BinAC2/Getting Started - Revision history

S Behnle at 17:10, 6 February 2026

2026-02-06T17:10:55Z

← Older revision		Revision as of 19:10, 6 February 2026
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	<source lang="bash">		<source lang="bash">
			#!/bin/bash
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
	#SBATCH --time=10:00		#SBATCH --time=10:00

F Bartusch at 07:19, 17 September 2025

2025-09-17T07:19:23Z

@@ Line 60: / Line 60: @@
 * is not actively used for computations in near future
-The <code>project</code> file system is available at <code>/pfs/10/project/</code>:
+The data is stored on HDDs. The primary focus of <code>project</code> is pure capacity, not speed.
 == Work File System ==

H Winkhardt: typo

2025-04-09T11:40:35Z

typo

← Older revision		Revision as of 13:40, 9 April 2025
Line 3:		Line 3:
	The Getting Started guide is designed for users who are new to HPC systems in general and to BinAC 2 specifically. After reading this guide, you should have a basic understanding of how to use BinAC 2 for your research.		The Getting Started guide is designed for users who are new to HPC systems in general and to BinAC 2 specifically. After reading this guide, you should have a basic understanding of how to use BinAC 2 for your research.

	Please note that this guide does not cover basic Linux command-line skills. If you're unfamiliar with commands such as listing directory contents or using a text editor, we recommend first exploring the Linux module on the [[https://training.bwhpc.de~~/bwHPC\|~~bwHPC training platform]].		Please note that this guide does not cover basic Linux command-line skills. If you're unfamiliar with commands such as listing directory contents or using a text editor, we recommend first exploring the Linux module on the [https://training.bwhpc.de bwHPC training platform].

	This guide also doesn't cover every feature of the system but aims to provide a broad overview. For more detailed information about specific features, please refer to the dedicated Wiki pages on topics like the batch system, storage, and more.		This guide also doesn't cover every feature of the system but aims to provide a broad overview. For more detailed information about specific features, please refer to the dedicated Wiki pages on topics like the batch system, storage, and more.

F Bartusch: /* Software */

2025-02-13T09:14:57Z

Software

← Older revision		Revision as of 11:14, 13 February 2025
Line 224:		Line 224:
	= Software =		= Software =

	There are several mechanisms how software can be installed on BinAC.		There are several mechanisms how software can be installed on BinAC 2.
	If you need software that is not installed on BinAC ~~you can~~ open a ticket and we can find a way to provide the software on the cluster.		If you need software that is not installed on BinAC 2, open a ticket and we can find a way to provide the software on the cluster.

	== Environment Modules ==		== Environment Modules ==
Line 238:		Line 238:

	# Load a module		# Load a module
	$ module load bio/~~bowtie2~~/2.~~4.1~~		$ module load bio/samtools/1.21

	# Show the module's help		# Show the module's help
	$ module help bio/~~bowtie2~~/2.~~4.1~~		$ module help bio/samtools/1.21
	</source>		</source>

Line 247:		Line 247:

	Sometimes software packages have so many dependencies or the user wants a combination of tools, so that environment modules cannot be used in a meaningful way.		Sometimes software packages have so many dependencies or the user wants a combination of tools, so that environment modules cannot be used in a meaningful way.
	Then other solutions like ~~conda~~ environments or Singularity ~~container~~ (see below) can be used.		Then other solutions like Conda environments or Singularity containers (see below) can be used.

	== Conda Environments ==		== Conda Environments ==

	Conda environments is a nice possibility for creating custom environments on the cluster, as a majority of the scientific software is available in the meantime as conda packages.		Conda environments are a nice possibility for creating custom environments on the cluster, as a majority of the scientific software is available in the meantime as conda packages.
			BinAC 2 already provides Conda via Miniforge.
	First, you have to install Miniconda in your home directory.
			You can find a general documtation for using Conda on [[Development/Conda \| on this wiki page]].

			== Apptainer (formerly Singularity) ==
	<source lang="bash">
	# Download installer
	$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
	$ sh Miniconda3-latest-Linux-x86_64.sh
	$ source ~/.bashrc
	</source>

	Then you can create your first environment and install software into it:

	<source lang="bash">
	# Create an environment
	$ conda create --name my_first_conda_environment
	# Activate this environment
	conda activate my_first_conda_environment
	# Install software into this environment
	$ conda install scipy=1.5.2
	</source>

	You will need to add this line to your jobscripts such that the environments are available on the compute nodes:

	<source lang="bash">
	source $HOME/miniconda3/etc/profile.d/conda.sh
	conda activate <env_name>
	</source>

	When installing software conda will solve dependencies on the fly.
	But it is not guaranteed that conda will use the exact same package versions in the future.
	For the sake of reproducibility, you can write a file containing all conda packages together with their versions:

	<source lang="bash">
	# Export packages installed in the active environment
	$ conda list --explicit > spec-file.txt
	# Create a new environment with the exact same conda packages
	$ conda create --name myenv --file spec-file.txt
	</source>

	== Singularity Container ==

	Sometimes software is also available in a software container format.		Sometimes software is also available in a software container format.
	Singularity is installed on all BinAC nodes. You can pull ~~Singularity~~ or Docker ~~containers~~ from registries onto BinAC and use them.		Apptainer (formerly called Singularity) is installed on all BinAC 2 nodes. You can pull Apptainer containers or Docker images from registries onto BinAC 2 and use them.
	You can also build new ~~Singularity~~ containers on your own machine and copy them to BinAC.		You can also build new Apptainer containers on your own machine and copy them to BinAC.

	Please note that ~~Singularity~~ containers should be stored in the ~~work~~ file system.		Please note that Apptainer containers should be stored in the <code>project</code> file system.
	We configured ~~Singularity~~ such that containers stored in your home directory do not work.		We configured Apptainer such that containers stored in your home directory do not work.

F Bartusch: /* Batch System Basics */

2025-02-13T09:08:43Z

Batch System Basics

Show changes

F Bartusch: /* Temporary Data */

2025-02-13T08:24:49Z

Temporary Data

← Older revision		Revision as of 10:24, 13 February 2025
Line 89:		Line 89:
	As you can see from the file permissions, the resulting workspace can only be accessed by you, not by other group members or other users.		As you can see from the file permissions, the resulting workspace can only be accessed by you, not by other group members or other users.

	== ~~Temporary Data~~ ==		== Scratch ==

			Each compute node provides local storage, which is much faster than accessing <code>project</code> and <code>work</code> file systems.</br>
	If your job creates temporary data, you can use the fast SSD with a capacity of 211 GB on the compute nodes. The temporary directory for your job is available via the $TMPDIR environment variable.
			When you execute a job, a dedicated temporary directory will be assigned to it on the compute node. This is often referred to as the <code>scratch</code> directory.</br>
			Programs frequently generate temporary data only needed during execution. If the program you are using offers an option for setting a temporary directory,</br>
			please configure it to use the <code>scratch</code> directory.</br>
			You can use the environment variable <code>$TMPDIR</code>, which will point to your job's <code>scratch</code> directory.

	= Batch System Basics =		= Batch System Basics =

F Bartusch: /* Work File System */

2025-02-13T08:11:13Z

Work File System

@@ Line 74: / Line 74: @@
 == Work File System ==
 <source lang="bash">
-cd /beegfs/work/
+$ ll /pfs/10/work/
 </source>
 == Temporary Data ==

F Bartusch: Correct BinAC 2 Getting Started guide.

2025-02-13T07:43:07Z

Correct BinAC 2 Getting Started guide.

← Older revision		Revision as of 09:43, 13 February 2025
Line 1:		Line 1:
	== Purpose and Goals ==		== Purpose and Goals ==

	The ~~'''~~Getting Started~~'''~~ guide is designed for users who are new to HPC systems in general and to BinAC specifically. After reading this guide, you should have a basic understanding of how to use BinAC for your research.		The Getting Started guide is designed for users who are new to HPC systems in general and to BinAC 2 specifically. After reading this guide, you should have a basic understanding of how to use BinAC 2 for your research.

	Please note that this guide does not cover basic Linux command line skills. If you're unfamiliar with commands such as listing directory contents or using a text editor, we recommend first exploring the Linux~~-Modul~~ on the [[https://training.bwhpc.de/bwHPC\|bwHPC training platform]].		Please note that this guide does not cover basic Linux command-line skills. If you're unfamiliar with commands such as listing directory contents or using a text editor, we recommend first exploring the Linux module on the [[https://training.bwhpc.de/bwHPC\|bwHPC training platform]].

	This guide also doesn't cover every feature of the system but aims to provide a broad overview. For more detailed information about specific features, please refer to the dedicated Wiki pages on topics like the batch system, storage, and more.		This guide also doesn't cover every feature of the system but aims to provide a broad overview. For more detailed information about specific features, please refer to the dedicated Wiki pages on topics like the batch system, storage, and more.

	Some terms in this guide may be unfamiliar. You can look them up in the [[HPC_Glossary\|HPC ~~Glossray~~]].		Some terms in this guide may be unfamiliar. You can look them up in the [[HPC_Glossary\|HPC Glossary]].

	== General Workflow of Running a Calculation ==		== General Workflow of Running a Calculation ==

	On a '''HPC Cluster''', you do not simply ~~run~~ log in and your software, ~~but~~ you write a '''Batch Script''' that contains all commands to run and process your job ~~and~~ ~~send~~ ~~this~~ ~~into~~ a waiting queue to be ~~run~~ on one of several hundred '''Compute Nodes'''.		On an '''HPC Cluster''', you do not simply log in and run your software. Instead, you write a '''Batch Script''' that contains all the commands needed to run and process your job, then submit it to a waiting queue to be executed on one of several hundred '''Compute Nodes'''.

	== Get Access to the Cluster ==		== Get Access to the Cluster ==
Line 19:		Line 19:
	== Login to the Cluster ==		== Login to the Cluster ==

	~~Setup~~ service password and 2FA token ~~and~~ ~~login~~ to ~~the~~ ~~cluster~~. → [[~~BinAC~~/Login\|Login BinAC]]		Set up your service password and 2FA token, then log in to BinAC 2. → [[BinAC2/Login\|Login BinAC]]

	== Using the Linux ~~Commandline~~ ==		== Using the Linux command line ==

			It is expected that you have at least basic Linux and command-line knowledge before using bwForCluster BinAC 2.
⚫	HPC Wiki (external site) → [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC/The_Command_Line Introduction to Linux ~~Commandline~~]
			There are numerous resources available online for learning fundamental concepts and commands.
			Here are two:

	Training course → [https://training.bwhpc.de/ Linux course on training.bwhpc.de]		* bwHPC Linux Training course → [https://training.bwhpc.de/ Linux course on training.bwhpc.de]
		⚫	* HPC Wiki (external site) → [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC/The_Command_Line Introduction to the Linux command line]

	Also see: [[.bashrc Do's and Don'ts]]		Also see: [[.bashrc Do's and Don'ts]]
Line 31:		Line 34:
	= File System Basics =		= File System Basics =

			BinAC 2 offers several file systems for your data, each serving different needs.
	~~The~~ ~~details~~ of ~~the~~ ~~file~~ ~~systems~~ ~~are~~ ~~explained~~ [https://wiki.bwhpc.de/e/BwForCluster_BinAC_Hardware_and_Architecture#Storage_Architecture here].		These are explained here in a short and simple form. For more detailed documentation, visit: [https://wiki.bwhpc.de/e/BwForCluster_BinAC_Hardware_and_Architecture#Storage_Architecture here].

	== Home File System ==		== Home File System ==

	Home directories are ~~meant~~ for permanent ~~file~~ storage of ~~files~~ ~~that~~ ~~are~~ ~~keep~~ ~~being used~~ like source codes, configuration files, executable programs, conda environments, etc.		Home directories are intended for the permanent storage of frequently used files, such as like source codes, configuration files, executable programs, conda environments, etc.
	It is ~~backuped~~ daily and has a quota.		The home file system is backed up daily and has a quota.
	If that quota is reached, you ~~will usually~~ experience ~~problems~~ when working on ~~the~~ ~~cluster~~.		If that quota is reached, you may experience issues when working with BinAC 2.

			Here are some useful command line and bash tips for accessing the Home File system.

			<source lang="bash">
			# For changing to your home directory, simply run:
			cd

			# To access files in your home directory within your job script, you can use one of these:
			~/myFile # or
			$HOME/myFile
			</source>

			== Project File System ==

			BinAC 2 has a <code>project</code> file system intended for data that:
			* is shared between members of a compute project
			* is not actively used for computations in near future

			The <code>project</code> file system is available at <code>/pfs/10/project/</code>:

			<source lang="bash">
			$ ll /pfs/10/project/
			total 333
			drwxrwx---. 3 root bw16f003 33280 Dec 19 17:16 bw16f003
			drwxrwx---. 3 root bw16g002 25600 Dec 17 15:23 bw16g002
			[..]
			</source>

			As shown by the file permissions the project directories are only accessible to users belonging to the specific compute project.

	== Work File System ==		== Work File System ==

			The Work F

	Use the work file system and not your home directory for your calculations and data. Create a work directory, usually users use their username:		Use the work file system and not your home directory for your calculations and data. Create a work directory, usually users use their username:

F Bartusch: Copy and Paste getting started from BinAC to BinAC2

2024-11-06T08:51:22Z

Copy and Paste getting started from BinAC to BinAC2

New page

== Purpose and Goals ==

The '''Getting Started''' guide is designed for users who are new to HPC systems in general and to BinAC specifically. After reading this guide, you should have a basic understanding of how to use BinAC for your research.

Please note that this guide does not cover basic Linux command line skills. If you're unfamiliar with commands such as listing directory contents or using a text editor, we recommend first exploring the Linux-Modul on the [[https://training.bwhpc.de/bwHPC|bwHPC training platform]].

This guide also doesn't cover every feature of the system but aims to provide a broad overview. For more detailed information about specific features, please refer to the dedicated Wiki pages on topics like the batch system, storage, and more.

Some terms in this guide may be unfamiliar. You can look them up in the [[HPC_Glossary|HPC Glossray]].

== General Workflow of Running a Calculation ==

On a '''HPC Cluster''', you do not simply run log in and your software, but you write a '''Batch Script''' that contains all commands to run and process your job and send this into a waiting queue to be run on one of several hundred '''Compute Nodes'''.

== Get Access to the Cluster ==

Follow the registration process for the bwForCluster. → [[Registration/bwForCluster|How to Register for a bwForCluster]]

== Login to the Cluster ==

Setup service password and 2FA token and login to the cluster. → [[BinAC/Login|Login BinAC]]

== Using the Linux Commandline ==

HPC Wiki (external site) → [https://hpc-wiki.info/hpc/Introduction_to_Linux_in_HPC/The_Command_Line Introduction to Linux Commandline]

Training course → [https://training.bwhpc.de/ Linux course on training.bwhpc.de]

Also see: [[.bashrc Do's and Don'ts]]

= File System Basics =

The details of the file systems are explained [https://wiki.bwhpc.de/e/BwForCluster_BinAC_Hardware_and_Architecture#Storage_Architecture here].

== Home File System ==

Home directories are meant for permanent file storage of files that are keep being used like source codes, configuration files, executable programs, conda environments, etc.
It is backuped daily and has a quota.
If that quota is reached, you will usually experience problems when working on the cluster.

== Work File System ==

Use the work file system and not your home directory for your calculations and data. Create a work directory, usually users use their username:

<source lang="bash">
cd /beegfs/work/
mkdir $USER
chmod 700 $USER
cd $USER
</source>

Do not use the login nodes to carry out any calculations or heavy load file transfers.

=== How to share data with coworkers? ===

You can share data with coworkers who are members in the same compute project by modifying file ownership and permissions of a directory in the work filesystem.
Every compute project has its own group on BinAC, namely the project's acronym.

In this example, the user tu_iioba01 creates a directory and wants to share it with members of the compute project bw16f003.
<source lang="bash">
$ id tu_iioba01
uid=900102(tu_iioba01) gid=500001(tu_tu) groups=500001(tu_tu),500002(bw16f003)
</source>

In order to share data with coworkers in the same compute project, change the group of the directory you want to share to the project acronym.
You can also set the so-called SGID-Bit. Then new files and subdirectories will automatically belong to this group.

<source lang="bash">
# Change ownership. This command changes the ownwership for ALL files and subdirectories.
$ chown -R <username>:<acronym> /beegfs/work/<your directory>
# Set SGID-Bit
$ chmod g+s /beegfs/work/<your directory>
# Show the directory's permissions and owner
$ ls -ld /beegfs/work/<your directory>
drwxr-sr-x 3 tu_iioba01 bw16f003 1 Apr 16 15:06 /beegfs/work/<your directory>
</source>

The group of the directory is now bw16f003. The permissions for the group is 'r-s'. This means members of the group can access the directory content and newly created subdirectories/files automatically belong to the group bw16f003.

Now you can set the file permissions for your coworkers in this directory as needed by granting read, write, and execute permissions to files and subdirectories.

<source lang="bash">
# Some examples
# Coworkers can read,write,delete,execute files in the directory
$ chmod 770 /beegfs/work/<your directory>
# Coworkers can read, owner still can write/delete files
$ chmod 740 /beegfs/work/<your directory>/<important_dataset>
</source>

For a more detailed explanation of file permissions, please refer to [https://www.linuxfoundation.org/blog/blog/classic-sysadmin-understanding-linux-file-permissions this tutorial]

== Temporary Data ==

If your job creates temporary data, you can use the fast SSD with a capacity of 211 GB on the compute nodes. The temporary directory for your job is available via the $TMPDIR environment variable.

= Batch System Basics =

On cluster systems like BinAC you do not run your analysis by hand on the login node.
Instead, you write a script and submit it to the batch system, this is called a job.
The batch systems then tries to schedule the jobs on the available compute nodes.

== Queue/Job Basics ==

The cluster consists of compute nodes with different [https://wiki.bwhpc.de/e/BwForCluster_BinAC_Hardware_and_Architecture hardware features].
These hardware features (e.g. high-mem or GPUs) are only available when submitting the jobs to the [https://wiki.bwhpc.de/e/Queues specific queue].
Also, each queue has different settings regarding maximal walltime.
The most recent queue settings are displayed on login as message of the day on the terminal.

Get an overview of the number of running and queued jobs:

<source lang="bash">
$ qstat -q

Queue Memory CPU Time Walltime Node Run Que Lm State
---------------- ------ -------- -------- ---- --- --- -- -----
tiny -- -- -- -- 0 0 -- E R
long -- -- -- -- 850 0 -- E R
gpu -- -- -- -- 66 0 -- E R
smp -- -- -- -- 4 1 -- E R
short -- -- -- -- 131 90 -- E R
----- -----
1051 91
</source>

To check all running and queued jobs:

<source lang="bash">
qstat
</source>

Just your own jobs.

<source lang="bash">
qstat -u <username>
</source>

== Interactive Jobs ==

Interactive jobs are a good method for testing if/how software works with your data.

To start a 1 core job on a compute node providing a remote shell.
<source lang="bash">
qsub -q short -l nodes=1:ppn=1 -I
</source>

The same but requesting the whole node.
<source lang="bash">
qsub -q short -l nodes=1:ppn=28 -I
</source>

Standard Unix commands are directly available, for everything else use the modules.
<source lang="bash">
module avail
</source>

Be aware that we allow node sharing. Do not disturb the calculations of other users.

== Simple Script Job ==

Use your favourite text editor to create a script called 'script.sh'.

{|style="background:#deffee; width:100%;"
|style="padding:5px; background:#cef2e0; text-align:left"|
[[Image:Attention.svg|center|25px]]
|style="padding:5px; background:#cef2e0; text-align:left"|
Please note that there are differences between Windows and Linux line endings.
Make sure that your editor uses Linux line endings when you are using Windows.
You can check your line endings with <code>vim -b <your script></code>. Windows line endings will be displayed as <code>^M</code>.
|}

<source lang="bash">
#PBS -l nodes=1:ppn=1
#PBS -l walltime=00:05:00
#PBS -l mem=1gb
#PBS -S /bin/bash
#PBS -N Simple_Script_Job
#PBS -j oe
#PBS -o LOG
cd $PBS_O_WORKDIR
echo "my Username is:"
whoami
echo "My job is running on node:"
uname -a
</source>

Submit the job using
<source lang="bash">
qsub -q tiny script.sh
</source>

Take a note of your jobID. The scheduler will reserve one core and 1 gigabyte of memory for 5 minutes on a compute node for your job.
The job should be scheduled within minute if the tiny queue is empty and write your username and the execution node into the output file.

There are tons of options, details and caveats. Most of the options are explained on [https://wiki.bwhpc.de/e/Batch_Jobs this page], but be aware that there are some [https://wiki.bwhpc.de/e/BwForCluster_BinAC_Specific_Batch_Features differences on BinAC].

If your job needs GPUs, you have to specify how many GPUs you want. Just submitting the job to the GPU queue does not work:

<source lang="bash">
#PBS -l nodes=1:ppn=1:gpus=1
#PBS -q gpu
</source>

If you encounter any problems, just send a mail to hpcmaster@uni-tuebingen.de.

== Killing a Job ==
Let's assume you build a Homer and want to stop/kill/remove a running job.
<source lang="bash">
qdel <jobID>
</source>

== Best Practices ==

The scheduler will reserve computational resources (nodes, cores, gpus, memory) for a specified period for you. By following some best practices, you can avoid some common problems beforehand.

=== Specify memory for your job ===

Often we get tickets with question like "Why did the system kill my job?".
Most often the user did not specify the required memory resources for the job. Then the following happens:

The job is started on a compute node, where it shares the resources other jobs. Let us assume that the other jobs on this node occupy already 100 gigabyte of memory. Now your job tries to allocate 40 gigabyte of memory. As the compute node has only 128 gigabyte, your job crashes because it cannot allocate that much memory.

You can make your life easier by specifying the required memory in your job script with:
<source lang="bash">
#PBS -l mem=xxgb
</source>
Then you have the guarantee that your job can allocate xx gigabyte of memory.

If you do not know how much memory your job will need, look into the documentation of the tools you use or ask us.
We also started [https://wiki.bwhpc.de/e/Memory_Usage a wiki page] on which we will document some guidelines and pitfalls for specific tools.

=== Use the reserved resources ===

Reserved resources (nodes, cores, gpus, memory) are not available to other users and their jobs.
You have the responsibility that your programs utilize the reserved resources.

An extreme example: You request a whole node (node=1:ppn=28), but your job uses just one core. The other 27 cores are idling. This is bad practice, so take care that the used programs really use the requested resources.

Another example are tools that do not benefit from a increasing number of cores.
Please check the documentation of your tools and also check the feedback files that report the CPU efficiency of your job.

<source lang="bash">
[...]
CPU efficiency, 0-100% | 25.00
[...]
</source>
This job for example used only 25% of the available CPU resources.

= Software =

There are several mechanisms how software can be installed on BinAC.
If you need software that is not installed on BinAC you can open a ticket and we can find a way to provide the software on the cluster.

== Environment Modules ==

Environment modules is the 'classic' way for providing software on clusters.
A module consists of a specific software version and can be loaded.
The module system then manipulates the PATH and other environment variables such that the software can be used.

<source lang="bash">
# Show available modules
$ module avail

# Load a module
$ module load bio/bowtie2/2.4.1

# Show the module's help
$ module help bio/bowtie2/2.4.1
</source>

A more detailed description of module environments can be found [https://wiki.bwhpc.de/e/Environment_Modules on this wiki page]

Sometimes software packages have so many dependencies or the user wants a combination of tools, so that environment modules cannot be used in a meaningful way.
Then other solutions like conda environments or Singularity container (see below) can be used.

== Conda Environments ==

Conda environments is a nice possibility for creating custom environments on the cluster, as a majority of the scientific software is available in the meantime as conda packages.
First, you have to install Miniconda in your home directory.

<source lang="bash">
# Download installer
$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ sh Miniconda3-latest-Linux-x86_64.sh
$ source ~/.bashrc
</source>

Then you can create your first environment and install software into it:

<source lang="bash">
# Create an environment
$ conda create --name my_first_conda_environment
# Activate this environment
conda activate my_first_conda_environment
# Install software into this environment
$ conda install scipy=1.5.2
</source>

You will need to add this line to your jobscripts such that the environments are available on the compute nodes:

<source lang="bash">
source $HOME/miniconda3/etc/profile.d/conda.sh
conda activate <env_name>
</source>

When installing software conda will solve dependencies on the fly.
But it is not guaranteed that conda will use the exact same package versions in the future.
For the sake of reproducibility, you can write a file containing all conda packages together with their versions:

<source lang="bash">
# Export packages installed in the active environment
$ conda list --explicit > spec-file.txt
# Create a new environment with the exact same conda packages
$ conda create --name myenv --file spec-file.txt
</source>

== Singularity Container ==

Sometimes software is also available in a software container format.
Singularity is installed on all BinAC nodes. You can pull Singularity or Docker containers from registries onto BinAC and use them.
You can also build new Singularity containers on your own machine and copy them to BinAC.

Please note that Singularity containers should be stored in the work file system.
We configured Singularity such that containers stored in your home directory do not work.