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Connect to the Enclave

1. Connect to LBL VPN

2. either https://vavdi.ornl.gov in browser and use the HTML client, or use the VMWare Horizon Client to connect to the same address.

3. Type in your passcode (six-digit personal PIN + RSA token) to log in the enclave

4. Connect to the Windows VM (mvp011-01) or either of the two Linux VMs (mvp011-02 and mvp011-03)

5. Login a VM with your KDI user name ([email protected]) and password, which will be set after you log in with the temporary password for the first time.

Connect to VASQL

• From Windows using Microsoft SQL Server Management Studio (SSMS):

  1. Launch Windows PowerShell
  2. Type SSMS.exe

• From Linux through sqlcmd:

  Example:

  $ /opt/mssql-tools/bin/sqlcmd -D -SMVPSQL -Q "SELECT TOP 10 * FROM CDWWork.Patient.Patient"

• From Linux through Azure Data Studio:

  Example:

  $ azuredatastudio

  Use VASQL as database name and choose Windows Authentication.

Data Processing

Read RDS files prepared by Ben McMahon:

>> import pyreadr
>> results = pyreadr.read_r('demo42.RDS')

The HPC Environment

Computer resources

VM

• Linux VM: Xeon Gold 6142, 8 threads, 64GB RAM, 100GB storage
• Windows limts maximum concurrent users to 2

The Computer cluster:

• 30 CPU nodes, 36 CPU cores, 128 GB RAM, 2TB HDD
• 15 GPU nodes, dual K80 GPUs, 36 CPU cores, 128 GB RAM, 2 TB HDD

• 3.2 PB Lustre file system

• 5 PB NFS and tape file system

The Relational Database

• 2 nodes, 40 cores, 3TB RAM, 11TB SSD storage, 167 TB HHD storage

System Repositories:

• CentOS 7 Base, CentOS 7 Updates, CentOS 7 Extras, EPEL

User Repositories:

• Anaconda, install by /usr/local/bin/condaenv
• CRAN
• PyPI

VM Project Shared folder 1.5 TB:

• Windows: file:\\vafs01\data\VA_MVP011_CDW

• Linux: /mnt/vafs01/data/

Murphy:

• project shared folder: /mnt/vafs01/data, available on login node only
• HPC shared folder: /lustre/valustre/VA_MVP011_CDW
• Local scratch: /localscratch

Connect to HPC

$ ssh va-murphy-login.kdi.local

Install Jupyter Notebook on Linux VM

$ python -m pip install jupyter

Install Anaconda on Linux VM

$ condaenv

Setting anaconda path will conflict with Linux VM remote desktop. Do not let the installer change the .bashrc file.

Using Jupyter Notebook on Murphy

From the Murphy Login node:

$ module load apps/python/anaconda/3/4.3.1
$ jupyter notebook --no-browser --ip=0.0.0.0

From VM:

$ ssh -N -f -L locahost:8889:localhost:8888 va-murphy-login.kdi.local

Type in a browser search bar: locahost:8889

Request new software

EMail [email protected], with

Subject: VA Tenant Software Change Request

Research Project Title:

Project Technical Contact:

Requestor Contact Information

Software Name:

Software Version(s), or Git revision/ SVN revision/Release updates:

Release Date:

License Agreement:

Software Homepage URL:

Installation Target OS:

Installation target(s) in KDI: specific VM, or cluster names

Prerequisites/dependencies:

Purpose/Justification:

Documentation

GitLab

https://code-va.kdi.local

Use Ad Login and your userid liux.mvp011w without the kdi.local part

• Getting Started http://operations.va.kdi.local/va-docs/user-guide/getting-started