweb_id_dsa.openssh”
  4. -T do not encrypt, -l8G 8000MB bandwidth. You can change this parameters but use the ascp command
  5. To download a file from ncbi: ascp-marcc anonftp@ftp.ncbi.nlm.nih.gov:gene/DATA /scratch/users/userid"
  1. Download Filezilla  (Web search)
  2. Install Filezilla
  3. Launch Filezilla. Your local machine files and folders should be visible on the left side
  4. Click on the top left “icon” or click File-> Site Manager. A new window pops up
  5. Click on New site and name it “MARCC”
  6. Click on “General”
    1. Host: gateway2.marcc.jhu.edu Port 22   (Type)
    2. Protocol: SFTP – SSH File Transfer Protocol   (select)
    3. Logon Type: Interactive (select)
    4. User: Your MARCC userid  (user-5s35@jhu.edu)  (Type)
    5. Password: Leave blank (recommended)
  7. Click on “Transfer Settings”
    1. Select Limit number of simultaneous connections and set it to “1”
  8. Click on “Connect”
  9. You should be connected. MARCC files and Folders should be visible on the right side
  10. Click and Drag files/folders

That is it.

 

HIPAA (Not available yet)

Yes, but you will need to provide some additional information regarding your study and you will need to include MARCC’s involvement as a research collaborator explicitly in your IRB protocol and in any consent signed by subjects
You should submit a change in protocol to your IRB to include MARCC’s involvement as a research collaborator on the protocol.
No. MARCC is a research resource and will collaborate with you on your research needs. MARCC is not a “covered entity,” as that term is defined in HIPAA and will not perform any “covered functions.” Research activities are generally not considered “covered functions” under HIPAA, so MARCC would not be functioning as a “business associate” under HIPAA.
While MARCC is not a “covered entity” or “business associate” under HIPAA, it does maintain security standards and safeguards consistent with the HIPAA Security Rule. Specifically,…[to be included once security standards have been established]
If you have confirmation that your dataset is de-identified as required by HIPAA or your data is not otherwise subject to HIPAA, you do not need to name MARCC in your research protocol.