Documentation
Server FAQs

Server FAQs

Basic server usage

Where can I get more information?

Most of the guides below apply to people who purchase hourly credits and don’t have their own physical servers, but there is still some useful information in these links:

How do I get a CBSU user account?

If you have a user account already created, you need to set your password: https://cbsu.tc.cornell.edu/lab/labpassreset.aspx

Type in your user id (should be the same as your NetID) and click submit. A link to set new password will be sent to your e-mail.

How do I access the server from an off-campus location?

To access server from off-campus:

  1. Download Cisco AnyConnect Secure Mobility Client
  2. Open program and connect to VPN: cuvpn.cuvpn.cornell.edu
  3. Use your Cornell NetID password when prompted
  4. More info here: https://cbsu.tc.cornell.edu/lab/doc/Remote_access.pdf

How do I access the server?

Connect to server:

  1. Launch Terminal (macOS/Linux only; for PC users see https://cbsu.tc.cornell.edu/lab/doc/Remote_access.pdf)
  2. Type ssh yournetid@cbsunt246.tc.cornell.edu
  3. Enter the password you created above

Once logged in, you will be in your network-mounted /home/yournetid/ directory. We also have a shared home directory for the lab with 2TB of backed up storage in /home/backup/. This is where we have been backing up important files (fastq and bam files, scripts, etc.) so far.

How do I transfer data?

To transfer files between your local computer and the server (good for <1-2 GB files):

  1. Connect to VPN if not on campus
  2. Open a new terminal window or tab (i.e. not a terminal already connected to the server)
  3. Use rsync to transfer data from the server to your computer with the command:
rsync -av -progress -e ssh yournetid@cbsunt246.tc.cornell.edu:/workdir/Path/To/Your/File.txt /Path/To/Your/Local/Directory/
  • to transfer data from your computer to the server, use:
rsync -av -progress /Path/To/Your/Local/File/ -e ssh yournetid@cbsunt246.tc.cornell.edu:/workdir/Path/To/Your/Directory/

How do I check memory usage?

Keep an eye on memory and node usage with the top or fancier htop commands:

htop

# or #

top

A window showing jobs on all 56 nodes and total memory usage will appear. (Be careful not to exceed the 252GB memory, or the server will crash.) Close the window with Control+c. You can also list jobs that are running but aren’t taking up CPU (e.g. crashed jobs) using:

ps –ef | grep yournetid

How do I check the disk usage?

To check how much space each directory on the /workdir/ is taking up:

du -sh /workdir/*

To check how much free space is left:

df -h /workdir/

Data backup

Where should we store the backup files?

  • For sequencing data and other large files (>30MB), you should use /workdir/backup/.
  • For small files such as scripts, markdown files, certain figures, and others, you can store them under your project directory, which should also be a GitHub repo. You can then use GitHub to back up these files.
  • For sample metadata, you should use lab Google Drive to back them up.

What should be backed up?

  1. Zipped raw fastq files (essential)
  2. Zipped ready to map (adapter trimmed and renamed (demultiplexed if applicable) (optional)
  3. Raw bam files (unmapped reads removed, but not filtered for mapping quality etc). Only save .bam files here, never .sam. When we have multiple fastq files per individual, map first, then merge bams (optional)
  4. Realigned, filtered bam files (following indel re-alignment, filtering on mapping quality, removal of duplicates). If there are multiple bam files per individual, merge before cleaning, esp. before removing duplicates.
  5. Sample lists (needed for keeping track of the bam files) - put on Github
  6. SNP lists (lists of called SNP sets used for downstream analysis) - put on Github
  7. Major result files used for downstream analysis (e.g. mafs files) (optional)
  8. Ones that take a long time to run and that you’ll need to re-use
  9. All scripts used to process the data. There should be one master scripts that will run the full analysis pipeline (essential), but all intermediate scripts should be saved as well.

When should files be backed up?

  • You should back up the raw fastq files and sample metadata as soon as possible.
  • You should back up the analysis scripts often while you are working on them.
  • You can start backing up the other files as long as moving them do not interfere with your workflow. Do note that you should avoid reading and (especially) writing under /workdir/backup/ as much as possible.

What should be deleted, and when?

  • TODO

What are the practices that should be avoided?

  • Don’t move things around or re-name files unless there is reason to (it’s ok to do if there is)
  • Don’t work directly in the backup folder, i.e. don’t have your mapping program write sam files into the backup folder and then convert. Do that in your working directory and then move over the bam files to be backed up.
  • Don’t store files in multiple places

Running programs on the server

Where do I run programs?

All processes (except really tiny jobs) must be done on the local server, /workdir/. To connect to the local server: cd /workdir/

How do I install programs?

  • There are many programs installed system-wide. A list of software and details on how to use it, see https://cbsu.tc.cornell.edu/lab/labsoftware.aspx.
  • You can request installation of software not listed on the CBSU website using the Contact Us link, but installation may take a few days.
  • You may also install programs locally yourself. Please always intall new programs under /workdir/programs/. You should also keep track of the version number of the program by first creating a new directory with the program name and version number, and install the program in this directory.

How do I check job status?

To see the job status of all jobs running on the server, use htop

To see only the status of jobs that you are running, use ps -aux | grep user_name

How do I kill a job?

Get the job ID using htop (this shows all jobs being run; look for the PIDs matching your username). To see only the job numbers that you are currently running, type pgrep -u USERNAME

To kill a specific job, use kill JOBNUM

To kill all jobs associated with your user name, use nohup pkill -u USERNAME

How do I make scripts executable?

If you use shell scripts to run commands, make them executable with chmod +x filename

You can use chmod to change permissions on files as well. See man chmod.

How do I control the number of threads a program uses?

For program that automatically use all available nodes, you can limit the number of nodes used with

export OMP_NUM_THREADS=8

How do I set the priority of a process?

To change the CPU usage of a program or command (i.e., give the process more or less CPU time than other processes), you can set the priority using the nice command, or renice if the process is already running.

  • The priority of a process (PR or PRI) and its niceness value (NI) can be seen using top or htop.
  • PR or PRI is the process’s actual priority used by the Linux kernel to schedule a task.
  • NI is the niceness value that the user can set to control the priority of a process.
  • NI ranges from -20 (highest priority value) to 19 (lowest priority value), with a default of 0.
  • Any user may decrease the priority of a process, but root permissions are required to increase priority. By increasing the niceness of your process, it will decrease the priority and get less amount of CPU compared to processes with lower niceness values.

If you are running some shell script myscript.sh, you can start the process with the niceness value in the command: nice -n 10 sh myscript.sh &

To change the niceness value of a running process, use the process ID and run renice -n nice_val -p [pid]

To change the niceness values of all processes by a user, run renice -n nice_val -u [user]

Using R on the server

How to run RStudio on the server?

  1. Run this command to start RStudio server

/programs/rstudio_server/rstudio_start

  1. From a browser on your laptop/desktop computer, go to

http://cbsunt246.biohpc.cornell.edu:8015

Sometimes, you might need to reshresh the page once. Log in using your biohpc username and password

  1. If you want to stop the RStudio Server, using this command:

/programs/rstudio_server/rstudio_stop

How to avoid plotting figures all over again every time when knitting an Rmd file?

You can set eval=F in the code block, run it manually, and save the figure to a file. Then, you can start a new code block, set eval=T, and use include_graphics("path_to_the_figure") to show the figure. Note that if you are knitting to a GitHub formatted md file, the figure needs to be pushed to GitHub as well for it to show up on the GitHub site.

How to use Positron (RStudio successor) on the server

Positron is an data science IDE developed by Posit, the developers of RStudio. It’s designed to be the successor to the RStudio software by being a flexible, user-friendly workspace. For more info, check out this video for a full breakdown of Positron’s features. Positron is effectively a reskinned version of Visual Studio Code but with some extra R-specific features, such as customizable plotting and the ability to see all environment variables and dataframes. Beyond R, Positron also supports Python interpreters and has a seamless GitHub integration. Like VS Code, Positron features a marketplace of useful extensions for a variety of tasks.

Positron is currently in beta, meaning that some features remain in-progress or missing and you may run into bugs. However, you can still install it via its GitHub Releases page. To get it working on our server, you will first need to go into the Settings (File > Preferences > Settings) and search for Kallichore, and check Kallichore Supervisor: Enable. You will then need to connect via ssh by hitting Ctrl + Shift + P on your keyboard and typing in Remote-SSH: Connect to Host. You will be prompted to enter your ssh host address, which should be yournetid@cbsunt246.biohpc.cornell.edu. A new window should open, and you will need to enter your BioHPC password. You can then select your working directory by going to the Explorer panel and selecting Open Folder and pointing to your desired working directory.

For more information on customizing Positron, check out this link, which is a bit outdated but contains some useful info on settings and extensions you can implement for a good experience.

Using GitHub on the server

What are some basic things I need to know to use GitHub on the server?

Check out this cheat sheet. It has most of the information that you will need.

How can I skip logging in each time that I use GitHub?

Run git config --global credential.helper "cache --timeout=3600". You can modify the number after timeout=. timeout=3600, for example, will save your login information for one hour.

Lab conventions

How do we name files, directories, objects, functions, and others?

GitHub repos: kebab (dashes in place of spaces)

Directories on the server: snake-case (all lowercase with _ in place of spaces)

Shell scripts: all uppercase for variable names, snake-case for almost everything else

R scripts: snake-case for object and function names

Others: snake-case for almost everything else

How do we keep our analysis logs?

We use a github formatted markdown file to keep track of our analysis pipeline. You can use Rmd to generate this markdown file.

What are some good coding practices recommended by the lab?

Please read https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745 and https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510

Miscellaneous tips

How do I download files from NCBI’s Short Read Archive (SRA)?

Navigate to the SRA (https://trace.ncbi.nlm.nih.gov/Traces/sra/) and retreive the SRA run accession number: these are coded as SRR####### e.g., SRR7973881

On the server, navigate to the backup directory (see below) or any directory where you would like to deposit the files

Use the sra toolkit (installed on the server) to download files

fastq-dump --split-files --gzip SRR#######

–split-files splits paired-end reads, do not use this for single-end reads –gzip zips the read files upon downloading

You need only to enter toe SRA accession as is, the sra toolkit will connect to NCBI automatically

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