LWP-Wiki - User contributions [en]

Software recommendations

2024-06-24T13:45:48Z

Sebastian: Create page with a few example programs

The LWP comes with some software preinstalled as it is based on a regular Ubuntu installation and we add some packages for convenience. As a one-fits-it-all installation, we can't add too much software by default to avoid bloat. You can however install most software yourself [[install packages|system-wide on personal machines]] or in your [[home directory|$HOME directory on shared machines]].

Below you can find some recommended programs for various purposes.

= Office =

* LibreOffice: free and open source writing (LibreOffice Writer), presentation (LibreOffice Impress), drawing (LibreOffice Draw) and more programs similar to other *Office solutions. Largely compatible with proprietary document types, but promoting open document types (ODF/ODT) or export to PDF for portability and interoperability.

= File editing, coding =

* gedit: simple GUI editor, installed by default on Ubuntu
* Kate: GUI, split windows, syntax highlighting
* VIM: command line editor, heavily customizable and extendable
* Emacs: command line, "the extensible, customizable, self-documenting, real-time display editor"
* VSCode: popular development tool, but bloated (more of an IDE) and developed by [https://www.ecis.eu/documents/Finalversion%20Consumerchoicepaper.pdf Microsoft]

Git

* [https://github.com/jesseduffield/lazygit lazygit]: simple terminal UI for git commands

= Desktop =

* screenshots and screen recording
** Spectacle: (full) window, time-delayed screenshot, rectangular selection, etc. with configurable keyboard shortcuts.
** Open Broadcaster Software (OBS): free and open source software for video recording and live streaming

= Maths, Visualization and Computer Algebra =

* Mathematica
* MatLab
* Python: Matplotlib, Seaborn

Software

2024-06-17T13:24:47Z

Sebastian: Add link to future page software recommendations

[[Category:software-faq]]
General
* [[choose packages|How to figure out which package to install/request]]
* [[install packages|How to install packages from the available repositories]]
* [[Using LWP software from a non-LWP]]
* [[software recommendations|Recommended software by categories]]
* [[How to set a default program]]

Specific Software
* [[software arb|Using "ARB" (microbiology software)]]
* [[software gurobi|Using "Gurobi" (mathematical programming optimization software)]]
* [[Using the Intel Fortran compiler]]
* [[How to disable the emacs splash screen]]
* [[Using newer gcc in /opt/netapps]]
* [[Skype can't hear me]]
* [[Subversion (svn) authentication fails]]
* [[GSI-software| Configure your LWP for use with Global GSI-software system]]
* [[Gromacs 2016.3 on /opt/netapps]]
* [[VOTCA on /opt/netapps]]
* [[DAMASK on /opt/netapps]]
* [[code::blocks on /opt/netapps]]
* [[Dropbox]]
* [[Paraview]]
* [[OpenFOAM]]
* [[Bagel4]]
* [[EESSI]]
* [[LaTeX]]

Git server

2024-06-17T13:22:25Z

Sebastian: Mention GitLab server git.lwp.rug.nl

[[Category:misc-faq]]
__TOC__

This describes how to create repositories on the [https://vcs.service.rug.nl Git server of the RUG (vcs.service.rug.nl)] and enable other people to access them over the internet.

The LWP team additionally provides a [https://git.lwp.rug.nl GitLab instance, git.lwp.rug.nl], running within the CIT facilities. The university-wide login with S/P-number can be used to use this server.

= vcs.service.rug.nl =

Familiarity is assumed with Git and SSH.

== Repository directory ==

Staff members can get a directory in which they can create repositories.

To get an account with a repository directory, please provide us with:

; ''Your e-mail address''
: For accounts that can create repositories, <code>@rug.nl</code> addresses are required.
; ''Your SSH public key''
: This is a small text file (~ 1kb). If you use OpenSSH, it is by default <code>~/.ssh/id_rsa.pub</code>. Getting an SSH public key is outside the scope of this manual.
; ''Directory name''
: This will become part of the URL to your repositories. An obvious name could be the acronym of your department, project, or just your initials.

== Checking access ==

Run this command to check your access to the server:

<pre>ssh git@vcs.service.rug.nl info</pre>
Anybody whose SSH public key was registered with the server can run this command. If successful, it lists the repositories you have access to, and your permissions to them.

Example output:

<pre>C abc/..*
R W one/example
R doc</pre>
Which means:

* You can create repositories inside the directory <code>abc</code>.
* You can read and write to a repository called <code>one/example</code>.
* You can read the repository <code>doc</code>.

== Creating a repository ==

To create a new repository, just clone from the directory where you have permissions to create repositories. Repositories that do not exist yet, will be created on the fly:

<pre>git clone git@vcs.service.rug.nl:abc/example</pre>
Breakdown of the URL:

; “git”
: The username for SSH. This is always “git”.
; “vcs.service.rug.nl”
: DNS name of the Version Control Server. This is always “vcs.service.rug.nl”.
; “abc”
: This is the directory where you can create repositories.
; “example”
: Name of the (new) repository.

When you create a repository, you will be registered as the owner of it. This enables you to grant access permissions to other persons.

== Granting access to others ==

To enable third party persons to access the server, please provide their:

* E-mail address
* SSH public key

At this moment new accounts will need to be registered on the server manually by the server admins. In the future a web application may automate this.

Once they’re registered, you can grant them access to repositories you own (or are allowed to administrate) by assigning ''roles'' to their e-mail address.

E.g. to enable John Doe to write to your repository <code>abc/example</code>, run the <code>perms</code> command using SSH like this:

<pre>ssh git@vcs.service.rug.nl perms abc/example + WRITERS john.doe@somehere.net</pre>
In this command, “WRITERS” is called a ''role''. If you would want to grant John Doe only read access to the repository, you could specify “READERS” instead.

To ''revoke'' a role instead, replace the ‘+’ in the command with a ‘-’:

<pre>ssh git@vcs.service.rug.nl perms abc/example - WRITERS john.doe@somehere.net</pre>

=== Roles ===

There are more levels of access than just “READERS” and “WRITERS”. Here is the entire list of roles with their permissions:

; ''READERS''
: Only reading is allowed, i.e.:
;* clone
;* fetch
;* pull
; ''WRITERS''
: In addition to what READERS can do:
;* Fast-forward push (except to the “master” branch).
;* Create new branches.
;* Create tags.
; ''MASTERS''
: In addition to what WRITERS can do:
;* Fast-forward push to “master”.
; ''MANAGERS''
: In addition to what MASTERS can do:
;* Delete branches.
;* Delete tags.
;* Non fast-forward push, i.e. push amended commits, rebased or rewound branches.
; ''ADMINS''
: In addition to what MANAGERS can do:
;* Managing access to the repository by assigning/revoking roles, just like the owner of the repository.

If more than one role is assigned, the role which allows the most will be in effect.

To list which roles are assigned for a repository, run the <code>perms</code> with the <code>-l</code> option command using SSH:

<pre>ssh git@vcs.service.rug.nl perms abc/example -l</pre>
; '''Note #1:'''
: The <code>-l</code> option should be the last argument on the command line.
; '''Note #2:'''
: Do not omit the <code>-l</code> option without knowing what you’re doing! This will invoke “batch mode” and if you leave the input empty (even by pressing <code>ctrl-c</code>) it will erase all permissions! The only correct way to bail out of this is to enter literally: <code>cancel</code> and press <code>enter</code>.

== Further information ==

* “Gitolite” is used for hosting Git on this server. So for all the details, refer to Gitolite’s documentation: http://gitolite.com/
* A quick tutorial about SSH public keys is here: http://git-scm.com/book/tr/v2/Git-on-the-Server-Generating-Your-SSH-Public-Key

LaTeX

2024-04-22T11:44:30Z

Sebastian:

[[Category:software-faq]]

== Using LaTeX on LWP ==

A comprehensive LaTeX installation (TexLive) is provided under <code>/opt/netapps/texlive/current</code>. This should be available to you, but you can ensure that is the case by adding the directory <code>/opt/netapps/texlive/current/bin/x86_64-linux</code> to your <code>$PATH</code> environment variable, e.g. by adding

<pre>
export PATH="/opt/netapps/texlive/current/bin/x86_64-linux:$PATH"
</pre>

to your <code>~/.bashrc</code> file.

Verify the installation e.g. with

<pre>
tlmgr --version
</pre>

LaTeX

2024-04-22T10:59:44Z

Sebastian: Add page on LaTeX through lwp16:netapps

== Using LaTeX on LWP ==

A comprehensive LaTeX installation (TexLive) is provided under <code>/opt/netapps/texlive/current</code>. This should be available to you, but you can ensure that is the case by adding the directory <code>/opt/netapps/texlive/current/bin/x86_64-linux</code> to your <code>$PATH</code> environment variable, e.g. by adding

<pre>
export PATH="/opt/netapps/texlive/current/bin/x86_64-linux:$PATH"
</pre>

to your <code>~/.bashrc</code> file.

Verify the installation e.g. with

<pre>
tlmgr --version
</pre>

Software

2024-04-22T09:51:03Z

Sebastian: Add ref LaTeX

[[Category:software-faq]]
General
* [[choose packages| How to figure out which package to install/request]]
* [[install packages| How to install packages from the available repositories]]
* [[Using LWP software from a non-LWP]]
* [[How to set a default program]]

Specific Software
* [[software arb|Using "ARB" (microbiology software)]]
* [[software gurobi|Using "Gurobi" (mathematical programming optimization software)]]
* [[Using the Intel Fortran compiler]]
* [[How to disable the emacs splash screen]]
* [[Using newer gcc in /opt/netapps]]
* [[Skype can't hear me]]
* [[Subversion (svn) authentication fails]]
* [[GSI-software| Configure your LWP for use with Global GSI-software system]]
* [[Gromacs 2016.3 on /opt/netapps]]
* [[VOTCA on /opt/netapps]]
* [[DAMASK on /opt/netapps]]
* [[code::blocks on /opt/netapps]]
* [[Dropbox]]
* [[Paraview]]
* [[OpenFOAM]]
* [[Bagel4]]
* [[EESSI]]
* [[LaTeX]]

User:Sebastian

2024-04-22T09:23:21Z

Sebastian:

[https://www.rug.nl/staff/s.erfort/ Sebastian Erfort] [mailto:s.erfort@rug.nl <s.erfort@rug.nl>] 
Linux System Administrator 
Team LWP

User:Sebastian

2024-04-22T09:22:35Z

Sebastian:

[https://www.rug.nl/staff/s.erfort/ Sebastian Erfort] [http://mailto:s.erfort@rug.nl <s.erfort@rug.nl>] 
Linux System Administrator 
Team LWP

User:Sebastian

2024-04-22T09:21:51Z

Sebastian:

[https://www.rug.nl/staff/s.erfort/ Sebastian Erfort] <s.erfort@rug.nl> 
Linux System Administrator 
Team LWP

User:Sebastian

2024-04-22T09:20:55Z

Sebastian: Created page with "[https://www.rug.nl/staff/s.erfort/ Sebastian Erfort] <s.erfort@rug.nl> Team LWP"

[https://www.rug.nl/staff/s.erfort/ Sebastian Erfort] <s.erfort@rug.nl>
Team LWP

Install packages

2023-08-03T12:07:57Z

Sebastian: Remove sudo from commands it isn't required for (search etc.)

[[Category:software-faq]]
It is possible for users to install packages from the standard repositories we provide on their own LWP's. Students (i.e. those logging in with S-numbers) are excluded from this feature, because the PCs in the computer rooms need to diverge as little as possible and new versions of packages can cause trouble with upgrades of packages provided by Ubuntu.

'''If you wish your software to be installed on all LWP's, e.g. because you need it for a course, please fill out [[Special:Contact/swreq|this software request form]].'''

We've added many extra repositories, for special packages, but they've been given a lower install priority. We've done this, so you have to deliberately install the package version you want and no accidental installs happen. You can also install anything that can be found in the ''Ubuntu Software Center''. 
----
Here are the most useful commands on the command line. 
* To search for the actual package name:
apt-cache search <name of the program>
* See the available versions of a package and in what repository with what priority they can be found:
apt-cache policy <package>
* Installing a package from
:1. the standard ''Ubuntu'' repositories:
sudo apt-get install <package>
:2. the extra repositories:
sudo apt-get install -t o=<origin> <package>
* With the '-t' option you can provide the <origin> of the package.
:1. If you know the repository name, the origin (o=...) can be found in the preferences file of the repository of the package:
cat /etc/apt/preferences.d/<repository_name>.pref
:2. If you don't know the repository name, you can use the following commands:
apt-cache policy <package>
apt-cache policy | grep -A2 <package source> | grep -o "o=.*" | cut -d"," -f1 | uniq

'''e.g.''' If you would like to install the latest version of Libreoffice on your system. It isn't available from the main repository, but it is available in one of the extra's with a lower (400) priority. (version numbers may differ)
'''sudo apt-cache policy libreoffice'''
[sudo] password for <you>:
libreoffice:
Installed: 1:3.5.7-0ubuntu5
Candidate: 1:3.5.7-0ubuntu5
Version table:
1:4.2.1-0ubuntu1~trusty 0
400 http://deb.rug.nl/ppa/mirror/ppa.launchpad.net/libreoffice/ppa/ubuntu/ precise/main amd64 Packages
*** 1:3.5.7-0ubuntu5 0
500 http://osmirror.rug.nl/ubuntu/ trusty-updates/main amd64 Packages
100 /var/lib/dpkg/status
1:3.5.4-0ubuntu1.1 0
500 http://security.ubuntu.com/ubuntu/ trusty-security/main amd64 Packages
1:3.5.2-2ubuntu1 0
500 http://osmirror.rug.nl/ubuntu/ trusty/main amd64 Packages
We can see that version 1:4.2.1 is the latest, but 1:3.5.7 is installed. 
First we'll pretend we don't know the repository file is named libreoffice.* and try to determine the origin of the package with a command:
'''sudo apt-cache policy | grep -A2 http://deb.rug.nl/ppa/mirror/ppa.launchpad.net/libreoffice/ppa/ubuntu/ | grep -o "o=.*" | cut -d"," -f1 | uniq'''
o=LP-PPA-libreoffice
If you do know the file to look in, you can do this:
'''cat /etc/apt/preferences.d/libreoffice.pref'''
# libreoffice
Explanation: : libreoffice
Package: *
Pin: release o=LP-PPA-libreoffice
Pin-Priority: 400
The "'''o=...'''" parameter is the origin, so now we can install the latest version with the addition of "'''-t o=LP-PPA-libreoffice'''" to the normal apt-get command:
'''sudo apt-get install -t o=LP-PPA-libreoffice libreoffice'''
<long list of packages and extra packages>
[y/n] y
<even longer list of stuff the system is doing>
It might ask you if you want to keep some configuration files. Usually the default (keep the config file on the system) is the best choise... unless you want to begin with a completely clean install, because of problems. When it's done, you'll have the latest version of Libreoffice installed.

Can I have root rights?

2023-08-03T11:14:08Z

Sebastian:

[[Category:misc-faq]]
We strive to make the LWP such that you do not need sudo and can only provide limited support for users with full permissions, since we do not know anymore how your system has changed.
Permissions can be given for certain commands, in fact you can already install all packages from all the repositories that we
have pre-configured. Example:

$ sudo apt-get install <somepackage>

For details, refer to [[install packages]].

If you need some software that is not in these repositories we have
rather that you ask us to provide it. That way we can keep track on what
is important for users and what is not.

That said you can of course install whatever you like in your [[Home directory|home directory]] or
on the local /mnt/D partition.

Examples:
$ conda create -n foo python=3.7 numpy keras
$ npm install <something>
$ pip install --user <some package> # use conda instead of pip
$ make && make install PREFIX=$HOME/local

If you tell us what it is that you want to achieve with sudo rights then
we can try to find a way do it without sudo rights (or why you should not
do that).

However, if you're still convinced you need sudo rights on your system, send [mailto:lwp@rug.nl us] a request mentioning your PC's hostname and/or WKS-number. Please note that you cannot get root rights to shared PC's.

FAQ

2023-08-03T09:58:18Z

Sebastian: Add page on root/sudo rights to FAQs

[[Category:faq]]
Here we try to write down solutions to most common issues. If you think something is missing, please let [mailto:lwp@rug.nl us] know.
----
 
* [[Installing]]
* [[Remote access]]
* [[Software]]
* [[Printing]]
* [[Networking]]
* [[Graphics]]
* [[Home directory]]
* [[Docker]]
* [[Anaconda]]
* [[Miscellaneous]]
* [[Data retention policy]]
* [[Can_I_have_root_rights%3F|root/sudo rights]]

Anaconda

2023-06-29T15:19:58Z

Sebastian:

[[Category:anaconda-faq]][[Category: Python]]
The '''Anaconda''' Python distribution allows you to set up a personal environment to install Python libraries/packages/modules in your Home directory, including different versions of Python. This is helpful for example if you require a newer Version than is installed on your system. Anaconda is available on LWP through a NFS mount. In order to use it on LWP instead of the locally installed Python, you need to load some environment variables into your shell.

To make Anaconda available in just your current ''bash'' session:

'''bash$''' source /opt/netapps/anaconda-lwp4/etc/profile.d/conda.sh
'''bash$''' conda activate

To have your shell startup files managed by Anaconda, so it will be available any time you start your shell:

'''bash$''' conda init

And after this, close and re-open your shell. Note that this last command also works with a select few other shells.

====Custom environments====

In order to be able to install additional packages using <code>conda install <package></code> you'll need to your own ''environment''. Such environment is stored in your home directory so it can be written to by you. By the commands above activate anaconda's default environment ''base'' and because it is stored centrally on the network it's not writeable.

To create your own environment called "xmpl" (it's recommended to keep the name short):

'''bash$''' conda create --name xmpl

Activate this with:

'''bash$''' conda activate xmpl

Custom environments also allow you to use specific versions of python itself and/or module packages, for example

'''bash$''' conda install python=3.11

For more information see:
* [https://conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-environments the conda documentation about environments].
* https://en.wikipedia.org/wiki/Anaconda_(Python_distribution)
* https://docs.anaconda.com/anaconda/user-guide/

Anaconda

2023-06-29T15:18:23Z

Sebastian:

[[Category:anaconda-faq]]
The '''Anaconda''' Python distribution allows you to set up a personal environment to install Python libraries/packages/modules in your Home directory, including different versions of Python. This is helpful for example if you require a newer Version than is installed on your system. Anaconda is available on LWP through a NFS mount. In order to use it on LWP instead of the locally installed Python, you need to load some environment variables into your shell.

To make Anaconda available in just your current ''bash'' session:

'''bash$''' source /opt/netapps/anaconda-lwp4/etc/profile.d/conda.sh
'''bash$''' conda activate

To have your shell startup files managed by Anaconda, so it will be available any time you start your shell:

'''bash$''' conda init

And after this, close and re-open your shell. Note that this last command also works with a select few other shells.

====Custom environments====

In order to be able to install additional packages using <code>conda install <package></code> you'll need to your own ''environment''. Such environment is stored in your home directory so it can be written to by you. By the commands above activate anaconda's default environment ''base'' and because it is stored centrally on the network it's not writeable.

To create your own environment called "xmpl" (it's recommended to keep the name short):

'''bash$''' conda create --name xmpl

Activate this with:

'''bash$''' conda activate xmpl

Custom environments also allow you to use specific versions of python itself and/or module packages, for example

'''bash$''' conda install python=3.11

For more information see:
* [https://conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-environments the conda documentation about environments].
* https://en.wikipedia.org/wiki/Anaconda_(Python_distribution)
* https://docs.anaconda.com/anaconda/user-guide/

Anaconda

2023-06-29T14:59:12Z

Sebastian: State use of Anaconda at beginning, add example of installing specific Python version

[[Category:anaconda-faq]]1
The '''Anaconda''' Python distribution allows you to set up a personal environment to install Python libraries/packages/modules in your Home directory, including different version of Python. This is helpful if you require a newer Version than is available on your system. Anaconda is available on LWP through a NFS mount. In order to use it on LWP instead of the locally installed Python, you need to load some environment variables into your shell.

To make Anaconda available in just your current ''bash'' session:

'''bash$''' source /opt/netapps/anaconda-lwp4/etc/profile.d/conda.sh
'''bash$''' conda activate

To have your shell startup files managed by Anaconda, so it will be available any time you start your shell:

'''bash$''' conda init

And after this, close and re-open your shell. Note that this last command also works with a select few other shells.

====Custom environments====

In order to be able to install additional packages using <code>conda install <package></code> you'll need to your own ''environment''. Such environment is stored in your home directory so it can be written to by you. By the commands above activate anaconda's default environment ''base'' and because it is stored centrally on the network it's not writeable.

To create your own environment called "xmpl" (it's recommended to keep the name short):

'''bash$''' conda create --name xmpl

Activate this with:

'''bash$''' conda activate xmpl

Custom environments also allow you to use specific versions of python itself and/or module packages, for example

'''bash$''' conda install python=3.11

For more information see:
* [https://conda.io/projects/conda/en/latest/user-guide/getting-started.html#managing-environments the conda documentation about environments].
* https://en.wikipedia.org/wiki/Anaconda_(Python_distribution)
* https://docs.anaconda.com/anaconda/user-guide/

EESSI

2023-04-17T15:00:33Z

Sebastian: /* Available software */

[[Category:software-faq]]
The European Environment for Scientific Software Installations (EESSI, pronounced as "easy") is a collaboration between different European partners in HPC community. 
The goal of this project is to build a common stack of scientific software installations for HPC systems and beyond, including laptops, personal workstations and cloud infrastructure. 
For more information visit https://eessi.github.io/docs/. 

== EESSI pilot software stack (2021.12) ==
=== Caveats ===
The current EESSI pilot software stack (version 2021.12) is the 7th iteration, and there are some known issues and limitations, please take these into account.
First of all: the EESSI pilot software stack is NOT READY FOR PRODUCTION!
Do not use it for production work, and be careful when testing it on production systems!
=== Set up your EESSI environment ===
Run the following command first (add this line to your .bashrc file to make it permanent):
export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libgtk3-nocsd.so.0
You can set up the environment by sourcing the provided init script:
source /cvmfs/pilot.eessi-hpc.org/versions/2021.12/init/bash
If all goes well, you should see output like this:
Found EESSI pilot repo @ /cvmfs/pilot.eessi-hpc.org/versions/2021.12!
Using x86_64/intel/haswell as software subdirectory.
Using /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/modules/all as the directory to be added to MODULEPATH.
Found Lmod configuration file at /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/.lmod/lmodrc.lua
Initializing Lmod...
Prepending /cvmfs/pilot.eessi-hpc.org/versions/2021.12/software/linux/x86_64/intel/haswell/modules/all to $MODULEPATH...
Environment set up to use EESSI pilot software stack, have fun!
[EESSI pilot 2021.12] $
Now you're all set up! Go ahead and explore the software stack using <code>module avail</code>, and go wild with testing the available software installations!

=== Testing the EESSI pilot software stack ===
Please test the EESSI pilot software stack as you see fit: running simple commands, performing small calculations or running small benchmarks, etc. 
Test scripts that have been verified to work correctly using the pilot software stack are available at https://github.com/EESSI/software-layer/tree/main/tests.

=== Giving feedback or reporting problems ===
Any feedback is welcome, and questions or problems reports are welcome as well, through one of the EESSI communication channels:
* (preferred!) EESSI software-layer GitHub repository: https://github.com/EESSI/software-layer/issues
* EESSI mailing list (eessi@list.rug.nl)
* EESSI Slack: https://eessi-hpc.slack.com (get an invite via https://www.eessi-hpc.org/join)
* monthly EESSI meetings (first Thursday of the month at 2pm CEST)

=== Available software ===
''(last update: Mar 21st 2022)''
EESSI currently supports the following HPC applications as well as all their dependencies (see [https://eessi.github.io/docs/pilot/#available-software Documentation]):

* GROMACS (2020.1 and 2020.4)
* OpenFOAM (v2006 and 8)
* R (4.0.0) + R-bundle-Bioconductor (3.11) + RStudio Server (1.3.1093)
* TensorFlow (2.3.1) and Horovod (0.21.3)
* OSU-Micro-Benchmarks (5.6.3)
* ReFrame (3.9.1)
* Spark (3.1.1)
* IPython (7.15.0)
* QuantumESPRESSO (6.6) (currently not available on ppc64le)
* WRF (3.9.1.1)