This page provides tools and utilities that make your life on ZIH systems more comfortable.
Terminal multiplexers are particularly well-suited for aiding you as a computer scientist in your daily trade. We generally favor tmux as it's newer than certain others and allows for better customization.
As there is already plenty of documentation on how to use tmux, we won't repeat that here. But instead, we would like to point you to those documents:
Tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background), and reattach them to a different terminal.
The huge advantage is, that as long as your tmux session is running, you can connect to it and your settings (e.g., loaded modules, current working directory, ...) are in place. This is beneficial when working within an unstable network with connection losses (e.g., traveling by the train in Germany), but also speed-ups your workflow in the daily routine.
marie@compute$ tmux new-session -s marie_is_testing -d marie@compute$ tmux attach -t marie_is_testing echo "hello world" ls -l Ctrl+b & d
If you want to jump out of your tmux session, hold the Control key and press 'b'. After that, release both keys and press 'd'. With the first key combination, you address tmux itself, whereas 'd' is the tmux command to "detach" yourself from it. The tmux session will stay alive and running. You can jump into it any time later by just using the aforementioned "tmux attach" command again.
Using a More Recent Version¶
More recent versions of tmux are available via the module system. Using the well know module commands, you can query all available versions, load and unload certain versions from your environment, e.g.,
marie@login$ module load tmux/3.2a
Error: Protocol Version Mismatch¶
When trying to connect to tmux, you might encounter the following error message:
marie@compute$ tmux a -t juhu protocol version mismatch (client 7, server 8)
To solve this issue, make sure that the tmux version you invoke
is the same as the tmux server that is running.
In particular, you can determine your client's version with the command
Try to load the appropriate tmux version to match with your
client's tmux server like this:
marie@compute$ tmux -V tmux 1.8 marie@compute$ module load tmux/3.2a Module tmux/3.2a-GCCcore-11.2.0 and 5 dependencies loaded. marie@compute$ tmux -V tmux 3.2a
When your client's version is newer than the server version, the aforementioned approach won't help you. In that case, you need to unload the loaded tmux module to downgrade the client to the client version that is supplied with the operating system (which should have a lower version number).
Using Tmux on Compute Nodes¶
At times it might be quite handy to have tmux sessions running inside your computation jobs, such that you perform your computations within an interactive tmux session. For this purpose, the following shorthand is to be placed inside the job file:
#!/bin/bash #SBATCH [...] module load tmux/3.2a tmux new-session -s marie_is_computing -d sleep 1; tmux wait-for CHANNEL_NAME_MARIE srun [...]
You can then connect to the tmux session like this:
marie@login$ ssh -t "$(squeue --me --noheader --format="%N" 2>/dev/null | tail -n 1)" \ "source /etc/profile.d/10_modules.sh; module load tmux/3.2a; tmux attach"
Where Is My Tmux Session?¶
Please note that, as there are thousands of compute nodes available, there are also multiple login nodes. Thus, try checking the other login nodes as well:
marie@login3$ tmux ls failed to connect to server marie@login3$ ssh login4 tmux ls marie_is_testing: 1 windows (created Tue Mar 29 19:06:26 2022) [105x32]
Architecture Information (lstopo)¶
The page HPC Resource Overview holds a general and fast
overview about the available HPC resources at ZIH.
Sometime a closer look and deeper understanding of a particular architecture is needed. This is
where the tool
lstopo comes into play.
The tool lstopo displays the topology of a system in a variety of output formats.
lstopo-no-graphics are available from the
hwloc modules, e.g.
marie@login$ module load hwloc/2.5.0-GCCcore-11.2.0 marie@login$ lstopo
The topology map is displayed in a graphical window if the
DISPLAY environment variable is set.
Otherwise, a text summary is displayed. The displayed topology levels and granularity can be
controlled using the various options of
lstopo. Please refer to the corresponding man page and
help message (
It is also possible to run this command using a job file to retrieve the topology of a compute nodes.
#!/bin/bash #SBATCH --job-name=topo_haswell #SBATCH --ntasks=1 #SBATCH --cpus-per-task=1 #SBATCH --mem-per-cpu=300m #SBATCH --partition=haswell #SBATCH --time=00:05:00 #SBATCH --output=get_topo.out #SBATCH --error=get_topo.err module purge module load hwloc/2.5.0-GCCcore-11.2.0 srun lstopo
Working with Large Archives and Compressed Files¶
Parallel Gzip Decompression¶
There is a plethora of
gzip tools but none of them can fully utilize multiple cores.
The fastest single-core decoder is
igzip from the
Intelligent Storage Acceleration Library.
In tests, it can reach ~500 MB/s compared to ~200 MB/s for the system-default
If you have very large files and need to decompress them even faster, you can use
Currently, it can reach ~1.5 GB/s using a 12-core processor in the above-mentioned tests.
Pragzip is available on PyPI and can be installed via pip. It is recommended to install it inside a Python virtual environment.
marie@compute$ pip install pragzip
It can also be installed from its C++ source code. If you prefer that over the version on PyPI, then you can build it like this:
marie@compute$ git clone https://github.com/mxmlnkn/pragzip.git marie@compute$ cd pragzip marie@compute$ mkdir build marie@compute$ cd build marie@compute$ cmake .. marie@compute$ cmake --build . pragzip marie@compute$ src/tools/pragzip --help
The built binary can then be used directly or copied inside a folder that is available in your
PATH environment variable.
Pragzip can be used like this:
marie@compute$ pragzip -d <file_to_decompress>
For example, if you want to decompress a file called
marie@compute$ pragzip -d data.gz
Furthermore, you can use it to speed up extraction of a file
my-archive.tar.gz like this:
marie@compute$ tar --use-compress-program=pragzip -xf my-archive.tar.gz
Pragzip is still in development, so if it crashes or if it is slower than the system
please open an issue on GitHub.
Direct Archive Access Without Extraction¶
In some cases of archives with millions of small files, it might not be feasible to extract the
whole archive to a filesystem.
archivemount tool has performance problems with such archives even if they are simply
uncompressed TAR files.
archivemount the archive would have to be reanalyzed whenever a new job is started.
Ratarmount is an alternative that solves these performance issues.
The archive will be analyzed and then can be accessed via a FUSE mountpoint showing the internal
Access to files is consistently fast no matter the archive size while
archivemount might take
minutes per file access.
Furthermore, the analysis results of the archive will be stored in a sidecar file alongside the
archive or in your home directory if the archive is in a non-writable location.
Subsequent mounts instantly load that sidecar file instead of reanalyzing the archive.
Ratarmount is available on PyPI and can be installed via pip. It is recommended to install it inside a Python virtual environment.
marie@compute$ pip install ratarmount
After that, you can use ratarmount to mount a TAR file using the following approach:
marie@compute$ ratarmount <compressed_file> <mountpoint>
Thus, you could invoke ratarmount as follows:
marie@compute$ ratarmount inputdata.tar.gz input-folder # Now access the data as if it was a directory, e.g.: marie@compute$ cat input-folder/input-file1
Ratarmount is still in development, so if there are problems or if it is unexpectedly slow, please open an issue on GitHub.
There also is a library interface called ratarmountcore that works fully without FUSE, which might make access to files from Python even faster.