Search Results for: Biowulf

If you experience difficulties with running R on Biowulf, you should: Read the R docs on Biowulf . Contact the HPC team at staff@hpc.nih.gov Attend monthly HPC walk-in virtual consultations Also, please feel Read More...

Let's connect remotely to Biowulf. ssh username@biowulf.nih.gov Enter your password and hit enter . Navigate to your /data/$USER directory. cd /data/$USER Get an interactive session. sinteractive --gres=lscratch:5 Let's Read More...

Additional Resources HPC Biowulf Resources Biowulf User Guide R/Bioconductor on Biowulf R on Biowulf Training by the HPC team Other Resources What they forgot to teach you about R usethis package reference Controlling R Read More...

To connect to Biowulf, you must be on the NIH network, either on campus or via VPN. We will then connect using an ssh protocol. Open your terminal if on a mac or the command Read More...

08/14/2025 - Biowulf isthe NIH Unix-based high-performance computer (HPC). Unix is a command driven computer operating system. Biowulf has more computational power than the average laptop, which makes it ideal for analyzing Next Generation Sequencing (NGS) Read More...

Due to limits on computational resources, you may be interested in running your analysis on an HPC. Biowulf is the NIH high performance compute cluster. It has greater than 90k processors, and can easily perform Read More...

01/22/2024 - This is the first lesson in the Introduction to Unix on Biowulf, January 2024 series. In this lesson, participants will learn to log onto Biowulf and receive an overview of Unix command line as well Read More...

As mentioned previously, QIIME 2 is installed on Biowulf. To see available versions use module avail qiime Also, check out the QIIME2 Biowulf help page . The default version on Biowulf is qiime2-2021.4, and the latest Read More...

If you wish to use R on Biowulf, you can view modules available using module -r avail '^R$' . Loading the module requires an interactive session, sinteractive (unless submitting a job). Example of module load module Read More...

There are also versions of qiime2 available as modules on Biowulf, NIH’s high performance computing system. To see available versions use module avail qiime The default version on Biowulf is qiime2-2021.4, and the Read More...

09/28/2023 - This is Lesson 4 of the Fall 2023 Introduction to Unix on Biowulf Series . Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

09/21/2023 - This is Lesson 3 of the Fall 2023 Introduction to Unix on Biowulf Series . Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

09/14/2023 - This is Lesson 2 of the Fall 2023 Introduction to Unix on Biowulf Series . Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

09/07/2023 - This is Lesson 1 of the Fall 2023 Introduction to Unix on Biowulf Series. Registering for this class will get you signed up for all four sessions in this course. Please make sure that you can Read More...

To complement this course, there is a module available on Biowulf with installed programs associated with the Biostar Handbook. During class, we will work on the command line on the GOLD system on DNAnexus. However, Read More...

Lesson 3 Biowulf https://hpc.nih.gov/training/intro_biowulf/biowulf-quiz/

Once you have your Biowulf account, you can connect remotely to Biowulf using a secure shell (SSH) protocol. If you have a macbook, you will need to open the terminal application. If you are using Read More...

Now that we are becoming more proficient at the command line, we can use these skills to begin working on Biowulf. Today's lesson will focus on submitting computational jobs on the Biowulf compute nodes.

Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and databases" ( https://hpc. Read More...

Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and databases" ( https://hpc. Read More...

Find the program "Terminal" on your machine, and enter the following statement at the prompt: ssh username@biowulf.nih.gov where "username" is your NIH/Biowulf login username. If this is Read More...

Find the program "Terminal" on your machine, and enter the following statement at the prompt: ssh username@biowulf.nih.gov where "username" is your NIH/Biowulf login username. If this is Read More...

Two introductory lessons on Biowulf were presented in this course series. You can access those here and here . The first contains an introduction to Biowulf including information regarding storage space and the module system. The Read More...

For your convenience, we have created a module on Biowulf that includes many of the same programs in the bioinfo environment from The Biostar Handbook . Instructions for using this module can be found at Additional Read More...

Logging into Biowulf You must be on VPN (Virtual Private Network) or the NIH campus internet to access Biowulf. Request VPN at NCI . If you have a Biowulf account but have not used it in 60 Read More...

If you are on a Mac, you do not need PuTTy. Find the program "Terminal" on your machine, and enter the following statement at the prompt: ssh username@biowulf.nih.gov where " Read More...

You must be on VPN (Virtual Private Network) or the NIH campus internet to access Biowulf. Request VPN at NCI . If you have a Biowulf account but have not used it in 60 days, please send Read More...

Open the command prompt and start an "SSH" (secure shell) session: ssh username@biowulf.nih.gov where "username" is your NIH/Biowulf login username. If this is your first time logging Read More...

Open the command prompt and start an "SSH" (secure shell) session: ssh username@biowulf.nih.gov where "username" is your NIH/Biowulf login username. If this is your first time logging Read More...

When you log into Biowulf, you are automatically in your home directory (/home). This directory is very small and not suitable for large data files or analysis. Change to your data directory as follows: 1. Use Read More...

Biostars on Biowulf To complement this course, there is a module available on Biowulf with installed programs associated with the Biostar Handbook. During class, we will work on the command line on the GOLD system Read More...

For this tutorial, you will be using either your own Biowulf account, or a student account. If you do not have a Biowulf account, see the instructor to get the login and password for a Read More...

Lessons focus on developing command line skills, getting started and working on Biowulf (the NIH HPC cluster), and downloading data from NCBI. Lesson 1 - Introduction to Unix and the Shell ( Recording ) Lesson 2 - Navigating file Read More...

On Biowulf, create the file /home/$USER/bin/R with the following content: mkdir ~/bin nano ~/bin/R Paste the following into nano: #! /bin/bash module load R/4.2 exec R "$@" Make /home/$USER/ Read More...

Lesson 1 will serve as a course introduction and refresher on Unix, Biowulf, and R.

Introduction to Biowulf (May – Jun, 2023) Introduction to Unix on Biowulf (Jan – Feb, 2023) Bioinformatics for Beginners: Module 1 Unix/Biowulf

If you do not already have a Biowulf account, you can obtain one by following the instructions here . NIH HPC accounts are available to all NIH employees and contractors listed in the NIH Enterprise Directory. Read More...

Understand how R can be deployed on Biowulf Understand how to access and use R modules Learn to create a custom R library on Biowulf

06/11/2025 - All Biowulf u er , and all tho e intere ted in u ing the y tem , are invited to call in to our Virtual Walk-in Con ult to di cu problem and concern , from Read More...

04/16/2025 - Please email staff@hpc.nih.gov for the meeting link. All Biowulf users, and all those interested in using the systems, are invited to call in to our Virtual Walk-in Consult to discuss problems Read More...

Those researchers who used the NCI CCR Sequencing Facility to get sequencing done will receive a link to their data. This data can be transferred to the "PartekFlow" folder on Biowulf using Globus. Read More...

HPC staff will create a folder called "PartekFlow" in the user's Biowulf data directory. This folder will hold all Partek Flow projects.

02/07/2024 - This the final (6th) lesson of the Introduction to Unix on Biowulf, January 2024 series. Participants will learn to view and edit text files as well as scripts and to perform basic wrangling tasks on Read More...

02/05/2024 - The fifth lesson in the Introduction to Unix on Biowulf, January 2024 series teaches participants to submit scripts to the Biowulf batch system, which enables automation of multi-step analyses. Meeting link: https://cbiit.webex.com/ Read More...

01/31/2024 - The fourth lesson of the Introduction to Unix on Biowulf, January 2024 series will introduce participants to bioinformatics software installed on Biowulf. Meeting link: https://cbiit.webex.com/cbiit/j.php?MTID=mb2b097ebdc0 Read More...

01/29/2024 - In the third lesson of the Introduction to Unix on Biowulf, January 2024 series participants will learn to copy, move, rename, and remove files and folder using Unix commands. Meeting link: https://cbiit.webex.com/ Read More...

If you are using a Windows PC, you will need to download and install the PuTTY program. https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html Go to the section "Alternative Binary Files& Read More...

When you log into Biowulf, you are automatically in your home directory (/home). This directory is very small and not suitable for large data files or analysis. Use the "cd" command to change Read More...

When you log into Biowulf, you are automatically in your home directory (/home). This directory is very small and not suitable for large data files or analysis. Use the "cd" command to change Read More...

ssh -Y username@biowulf.nih.gov cd results_dir sinteractive --mem=8g --gres=lscratch:5 Open a connection to biowulf.nih.gov with "NoMachine". Minimize this window and work at the command line. module Read More...

Swarm is a script for running a group of commands on Biowulf. Swarm reads a list of command lines and automatically submits them to the system. To create a swarm file, you can use " Read More...

Swarm is a script for running a group of commands on Biowulf. Swarm reads a list of command lines and automatically submits them to the system. To create a swarm file, you can use " Read More...

Lesson 3: Introduction to Biowulf

To disconnect the remote connection on Biowulf, use exit

https://hpc.nih.gov/training/intro_biowulf/biowulf-quiz/

To run jobs on Biowulf, you must designate them as interactive, batch or swarm. Failure to do this may result in termination of your account.

To run jobs on Biowulf, you must designate them as interactive, batch or swarm. Failure to do this may result in termination of your account.

Swarm is for running a group of commands (job array) on Biowulf. swarm reads a list of command lines and automatically submits them to the system as sub jobs. To create a swarm file, you Read More...

Quiz yourself using the hpc.nih.gov biowulf-quiz .

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR set up a file transfer program ( Filezilla ) for Mac or WinSCP for Windows PC. program to establish a Read More...

If you are already logged in, exit the remote connection and reconnect. Remember, you must be on the NIH network. {{Sdet}} Solution{{Esum}} ssh username@biowulf.nih.gov {{Edet}}

For your convenience, we have created a module on Biowulf that includes many of the same programs in the bioinfo environment from The Biostar Handbook . To use this module, please see the instructions documented under Read More...

There is extensive documentation on transferring data to and from Biowulf at hpc.nih.gov . If you simply would like to view .html files or other output, or you want to copy small files, consider Read More...

Slurm system: batch jobs, swarms jobs, interactive sessions Introduce parallel command Retrieve data from NCBI Trouble shooting jobs and job failures Help session: submitting jobs on Biowulf

Slurm system: batch jobs, swarms jobs, interactive sessions Introduce parallel command Retrieve data from NCBI Trouble shooting jobs and job failures Help session: submitting jobs on Biowulf

We have created a Biostars module on Biowulf for your convenience. Instructions for using this module are here , and the software included in the module are listed here . Let's get an interactive session and Read More...

Biowulf is the Unix/Linux-based high-performance computing (HPC) cluster at NIH. If you do not currently use Biowulf for your data analysis needs, consider the following advantages: Much more compute power as compared to a Read More...

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07/16/2025 - All Biowulf users, and all those interested in using the systems, are invited to call in to our Virtual Walk-in Consult to discuss problems and concerns, from scripting problems to node allocation, to strategies Read More...

01/15/2025 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

12/11/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

11/13/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

10/17/2024 - Please join us on Thursday for our third talk in the Biowulf 25th Anniversary Seminar Series: Explorations in use of Synthetic Images for Biomedical ML/AI Research This talk will be videocast at: https:// Read More...

10/16/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

09/25/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

08/14/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

07/17/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

06/12/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

05/15/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

03/13/2024 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

02/14/2024 - For inquires send email to staff@hpc.nih.gov Meeting ID: 160 198 9146 Passcode: 083637 Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited Read More...

01/24/2024 - This is the second lesson of the Introduction to Unix on Biowulf, January 2024 series. After this lesson, participants will  Know how to get help with Unix commands Know how to transfer data from local Read More...

01/17/2024 - For inquires send email to staff@hpc.nih.gov Meeting ID: 160 335 9291 Passcode: 640160 Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited Read More...

12/13/2023 - For inquires send email to staff@hpc.nih.gov Meeting ID: 161 385 0213 Passcode: 179891 Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited Read More...

11/15/2023 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

Hundreds of scientific programs, databases, and packages are maintained on the NIH HPC (Biowulf). These are mostly accessible as modules. To see a list of available software in modules use module avail module avail [appname| Read More...

Lesson 5: Working on Biowulf Lesson 4 Review Flags and command options Wildcards ( * ) Tab complete Accessing user history with the "up" and "down" arrows cat , head , and tail Working with file content (input, Read More...

How to download data from the Sequence Read Archive (NCBI/SRA) to your account on NIH HPC Biowulf You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR Read More...

There are instructions for running SRA-Toolkit on Biowulf here ([https://hpc.nih.gov/apps/sratoolkit.html])(https://hpc.nih.gov/apps/sratoolkit.html). To start with, we will start up an interactive node using the & Read More...

08/16/2023 - For inquires send email to staff@hpc.nih.gov Next edition of the NIH HPC monthly Zoom-In Consults! All Biowulf users, and all those interested in using the systems, are invited to stop by Read More...

Discover expert help with analysis, processing applications, and licensed software packages.

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx Program Manager The CREx Team is happy to announce Deepika Velampati as the new CREx Program Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Intramural Core Resources NHGRI Flow Cytometry Core The Core performs high quality single cell analysis through the Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New CREx User Survey The CREx Team is carrying out a CREx User Survey. We would greatly appreciate Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Research Festival The NIH Research Festival highlights the groundbreaking science and the vibrant NIH community driving our Read More...

Cores & Facilities From centralized laboratories to collaborative resources and technologies available to CCR Investigators. NCI Cores Centralized laboratories providing broad access to cutting-edge technologies and specialized expertise. Browse NCI Cores Collaborative Resources are technologies and Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Derive Greater Insights and Accelerate your Research Using Bioinformatic Tools! CREx is an NIH Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Resources Advance your research with the NIH Mouse Imaging Facility (MIF) The NIH Mouse Imaging Read More...

Our operational objectives are to provide state-of-the-art OMICS technologies in support of the Genetics Branch (GB) investigators and collaborators. Research Services Wet Lab Single cell isolation from fresh, frozen, and FFPE tissue, DNA/RNA extractions Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More New NIH Resource Spotlight The NIH Lab Managers Working Group have developed a new NIH-wide database of cold Read More...

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