Server instructions

This document explains how to request access, use and manage projects on the comp0.genomic.abi.am server

How to set up an account

Start with generating a SSH key pair, if you don’t have any. You may use the following documentation . Fill in this form .

The system administrator will email you the details, such as your new username.

How to access the server

In your Windows PowerShell or Unix terminal, type in the following

ssh YOURUSERNAME@comp0.genomic.abi.am

If you happen to have any issues while connecting, then run the following command and send the output to it-support@abi.am

ssh -v YOURUSERNAME@comp0.genomic.abi.am

How to use the server

Your home directory sits at /mnt/home/YOURUSERNAME and it is connected on per need basis. It becomes available when you log in, and it gets removed when you log out.

Your home directory has a quota of 10G

Your home directory is also private, no one has access to it except yourself. Keep it that way!

If you want to share files with others, you may use /mnt/user/YOURUSERNAME, which, unlike your home directory, can be read by others. For giving others write access, ask your system administrator

Your shared directory has a quota of 100G

As a project member, you shall always run your computation not directly, but rather with Slurm.

To learn the basics of Slurm, please follow this guide .

To specify the project, you can add the following to your Slurm Sbatch script.

#SBATCH -A ProjectName

As a user, you are limited to 4 cores of CPU (400% of cpu time) and 8GB of memory/RAM .

If you want to use more resources, then you’ll need to submit jobs as part of a project.

Applying for a Project

As a user, you should always be part of a project, if you want to have more resources.

To apply for a project, please use the following form . If you need to be part of an existing project, please ask your project lead to contact&nbs; it-support@abi.am .

Each project will have the followig resources by default:

64 CPU vCores
256 GB of RAM
5TB of Storage

If you require more (or less!) please mention in the form.

When your project is approved, you will see it mounted at the /mnt/proj/ProjecName directory.

If you want to see which groups you are a member of, then run the id command:

lilit@comp0:~$ id

uid=10001(lilit) gid=10001(lilit) groups=10001(lilit),15000(scientist),15001(microbiome)<

As you can see, the user lilit is part of the default group scientist and the project microbiome .

Each project sits at /mnt/proj/ProjectName , where the directory owner is the lead of the project, and the directory group is the project itself. This makes the project secure from unwanted writes, while keeping it usable for project members.

Requesting software

Software is installed globally.

If you’d like to find out where a software is, you may use the which command, i.e.

# which STAR

/usr/bin/STAR

Most software will be put into your $PATH, so doing a simple TAB will allow you to autocomplete software names.

Many custom installed software will be at /mnt/software/linux with their binaries installed at /mnt/software/linux/bin

If there is specific software that you need on the server, please use this form to request it.

Python version

In ABI we use pre-prepared VENVs to set default python version for our projects. Let's see how to that on an example of "fivepseq" project. Follow these steps to automatically activate a virtual environment named "fivepseq-env" when logging in:

Navigate to Your Home Directory: Open a terminal and navigate to your home directory. You can do this by running the following command:

cd ~

Open Your Bash Profile: Use a text editor to open your .bash_profile. This file is typically located in your home directory. You can open it with vim editor by running:

vim .bash_profile

Note: If .bash_profile doesn't exist, don't worry. You can create a new one. Simply run vim .bash_profile and start editing the file. Once you've added the necessary content, save the file and proceed to the next steps.

Add the Activation Line: In the .bash_profile file, add the following line at the end:

source /mnt/home/lilit/fivepseq-env/bin/activate

Save and Exit: After adding the line, save the changes and exit the text editor. In vim editor, you can do this by pressing Esc to exit editing mode, then typing :wq to save and quit.

Reload Bash Profile: To apply the changes, reload your .bash_profile. You can do this by running:

source .bash_profile

Verify Activation: You can verify that the virtual environment is activated by opening a new terminal session. Upon logging in, the virtual environment specified in the .bash_profile should be activated automatically.

That's it! Now, whenever you log in, the specified virtual environment will be automatically activated, allowing you to work within its isolated environment.

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If you have any questions, contact us at it-support@abi.am.

—
Ararat Hovhannisyan

Tags: Updates