Rivanna

Communication

We have a team discord at: uva-bii-community

https://discord.gg/7K2PQqxYz7

to be added, send laszewski@gmail.com an email with subject: Please add me to discord for bii_dsc_community

please subscribe if you work on rivanna and are part of the bii_dsc_community.

Rivanna at UVA

The official Web page for Rivanna is located at

• https://www.rc.virginia.edu/userinfo/rivanna/overview/

In case you need support you can ask the staff using a ticket system at

• https://www.rc.virginia.edu/support/
• This page also contains zoom office hours Tue 3-5 pm, Thu 10-12 pm

It is important that before you use Rivanna to attend a seminar that upon request is given every Wednesday. To sign up, use the link:

• Wednesday 3-4 pm Introduction

Please note that in this introduction we will provide you with additional inforamation that may make the use of Rivanna easier. We encourage you to add to this information and share your tips,

Getting Permissions to use Rivanna

To use Rivanna you need to have special authorization. In case you work with a faculty member you will need to be added to a special group (or multiple) to be able to access it. The faculty member will know which group it is. This is managed via the group management portal by the faculty member. Please do not use the previous link and instead communicate with your faculty member first.

• Note: For BII work conducted with Geoffrey Fox or Gregor von Laszewski, please contact Gregor at laszewski@gmail.com

TODO: IS THIS THE CASE?

Once you are added to the group, you will receive an invitation email to set up password for the research computing support portal. If you do not recive such an email, please visit the support portal at

TBD

This password is also the password that you will use to log into the system.

END TODO IS THIS THE CASE

After your account is set up, you can try to log in through the Web-based access. Please test it to make sure you have the proper access already.

However, we will typically notuse the online portal but instead use the more advanced batch system as it provides significant advantages for you when managing multiple jobs to Fivanna.

Accessing an HPC Computer via command line

If you need to use X11 on Rivanna you can finde documentation at the rivanna documentation. In case you need to run jupyter notebooks directly on Rivanna, please consult with the Rivanna documentation.

VPN (required)

You can access rivanna via ssh only via VPN. UVA requires you to use the VPN to access any computer on campus. VPN is offered by IT services but oficially only supported for Mac and Windows.

However, if you have a Linux machine you can follow the VPN install instructions for Linux. If you have issues installing it, attend an online support session with the Rivanna staff.

Access via the Web Browser

Rivanna can be accessed right from the Web browser. Although this may be helpful for those with systems where a proper terminal can not be accessed it can not leverage the features of your own desktop or laptop while using for example advanced editors or keeping the file system of your machine in sync with the HPC file system.

Therefore, practical experience shows that you benefit while using a terminal and your own computer for software development.

Additiional documentation by the rivanna system staff is provided at

• https://www.rc.virginia.edu/userinfo/rivanna/ood/overview/

Access Rivanna from macOS and Linux

To access Rivanna from macOS, use the terminal and use ssh to connect to it. We will provide an in depth configuration tutorial on this later on. We will use the same programs as on Linux and Windows so we have to only provide one documentation and it is uniform across platforms.

Please remember to use

$ eval `ssh-agent`
$ ssh-add

To activate ssh in your terminal

Access Rivanna from Windows

While exploring the various choices for accessing Rivanna from Windows you can use putty and MobaXterm.

However, most recently a possible better choice is available while using gitbash. Git bash is trivial to install. However, you need to read the configuration options carefully. READ CAREFULLY Let us know your options so we can add them here.

To simplify the setup of a Windows computer for research we have prepared a separate

• help page to set up your Windows computer.

It addresses the installation of gitbash, Python, PyCharm (much better than VSCode), and other useful tools such as chocolate.

With git bash, you get a bash terminal that works the same as a Linux bash terminal and which is similar to the zsh terminal for a Mac.

Set up the connection (mac/Linux)

The first thing to do when trying to connect to Rivanna is to create an ssh key if you have not yet done so.

To do this use the command

ssh-keygen

Please make sure you use a passphrase when generating the key. Make sure to not just skip the passphrase by typing in ENTER but instead use a real not easy to guess passphrase as this is best practice and not in violation violation of security policies. You always can use use ssh-agent and ssh-add so you do not have to repeatedly enter your passphrase.

The ssh-keygen program will generate a public-private keypair in the directory ~/.ssh/id_rsa.pub (public key) and ~/.ssh/id_rsa. Please never share the private key with anyone.

Next, we need to add the public key to Rivanna’s rivanna:~/.ssh/authorized_keys file. The easiest way to do this is to use the program ssh-copy-id.

ssh-copy-id username@rivanna.hpc.virginia.edu

Please use your password when using ssh-copy-id. Your username is your UVA computing id. Now you should be ready to connect with

ssh username@rivanna.hpc.virginia.edu

Commandline editor

Sometimes it is necessary to edit files on Rivanna. For this, we recommend that you learn a command line editor. There are lots of debates on which one is better. When I was young I used vi, but found it too cumbersome. So I spend one-day learning emacs which is just great and all you need to learn. You can install it also on Linux, Mac, and Windows. This way you have one editor with very advanced features that is easy to learn.

If you do not have one day to familiarize yourself with editors such as emacs, vim, or vi, you can use editors such as nano and pico.

The best commandline editor is emacs. It is extremely easy to learn when using just the basics. The advantage is that the same commands also work in the terminal.

PyCharm

The best editor to do python development is pyCharm. Install it on your desktop. The education version is free.

VSCode

An inferior editor for python development is VSCode. It can be configured to also use a Remote-SSH plugin.

Moving data from your desktop to Rivanna

To copy a directory use scp

If only a few lines have changed use rsync

To mount Rivannas file system onto your computer use fuse-ssh. This will allow you to for example use pyCharm to directly edit files on Rivanna.

Developers however often also use GitHub to push the code to git and then on Rivanna use pull to get the code from git. This has the advantage that you can use pyCharm on your local system while synchronizing the code via git onto Rivanna.

However often scp and rsync may just be sufficient.

Example Config file

Replace abc2de with your computing id

place this on your computer in ~/.ssh/config

ServerAliveInterval 60

Host rivanna
     User abc2de
     HostName rivanna.hpc.virginia.edu
     IdentityFile ~/.ssh/id_rsa.pub
     
Host b1
     User abc2de
     HostName biihead1.bii.virginia.edu
     IdentityFile ~/.ssh/id_rsa.pub
     
Host b2
     User abc2de
     HostName biihead2.bii.virginia.edu
     IdentityFile ~/.ssh/id_rsa.pub

Adding it allows you to just ssh to the machines with

ssh rivanna
ssh b1
ssh b2

Rivanna’s filesystem

The file systems on Rivanna have some restrictions that are set by system wide policies that you need to be inspecting:

• TODO: add link here

You can alls see your quote with

rivanna>
  hdquota

we distinguish

• home directory: /home/<uvaid> or ~
• /scratch/bii_dsc_community/<uvaid>
• /project/bii_dsc_community/projectname/<uvaid>

Y In your home directory, you will find system directories and files such as ~/.ssh , ~/.bashrcand ~/.zshrc

The difference in the file systems is explained at

• https://www.rc.virginia.edu/userinfo/rivanna/storage/.

Dealing with limited space under HOME

As we conduct research you may find that the file space in your home directory is insufficient. This is especially the case when using conda. Therefore, it is recommended that you create softlinks from your home directory to a location where you have more space. This is typically somewhere under /project.

We describe next how to relocate some of the directories to /project

In ~/.bashrc, add the following lines, for creating a project directory.

$ vi ~/.bashrc

$ PS1="\w \$"
$ alias project='cd /project/bii_dsc_community/$USER'
$ export PROJECT="/project/bii_dsc_community/$USER"

At the end of the .bashrc file use

$ cd $PROJECT

So you always cd directly into your project directory instead of home.

The home directory only has 50GB. Installing everything on the home directory will exceed the allocation and have problems with any execution. So it’s better to move conda all other package installation directories to $PROJECT.

First, explore what is in your home directory and how much space it consumes with the following commands.

cd $HOME
$ ls -lisa
$ du -h .

Select from this list of directories that you want to move (those that you not already have moved).

Let us assume you want to move the directories .local, .vscode-server, and .conda. Important is that you want to make sure that .conda and .local are moved as they may include lots of files and you may run out of memory quickly. Hence you do next the following.

rivanna>
  $ cd $PROJECT
  $ mv ~/.local .
  $ mv ~/.vscode-server .
  $ mv ~/.conda .

Then create symbolic links to the home directory installed folder.

rivanna>
  $ cd $PROJECT
  $ ln -s $PROJECT/.local ~/.local
  $ ln -s $PROJECT/.vscode-server ~/.vscode-server
  $ ln -s $PROJECT/.conda ~/.conda

Check all symbolic links:

rivanna>
  $ ls -lisa

20407358289   4 lrwxrwxrwx    1 $USER users          40 May  5 10:58 .local -> /project/bii_dsc_community/djy8hg/.local
20407358290   4 lrwxrwxrwx    1 $USER users          48 May  5 10:58 .vscode-server -> /project/bii_dsc_community/djy8hg/.vscode-server

Singularity Cache

In case you use singularity you can build images you need to set the singularity cache. This is due to the fact that the cache usually is created in your home directory and is often far too small for even our small projects. Thus you need to set it as follows

rivanna>
  mkdir -p /project/$USER/.singularity/cache
  export SINGULARITY_CACHEDIR=/project/$USER/.singularity/cache

`

Python

In case you use python venv, do not place them in home but under project.

rivanna>
  module load python3.8
  python -m venv $PROJECT/ENV3
  source $PROJECT/ENV3/bin/activate

If you succeed, you can also place the source line in your .bashrc file.

In case you use conda and python, we also recommend that you create a venv from the conda python, so you have a copy of that in ENV3 and if something goes wrong it is easy to recreate from your default python. Those that use that path ought to improve how to do this here.

Adding cloudmesh rivanna specific commands and tools

On your computer in your ENV3 add the following to enable the commands

computer> 
  pip install pip -U
  pip install cloudmesh-common
  pip install cloudmesh-rivanna
  pip install cloudmesh-sbatch
  pip install cloudmesh-vpn

On Rivanna in ENV3 also add the gpu monitor

computer> 
  pip install pip -U
  pip install cloudmesh-common
  pip install cloudmesh-gpu
  pip install cloudmesh-rivanna
  pip install cloudmesh-sbatch

Note: Please send me a mail to laszewski@gmail.com if any requirements are missing as I may not yet have included all of them in the pip package.

Once you have activated it the cloudmesh rivanna command shows you combinations of SBATCH flags that you can use.

To see them type in

cms rivanna slurm list

To login into a specific node you can say (lest assume you like to log into a k80

cms rivanna login k80

Please be reminded that interactive login is only allowed for debugging all jobs must be submitted through sbatch.

To get the directives template to use that GPU, use

cms rivanna slurm k80

cloudmesh sbatch

Cloudmesh-sbatch is a super cool extension to sbatch allowing you to outomatically run parameters studies while creating permuattions on experiment parameters. At this time we try to create some sampel applications, but you can also ararnge a 30 minute meeting with Gregor so we try setting it up for your application with his help

See also:

• https://pypi.org/project/cloudmesh-sbatch/
• Example application: https://github.com/laszewsk/mlcommons/tree/main/benchmarks/cloudmask/target/rivanna
  • make project; make submit
  • see Makefile for how to use it.
• Hybrid Reusable Computational Analytics Workflow Management with Cloudmesh

cloudmesh vpn command

cloudmesh has a simple commandline vpn command that you can use to switch on and off vpn for UVA (and other vpn’s, we can add that feature ;-))

computer> 
  cms vpn connect
  ... do your work in vpn such as working on rivanna
  cms vpn disconnect
  ... work on your regular network 

Load modules

Modules are preconfigured packages that allow you to use a specific software to be loaded into your environment without needing you to install it from source. To find out more about a particular package such as cmake you can use the command

rivanna>
  module spider cmake # check whether cmake is available and details

Load the needed module (you can add version info). Note that some modules are dependent on other modules (clang/10.0.1 depends on gcc/9.2.0 so gcc needs to be loaded first.

rivanna>
  # module load gcc/9.2.0 clang/10.0.1
  module load clanggcc
  module load cmake/3.23.3 git/2.4.1 ninja/1.10.2-py3.8 llvm cuda/11.4.2

check currently loaded modules

rivanna>
  module list

clean all the modules

rivanna>
  module purge

Request GPUs to use interactively

TODO: explain what -A is

rivanna$ ijob -c number_of_cpus
              -A group_name
	      -p queue_name
	      --gres=gpu:gpu_model:number_of_gpus
	      --time=day-hours:minutes:seconds

An example to request 1 cpu with 1 a100 gpu for 10 minutes in ‘dev’ partition is

rivanna$ ijob -c 1 -A bii_dsc_community -p gpu --gres=gpu:a100:1 --time=0-00:10:00

Rivanna has different partitions with different resource availability and charging rate. dev is free but limited to 1 hour for each session/allocation and no GPU is available. To list the different partitons use qlist to check partitions

Last Checked July 28th, note thes values may change.

To list the limits, use the command qlimits

Last Checked July 28th, note these values may change.

Linux commands for HPC

Many useful commands can be found in Gregor’s book at

• https://cloudmesh-community.github.io/pub/vonLaszewski-linux.pdf

The following additional commands are quite useful on HPC systems

SLURM Batch Parameters

We present next a number of default parameters for using a variety of GPUs on rivanna. Please note that you may need to adopt some parameters to adjust for cores or memory according to your application.

Running on v100

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=12:00:00
#SBATCH --partition=bii-gpu
#SBATCH --account=bii_dsc_community
#SBATCH --gres=gpu:v100:1
#SBATCH --job-name=MYNAME
#SBATCH --output=%u-%j.out
#SBATCH --error=%u-%j.err

Running on a100-40GB

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=12:00:00
#SBATCH --partition=bii-gpu
#SBATCH --account=bii_dsc_community
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=MYNAME
#SBATCH --output=%u-%j.out
#SBATCH --error=%u-%j.err

Running on special fox node a100-80GB

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=12:00:00
#SBATCH --partition=bii-gpu
#SBATCH --account=bii_dsc_community
#SBATCH --gres=gpu:a100:1
#SBATCH --job-name=MYNAME
#SBATCH --output=%u-%j.out
#SBATCH --error=%u-%j.err
#SBATCH --reservation=bi_fox_dgx
#SBATCH --constraint=a100_80gb

Some suggestions

When compiling large projects, you may neeed to make surue you have enough time and memory to conduct such compiles. This can be best achieved by using an interactive node, possibly from the large memory partition.

References

• Presentation about SLURM on rivanna
• Tutorial on using Rivanna
• Gregors book chapters
  • https://github.com/cloudmesh-community/book/tree/main/chapters
• MPI with python:
  • https://cloudmesh.github.io/cloudmesh-mpi/report-mpi.pdf
  • https://github.com/cloudmesh/cloudmesh-mpi
  • Tutorials about cybertraining: https://cybertraining-dsc.github.io/docs/tutorial/
  • Modules about cybertraining: https://cybertraining-dsc.github.io/docs/modules/

Help Support

When requesting help from Gregor or anyone make sure to completely specify the issue, a lot of things cannot be solved if you are not clear on the issue and where it is occurring. Include:

• The issue you are encountering.
• Where it is occurring.
• What you have done to try to resolve the issue.

A good example is:

I ran the application xyz, from url xyz on Rivanna. I placed code in the directory /project/…. or I placed the data in /project/… The download worked and I placed about 600GB. However when I uncompress the data with the command xyz I get the error xyz. What should we do now?