Index

Python and Jupyter

Jupyterhub was the topic of the HPC Cafe in October 2020. https://jupyterhub.rrze.uni-erlangen.de/ is an experimental service.

This page will address some common pitfalls when working with python and related tools on a shared system like a cluster.

The following topics will be discussed in detail on this page:

• Available python versions
• Installing packages
• Conda environment
• Jupyter notebook security

Available python versions

All unix systems come with a system wide python installation, however for the cluster it is highly recommended to use one of the anaconda installations provided as a modules.

# reminder
module avail python
module load python/XY

These modules come with a wide range of preinstalled packages.

Installing packages

There are different ways of managing python packages on the cluster. This list is not complete, whoever it highlights methods which are known to work well with the local software stack.

As a general note. It is recommended to build packages using an interactive job on the target cluster to make sure all hardware can be used properly.
Make sure to load modules that might be needed by your python code (e.g. CUDA for gpu support)
set if external repositories are needed
export http_proxy=http://proxy:80
export https_proxy=http://proxy:80

Using pip

Pip is a package manager for python. It can be used to easily install packages and manage their versions.
By default pip will try to install packages system wide, which will not be possible due to missing permissions.
The behaviour can be changed by adding --user to the call.
pip install --user package-name
or %pip install —user —proxy http://proxy:80 package-name from within Jupiter-nootbooks

By defining the variable PYTHONUSERBASE (best done in your bashrc/bash_profile) we change the installation location from ~/.local to a different path. Doing so will prevent your home folder from cluttering with stuff that does not need a backup and hitting the quota.
export PYTHONUSERBASE=$WOODYHOME/software/privat
If you intend to share the package with your coworkers consider wrapping the python package inside a module.
For information on the module system see your HPC-Cafe from March 2020.

Setup and define the target folder with PYTHONUSERBASE.
Install the package as above.
Your module file needs to add to PYTHONPATH the site-packages folder
and to PATH the bin folder, if the package comes with binaries.

For an example see the module quantumtools on woody.

Conda envirenment

In order to use conda environments on the HPC cluster some preparation has to be done.
Remember a python module needs to be loaded all the time – see module avail python.

run
conda init bash if you use a different shell replace bash by the shell of your choice
source ~/.bashrc if you use a different shell replace .bashrc if you use a different shell.

The process was successful if you prompt starts with (base).

Create a ~/.profile with the content
if [ -n "$BASH_VERSION" ]; then
# include .bashrc if it exists
if [ -f "$HOME/.bashrc" ]; then
. "$HOME/.bashrc"
fi
fi
Some scientific software comes in form of a Conda environment (e.g. https://docs.gammapy.org/0.17/install/index.html).
By default such an environment will be installed to ~/.conda. However the size can be several GB therefore you should configure Conda to a different path. This will prevent your home folder from hitting the quota. It can be done by following these steps:

conda config # create ~/.condarc
Add the following lines to the file (replace the path if you prefer a different location)
pkgs_dirs:
- ${WOODYHOME}/software/privat/conda/pkgs
envs_dirs:
- ${WOODYHOME}/software/privat/conda/envs
You can check that this configuration file is properly read by inspecting the output of conda info
For more options see https://conda.io/projects/conda/en/latest/user-guide/configuration/use-condarc.html
Conda environments can also be used for package management (and more)

Create your own environment with
conda create --name myenv (python=3.9)
conda activate myenv
conda/pip install package-name packages will end up within the conda environment therefor no --user option is needed.
Conda environments come with the benefit of easy use with jupyterhub.rrze.uni-erlangen.de they show up as kernal option when starting a notebook.

Jupyter notebook security

When using Jupyter notebooks with their default configuration, they are protected by a random hashed password, which in some circumstances can cause security issues on a multiuser-system like cshpc or the cluster frontends.
We can change this with a few configuration steps by adding a password protection.

First generate a configuration file by executing
jupyter notebook --generate-config

Open a python terminal and generate a password
from notebook.auth import passwd; passwd()

Add the password hash to your notebook config file

# The string should be of the form type:salt:hashed-password.

c.NotebookApp.password = u''
c.NotebookApp.password_required = True

From now on your notebook will be password protected this comes also with the benefit that you can use bash functions for a more convenient use.

Quick reminder how to use the remote notebook

#start notebook on a frontend (e.g. woody)
jupyter notebook --no-browser --port=XXXX

on your client:
ssh -f user_name@remote_server -L YYYY:localhost:XXXX -N

Open the notebook in your local browser at https://localhost:YYYY
With XXXX and YYYY being 4 digit numbers.
Don’t forget to stop the notebook once you are done. Otherwise you will block resources that could be used by others!

Some useful functions/alias for lazy people 😉

alias remote_notebook_stop='ssh username@remote_server_ip "pkill -u username jupyter"'
Be aware this will kill ALL jupyter processes that you own!

start_jp_woody(){

nohup ssh -J username@cshpc.rrze.fau.de -L $1:localhost:$1 username@woody.rrze.fau.de " 
. /etc/bash.bashrc.local; module load python/3.7-anaconda ; jupyter notebook --port=$1 --no-browser" ;
echo ""; echo " the notebook can be started in your browser at: https://localhost:$1/ " ; echo ""
}

start_jp_emmy(){

nohup ssh -J username@cshpc.rrze.fau.de -L $1:localhost:$1 username@emmy.rrze.fau.de " 
. /etc/profile; module load python/3.7-anaconda ; jupyter notebook --port=$1 --no-browser" ;
echo ""; echo " the notebook can be started in your browser at: https://localhost:$1/ " ; echo ""
}

If you are using a cshell remove . /etc/bash.bashrc.local and . /etc/profile from the functions.

SSH – Secure Shell access to HPC systems

To use the HPC systems at RRZE, you have to log into a cluster frontend via an SSH (SecureShell) client. SSH is a common command-line tool for remotely logging into and executing commands on a different computer over the network. The following topics will be discussed in detail on this page:

• Basic usage
  • Connect to a remote host
  • Copy data to a remote host
• Graphical applications
• SSH public-key authentication
• SSH agent
• Configure host settings in ~/.ssh/config
• Security recommendations
  • SSH agent forwarding
  • X11 forwarding
  • Host keys
• Advanced usage
  • Proxy Jump
  • SSH config

Basic usage

Connect to a remote host

Under Linux, Mac and recent Windows 10 versions, a command-line SSH client is pre-installed. If you want to have a graphical user interface, you can use third-party clients like PuTTY (Windows, Linux) or MobaXterm (Windows).

Direct access to the cluster frontends is restricted to networks within the university. So if you are connected via such a network, or if you are using VPN, you can connect using the following command:

ssh USERNAME@CLUSTERNAME.rrze.fau.de

In this case, USERNAME is your HPC user name and CLUSTERNAME is the name of the cluster you want to log into, e.g. woody, emmy or meggie. If you want to access TinyFat, TinyGPU or TinyEth, you also have to connect to woody. You will be prompted for your HPC password or your SSH key passphrase if you are using SSH keys. After successful authentication, you have a login shell on the target system.

If you are outside of the university network and are not using VPN, you have to connect to the dialogserver first :

ssh USERNAME@cshpc.rrze.fau.de

You can then use the above SSH command to connect to the cluster front ends from there.

Copy data to a remote host

A secure mechanism for copying data to a remote host is also available in all OpenSSH distributions on Linux, Mac, and current Windows 10 versions. When running Windows, you can also use WinSCP, which has a graphical user interface.

For all command-line based options, the secure copy mechanism is invoked by the following command:

scp <filename> USERNAME@CLUSTERNAME.rrze.fau.de:<remote_directory>

This will copy the local file <filename> to the directory $HOME/<remote_directory> on the remote system. This directory must exist prior to the copy attempt. Keep in mind that nearly all available file systems are mounted on all frontends (see File Systems documentation). It is therefore sufficient to copy data to only one frontend, e.g. cshpc.

For WinSCP, it is possible to choose from different file transfer protocols, mainly scp and sftp. A comparison can be found on the WinSCP website. Especially for large files, scp is usually much faster, however, the transfer cannot be resumed.

For more complex file transfers or a larger amount of files, we recommend using rsync. It provides more extensive functionality than scp, e.g. resuming file transfers, excluding specific files, or checking if files already exist in the destination. It is, however, only available for Linux and Mac.

Graphical applications

We generally do not recommend to run graphical applications on the cluster frontends, since they normally consume much more resources and can, therefore, interfere with the work of other users on these shared systems. However, there are some cases where the use of graphical applications is necessary.

For applications that do not need many resources, it should be sufficient to enable X11 forwarding/X11 tunneling by your SSH client via the -X option:

ssh -X USERNAME@CLUSTERNAME.rrze.fau.de

However, this requires an X11-Server running on your local machine, which is generally not available by default on Mac and Windows. In this case, you need to activate X11 tunneling in your client configuration, as well as have an X Window server (e.g. Xming or MobaXTerm for Windows, XQuartz for Mac) running locally.

As an alternative, we recommend using remote desktop software to run graphical applications, e.g. NoMachine NX. A description of how to set up and use NoMachine NX on cshpc is available in the dialogserver description.

SSH public-key authentication

As an alternative to logging in with your HPC password when you connect to a server via SSH, you can also use public key authentication. It requires a so-called SSH key pair comprised of two matching parts – a public and a private key. The key pair is generated on your local machine. The public key is uploaded to the remote system, whereas the private key remains on your local machine. We recommend generating a separate SSH key pair for every system (workstation, laptop, …) you use for logging into the HPC clusters.

Generating key pairs is possible when your client has OpenSSH capabilities (Linux, Mac, Windows 10). If you are using PuTTY, you can generate keys with puttygen.exe.

When generating a key pair, you have to choose between different algorithms and key sizes. The recommendations which one to use are changing over time since also the capabilities to break encryptions increase. Currently, it is advised to use either rsa with a length of 4096 bits, ecdsa with 521 bits or ed25519. Use one of the following commands to generate a key pair:

ssh-keygen -t rsa -b 4096

ssh-keygen -t ecdsa -b 521

ssh-keygen -t ed25519

During the generation process, you will be prompted for a passphrase to encrypt your private key. We don’t recommend leaving this empty since in this case, your private key sitting on your computer as a plain text file.  If this unencrypted private key is copied/stolen by someone, they can access the corresponding server directly. In case it is encrypted by a passphrase, the attacker must first find out the passphrase in order to gain access to the server with the key.

By default, the key pair is generated into the folder .ssh in your home directory, with the files id_<algorithm> being your private and id_<algorithm>.pub being your public key. If you want to change the location and name of your key pair, use the following option:

ssh-keygen -f <path_to_keys>/<keyname> -t <algorithm>

The public key must then be copied to the server and added to the authorized_keys file to be used for authentication. This can be conveniently done using the ssh-copy-id tool:

ssh-copy-id -i ~/.ssh/id_<algorithm>.pub USERNAME@cshpc.rrze.fau.de

If this doesn’t work, you can also manually copy the public key and add it to ~/.ssh/authorized_keys:

cat id_rsa.pub | ssh USERNAME@cshpc.rrze.fau.de 'cat>> ~/.ssh/authorized_keys'

Once the public key has been configured on the server, the server will allow any connecting user that owns the private key to log in. Since your home directory is shared on all HPC systems at RRZE, it is sufficient to copy the key to only one system, e.g. cshpc. It will be automatically available on all others.

If you have changed the default name of your key pair, you have to explicitly specify that this key should be used for connecting to a specific host. This is possible by using the -i parameter:

ssh -i ~/<path_to_keys>/<keyname> USERNAME@CLUSTERNAME.rrze.fau.de

For frequent usage, this is quite cumbersome. Therefore, it is possible to specify these parameters (and many more) in the ~/.ssh/config file. A detailed description of how to do this is given below.

If you have problems using your key, e.g. when you are asked for your password despite the key, or in case authentication is not working for some other reason, try using the option ssh -v. This will cause SSH to print debugging messages about its progress, which can help locate the issue much easier.

SSH agent

If you have set a passphrase for your private SSH key, you will be prompted to enter the passphrase every time you use the key to connect to a remote host. To avoid this, you can use an SSH agent. After you have entered your passphrase for the first time, this small tool will store your private key for the duration of your session. This will allow you to connect to a remote host without re-entering your passphrase every time.

If you are using a current Linux distribution with a graphical desktop session (Unity, GNOME,…), an SSH agent will be started automatically in the background. Your private keys will be stored automatically and used when connecting to a remote host.

In case you are not using a graphical desktop session or your SSH agent does not start automatically, you will have to start it manually by typing the following into your local terminal session:

eval "$(ssh-agent -s)"

This will start the agent in the background. To add your private key to the agent, type the following:

ssh-add ~/.ssh/<keyname>

After you have successfully entered your passphrase, you will get a confirmation message that your identity file was successfully added to the agent. This will allow you to use your key to sign in without having to enter the passphrase again in the current terminal session.

You can also list the keys which are currently managed by the SSH agent via:
ssh-add -l

For more information about the SSH agent, type man ssh-add on your terminal.

Configure host settings in ~/.ssh/config

If you are regularly connecting to multiple remote systems over SSH, you’ll find that typing all the remote hostnames, different usernames, identity files, and various more options is quite cumbersome. However, there is a much simpler solution to define shortcuts for different hosts and store SSH settings for each remote machine you connect to.

The client-side configuration file is named config and is located in the .ssh folder in your home directory. If it does not exist, you can create it manually.

The configuration file is organized in different sections for each host. You can use wildcards to match more than one host. The SSH client reads the configuration file line by line, so later matches can override earlier ones. Because of this, you should put your most general matches at the top of the file.

One simple example to create a shortcut for connection to cshpc is given below. The following is added to ~/.ssh/config:

Host cshpc
  HostName cshpc.rrze.fau.de
  User USERNAME
  IdentitiyFile ~/.ssh/private_ssh_key_name

With this configuration, you can now connect via

ssh cshpc

instead of typing

ssh -i ~/.ssh/private_ssh_key_nameUSERNAME@cshpc.rrze.fau.de

A large number of different SSH options are available. Some options which are used more frequently or are especially useful are listed below. You can find a full list by typing man ssh_config in your terminal.

Security recommendations

In general, it is recommended not to trust systems that are accessible to multiple users or that someone else has root access to, which is true for all HPC systems. Even with best efforts by the administrators to keep the systems safe, it is always possible that attackers are able to gain root rights on the system, which makes them very powerful. An attacker may for example install keyloggers or hijack your running SSH-agent, just to name a few possibilities.

Thus it is often recommended

• not to log in via interactive passwords on untrusted hosts,
• not to use SSH agents on untrusted hosts,
• and not to use SSH agent forwarding to untrusted hosts.

It is generally more secure to use SSH public-private key pairs for authentication when accessing remote systems, as long as these rules are followed:

• Store no private keys on untrusted hosts. Private keys should only be placed on single-user systems (e.g. your laptop).
• Always use SSH private keys with strong passphrases.
• Use only one SSH key pair per system with shared homes.
• Use a separate key pair for every client (laptop, desktop,..).

To make it easier to jump between different systems at RRZE, we recommend generating a separate key for internal use only. This key may also be used for access to external systems (e.g. LRZ).

SSH agent forwarding

SSH agent forwarding is mostly used as a Single-Sign-On solution to connect from one remote host to another (e.g. from cshpc to other cluster frontend or between different cluster frontends). When you enable SSH agent forwarding, the query of the remote server for the private key is redirected to your local client where the SSH-agent is running. This eliminates the need for using password logins and for having private keys on remote machines. However, it is not recommended to use SSH agent forwarding to an untrusted host. Attackers with the ability to bypass file permissions on the remote machine can gain access to the agent on your local machine through the forwarded connection. An attacker cannot obtain key material from the agent, however, they can use the loaded keys to gain access to remote machines with your identity. An alternative to using SSH-agent forwarding is the ProxyJump functionality provided by SSH, which is described below.

X11 forwarding

Similar to SSH agent forwarding, X11 forwarding can be a security risk. If your SSH client is configured to generally allow applications on a remote server to render GUI windows on your screen, this can be exploited by an attacker. It is therefore recommended to specify ForwardX11 no for all hosts in ~/.ssh/config and only use -X on the command line when necessary.

Host keys

SSH host keys are used to verify a server’s identity before you sent any sensitive information like passwords to it. Each server has a unique host key, which is the server’s public key. It can be used by the client to decrypt an authentication message sent from the server when connecting. This makes sure that the remote host you connect to is really the one you intended to connect to, and that your connection is not secretly redirected to another server.

SSH clients automatically store host keys for all hosts they have connected to. These keys are normally stored in ~/.ssh/known_hosts. If the host key of a server you are trying to connect to has changed, you will get a warning message.

When you connect to a server for the first time, you cannot know if the key offered by the server is correct. Therefore, we provide the public system keys for the cluster frontends below, which can be directly added into the ~/.ssh/known_hosts file (you may need to generate the .ssh directory and/or the file if it does not exist yet) on your local machine.

cshpc.rrze.fau.de ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAIEAs0wFVn1PN3DGcUtd/JHsa6s1DFOAu+Djc1ARQklFSYmxdx5GNQMvS2+SZFFa5Rcw+foAP9Ks46hWLo9mOjTV9AwJdOcSu/YWAhh+TUOLMNowpAEKj1i7L1Iz9M1yrUQsXcqDscwepB9TSSO0pSJAyrbuGMY7cK8m6//2mf7WSxc=
cshpc.rrze.fau.de ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPSIFF3lv2wTa2IQqmLZs+5Onz1DEug8krSrWM3aCDRU
cshpc.rrze.fau.de ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBNVzp97t3CxlHtUiJ5ULqc/KLLH+Zw85RhmyZqCGXwxBroT+iK1Quo1jmG6kCgjeIMit9xQAHWjS/rxrlI10GIw=

emmy.rrze.fau.de ssh-rsa AAAAB3NzaC1yc2EAAAABIwAAAQEA2q7Ung+RdwLkMyQXiod/6BFsUBMcKlEnvG3pFR7cw7/wdLUcjUU4ubQR9ctNlQZok7XU9b2ttMVwUOYI3w2RZnQFwm9jzUbAAl00XRfBThI9cWlgJu0UR/I+W/iRJdBSAmffwsQYTYBzJ4cRTtKSLZ98yEbJVtwfRRG12PVMewNGVDsnmBOBX5zWG92tgaA1bXAiB0GVWBS79lV78+ii/1UR/PldZaA+RQtxDx0ckuc8vq10XK4GvXJijyrEzIsi3SeIFApMhr+W84uIGp5HjhaaYwVWMkBge8PX8bR8oXNaUFLVmaRUrX/WSchCmLp2YBh3npeZ/B9vAtb6LXoS7Q==
emmy.rrze.fau.de ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIBqBH0GRzrNUrTyOE25TkQXqY/30PLVUqUam93XArPMb
emmy.rrze.fau.de ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBEsYP0xDLyI/VHC68o4BqZ1RR5Ff7qMscZjKiKD1kEP2ckea0dMdH4oB4ahScShcEG5iZmQ2FlN41FbGX4zp6Go=

woody.rrze.fau.de ssh-rsa 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
woody.rrze.fau.de ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAIPC9x4/BNwKQro3+95Gwh4DZpHBT2tVHPjKouwIBOk6g
woody.rrze.fau.de ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBL7lrwFFhlZZ7mGBJ3f5gSxDEKcxvebrXLXd/bz0fH6A9Qk2GrJN2tL+sleVPRJHTboOFbdeaJy0igSwivqI2vc=

meggie.rrze.fau.de ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQCwi2jQPuIe88/SJRmaKmA1VOOse4UxyjWlqp6VHM+8gggkpajGz3l6xZD1BihqOpY10oIA6rRHBQipZmFGgDkgTT40jdMvP8sLzqtJqKoQILXJqQbGWrGgjEDwXdZHIWaiV5Q8XDAgqj9+4W9ZHfeGtgS2OqhzAlTdgHzx94h8m6J8JUc+QtPGlWGBr/Z2Ee+KFEG1siT09k7E72sOnL9VDqMHFlWtHUsGfcR+8f6hnKnSHBB2TpxGac2Yv0KpqtHFdGMLY22RzDgCoEeY42fLvOqF9xIU8NgWoqII4W1AcvvpPDe8EthnKkaMsQjqj6N1uJ1qpsOZry7TiwQQF2/D
meggie.rrze.fau.de ecdsa-sha2-nistp256 AAAAE2VjZHNhLXNoYTItbmlzdHAyNTYAAAAIbmlzdHAyNTYAAABBBNmjmhh6fMxEkmNybzP3Maau/KRbOTZECKF8FxZVH3a3rMirSyjRG8LLNswctajPJxeQCAb5OIh1A63PbsIA2g8=
meggie.rrze.fau.de ssh-ed25519 AAAAC3NzaC1lZDI1NTE5AAAAILOVhUpUyaugYDdwpHCuKfcgS0PQjZN+7KlbJ5ByZvhi

Please keep in mind that these keys are changed from time to time. So if you get a warning while connecting, first check the above keys if they have changed!

Advanced Usage

Proxy Jump

If you want to connect from one host to another without the risks involved by using SSH agent forwarding and without having to type your password each time, the ProxyJump functionality of SSH can be a good alternative. When using ProxyJump, the connection is forwarded through one or more jump hosts to the target destination host via SSH. This is the most secure method because encryption is end-to-end. You can use ProxyJump for example to connect to the emmy cluster frontend by using cshpc as the jump host. This can be achieved via the following additions to ~/.ssh/config:

Host emmy
  HostName emmy.rrze.fau.de
  ProxyJump cshpc.rrze.fau.de

SSH config

There are some options to use in ~/.ssh/config that can simplify your workflow. To see all available options, type man ssh_config in your terminal.

• Instead of defining the same identity file explicitly for every host, you can also define to always use the same key for a specific user:

  Match User JohnDoe
    IdentityFile ~/.ssh/private_ssh_key_name

• Specify that only the SSH keys listed in ~/.ssh/config should be tried for authentication. This can avoid a “Too many authentication failures” error, if the SSH agent offers many different keys.
  IdentitiesOnly yes
• It is possible to use wildcards (*,?,..) in hostnames to reduce the number of explicit entries. For example, it is possible to deny SSH agent and X11 forwarding for all hosts via:

  Host * 
    ForwardAgent no 
    ForwardX11 no

OpenFOAM

OpenFOAM (for “Open-source Field Operation And Manipulation”) is a C++ toolbox for the development of customized numerical solvers, and pre-/post-processing utilities for the solution of continuum mechanics problems, most prominently including computational fluid dynamics (CFD). It contains solvers for a wide range of problems, from simple laminar regimes to DNS or LES including reactive turbulent flows. It provides a framework for manipulating fields and solving general partial differential equations on unstructured grids based on finite volume methods. Therefore, it is suitable for complex geometries and a wide range of configurations and applications.

There are three main variants of OpenFOAM that are released as free and open-source software under a GPLv3 license: ESI OpenFOAM, The OpenFOAM Foundation, Foam Extend.

Availability / Target HPC systems

We provide modules for some major OpenFOAM versions, which were mostly requested by specific groups or users. If you have a request for a new version, please contact hpc-support@fau.de. Please note that we will only provide modules for fully released versions, which will be used by more than one user. If you need some specific custom configuration or version, please consider building it yourself. Installation guides are available from the respective OpenFOAM distributors.

The installed versions of OpenFOAM may differ between the different HPC clusters. You can check the available versions via module avail openfoam.

Production jobs should be run on the parallel HPC systems in batch mode.  It is NOT permitted to run computationally intensive OpenFOAM simulation runs or serial/parallel post-processing sessions with large memory consumption on login nodes.

Notes

• OpenFOAM produces per default lots of small files – for each processor, every step, and for each field. The parallel file system ($FASTTMP) is not made for such a finely grained file/folder structure. For more recent versions of OpenFOAM, you can use collated I/O, which produces somewhat less problematic output.
• Paraview is used for post-processing and is also available via the modules system on the HPC cluster. However, keep an eye on the main memory requirements for this visualization, especially on the frontends!

Sample job scripts

All job scripts have to contain the following information:

• Resource definition for the queuing system (more details here)
• Load OpenFOAM environment module
• Start command for parallel execution of solver of choice

For meggie/Slurm batch system: mpirun takes the parameters (nodes, tasks-per-node) that you specified in the header of your batch file. You don’t have to specify this again in your mpirun call (see also MPI on meggie).  In order that this works correctly, the total number of MPI tasks (nodes times tasks-per-node) must be equal to numberOfSubdomains inside system/decomposeParDict!

#!/bin/bash -l
#PBS -lnodes=4:ppn=40,walltime=24:00:00
#PBS -N my-job-name
#PBS -j eo

# number of cores to use per node
PPN=20
# load environment module
module load openfoam/XXXX

# change to working directory 
cd ${PBS_O_WORKDIR}

# count the number of nodes
NODES=`uniq ${PBS_NODEFILE} | wc -l`
# calculate the number of cores actually used
CORES=$(( ${NODES} * ${PPN} ))

# Please insert here your prefered solver executable!
mpirun -np ${CORES} -npernode ${PPN} icoFoam -parallel -fileHandler collated > logfile

#!/bin/bash -l
#SBATCH --job-name=my-job-name
#SBATCH --nodes=4
#SBATCH --tasks-per-node=20                   # for 20 physical cores on meggie
#SBATCH --time=24:00:00 
#SBATCH --export=NONE 

# load environment module 
module load openfoam/XXXX 

unset SLURM_EXPORT_ENV 

# Please insert here your prefered solver executable! 
mpirun icoFoam -parallel -fileHandler collated > logfile

Further information

• Tutorials and guides can be found in the official OpenFOAM.com documentation or the OpenFOAM.org User Guide.

Mentors

• please volunteer!

ANSYS CFX

ANSYS CFX is a general purpose Computational Fluid Dynamics (CFD) code. It provides a wide variety of physical models for turbulent flows, acoustics, Eulerian and Lagrangian multiphase flow modeling, radiation, combustion and chemical reactions, heat and mass transfer including CHT (conjugate heat transfer in solid domains). It is mostly used for simulating turbomachinery, such as pumps, fans, compressors and gas and hydraulic turbines.

Please note that the clusters do not come with any license. If you want to use ANSYS products on the HPC clusters, you have to have access to suitable licenses. These can be purchased directly from RRZE. To efficiently use the HPC resources, ANSYS HPC licenses are necessary.

Availability / Target HPC systems

Different versions of all ANSYS products are available via the modules system, which can be listed by module avail ansys. A special version can be loaded, e.g. by module load ansys/2020R1.

We mostly install the current versions automatically, but if something is missing, please contact hpc-support@fau.de.

Production jobs should be run on the parallel HPC systems in batch mode.

ANSYS CFX can also be used in interactive GUI mode for serial pre- and/or post-processing on the login nodes (Linux: SSH Option “-X”; Windows: using PuTTY and XMing for X11-forwarding). This should only be used to make quick simulation setup changes. It is NOT permitted to run computationally intensive ANSYS CFX simulation runs or serial/parallel post-processing sessions with large memory consumption on login nodes.

Alternatively, ANSYS CFX can be run interactively with GUI on TinyFat (for large main memory requirements) or on a compute node.

Getting started

The (graphical) CFX launcher is started by typing

cfx5launch

on the command line. If you want to use the separate pre- or postprocessing capabilities, you can also launch cfx5pre or cfx5post, respectively.

For running simulations in batch mode on the HPC systems, use the

cfx5solve

command. You can find out the available parameters via cfx5solve -help. One example call to use in your batch script would be

cfx5solve -batch -par-dist $NODELIST -double -def <solver input file>

The number of processes and the hostnames of the compute nodes to be used are defined in $NODELIST. For how to compile this list, refer to the example script below. Using SMT threads is not recommended.

Notes

• We recommend writing automatic backup files (every 6 to 12 hours) for longer runs to be able to restart the simulation in case of a job or machine failure. This can be specified in Output Control → User Interface → Backup Tab
• Furthermore, it is recommended to use the “Elapsed Wall Clock Time Control” in the job definition in ANSYS CFX Pre (Solver Control → Elapsed Wall Clock Time Control → Maximum Run Time → <24h). Also plan enough buffer time for writing the final output, depending on your application, this can take quite a long time!

Sample job scripts

All job scripts have to contain the following information:

• Resource definition for the queuing system (more details here)
• Load ANSYS environment module
• Generate a file with names of hosts of the current simulation run to tell CFX on which nodes it should run (see example below)
• Execute cfx5solve with appropriate command line parameters (available options via cfx5solve -help)

#!/bin/bash -l
#PBS -lnodes=4:ppn=40,walltime=24:00:00
#PBS -N cfx
#PBS -j eo

# specify the name of your input-def file
DEFFILE="example.def"
# number of cores to use per node
PPN=20
# load environment module
module load ansys/XXXX
# generate node list
uniq $PBS_NODEFILE | sed -e 's/$/*'$PPN'/' | paste -d ',' -s > NODELIST


# execute cfx with command line parameters (see cfx5solve -help for all available parameters)  
 cfx5solve -batch -double -par-dist  $NODELIST -def $DEFFILE

Further information

• Documentation is available within the application help manual. Further information is provided through the ANSYS Customer Portal for registered users.
• More in-depth documentation is available at LRZ. Please note: not everything is directly applicable to HPC systems at RRZE!

Mentors

• Dr.-Ing. Katrin Nusser, RRZE, hpc-support@fau.de
• please volunteer!

Tensorflow

TensorFlow is an Open Source Machine Learning Framework.

Availability / Target HPC systems

TensorFlow currently is not installed on any of RRZE’s HPC systems as new versions are very frequently released and all groups have their own special needs.

The following HPC systems are best suited:

• TinyGPU or GPU nodes in Emmy
• Woody smaller but many for CPU-only runs

Notes

Different routes can be take to get your private installation of TensorFlow. Don’t waste valuable storage in $HOME and use $WORK instead for storing your installation.

The pre-built Docker images might not work on the GTX980 nodes in TinyGPU as their host CPU is too old to support the required AVX instruction set.

cd $WORK
export SINGULARITY_CACHEDIR=$(mktemp -d)
singularity pull tensorflow-2.1.0-gpu-py3.sif docker://tensorflow/tensorflow:2.1.0-gpu-py3
rm -rf $SINGULARITY_CACHEDIR

./tensorflow-2.1.0-gpu-py3.sif  ./script.py

cd $WORK
export SINGULARITY_CACHEDIR=$(mktemp -d)
singularity pull tensorflow-ngc-20.03-tf2-py3.sif docker://nvcr.io/nvidia/tensorflow:20.03-tf2-py3
rm -rf $SINGULARITY_CACHEDIR

./tensorflow-ngc-20.03-tf2-py3.sif  script.py

To check that your TensorFlow is functional and detects the hardware, you can use the following simple Python sequence:

from tensorflow.python.client import device_lib
print(device_lib.list_local_devices())

Further information

• https://www.tensorflow.org/
• https://github.com/tensorflow/tensorflow
• https://ngc.nvidia.com/catalog/containers/nvidia:tensorflow

Mentors

• please volunteer!

Test cluster

The RRZE test and benchmark cluster  is an environment for porting software to new CPU architectures and running benchmark tests. It comprises a variety of nodes with different processors, clock speeds, memory speeds, memory capacity, number of CPU sockets, etc. There is no high-speed network, and MPI parallelization is restricted to one node. The usual NFS file systems are available.

This is a testing ground. Any job may be canceled without prior notice. For further information about proper usage, please contact HPC@RRZE.

This is a quick overview of the systems including their host names (frequencies are nominal values) – NDA systems are not listed:

• aurora1: Single Intel Xeon “Skylake” Gold 6126 CPU (12 cores + SMT) @ 2.60GHz.
  Accelerators: 2x NEC Aurora “TSUBASA” 10B (48 GiB RAM)
• broadep2: Dual Intel Xeon “Broadwell” CPU E5-2697 v4 (2x 18 cores + SMT) @ 2.30GHz, 128 GiB RAM
• casclakesp2: Dual  Intel Xeon “Cascade Lake” Gold 6248 CPU (2x 20 cores + SMT) @ 2.50GHz, 384 GiB RAM
• hasep1: Dual Intel Xeon “Haswell” E5-2695 v3 CPU (2x 14 cores + SMT) @ 2.30GHz, 64 GiB RAM
• icx32: Dual Intel Xeon “Icelake” Platinum 8358 CPU (2x 32 cores + SMT) @ 2.60GHz, 256 GiB RAM
• icx36: Dual Intel Xeon “Icelake” Platinum 8360Y CPU (2x 36 cores + SMT) @ 2.40GHz, 256 GiB RAM
• interlagos1: Dual AMD Opteron 6276 “Interlagos” CPU (2x 16 cores) @ 2.3 GHz, 64 GiB RAM.
  Accelerator: AMD Radeon VII GPU (16 GiB HBM2)
• ivyep1: Dual Intel Xeon “Ivy Bridge” E5-2690 v2 CPU (2x 10 cores + SMT) @ 3.00GHz, 64 GiB RAM
• medusa: Dual Intel Xeon “Cascade Lake” Gold 6246 CPU (2x 12 cores + SMT) @ 3.30GHz, 192 GiB RAM.
  Accelerators:
  – NVIDIA GeForce RTX 2070 SUPER (8 GiB GDDR6)
  – NVIDIA GeForce RTX 2080 SUPER (8 GiB GDDR6)
  – NVIDIA Quadro RTX 5000 (16 GiB GDDR6)
  – NVIDIA Quadro RTX 6000 (24 GiB GDDR6)
• milan1: Dual AMD EPYC 7543 “Milan” CPU (32 cores + SMT) @ 2.8 GHz, 256 GiB RAM
  Accelerators: NVIDIA A40 (48 GiB GDDR6)
• naples1: Dual AMD EPYC 7451 “Naples” CPU (2x 24 cores + SMT) @ 2.3 GHz, 128 GiB RAM
• phinally: Dual Intel Xeon “Sandy Bridge” CPU E5-2680 (8 cores + SMT) @ 2.70GHz, 64 GiB RAM
• rome1: Single AMD EPYC 7452 “Rome” CPU (32 cores + SMT) @ 2.35 GHz, 128 GiB RAM
• rome2: Dual AMD EPYC 7352 “Rmome” CPU (24 cores + SMT) @ 2.3 GHz, 256 GiB RAM
  Accelerators: AMD MI100 (32 GiB HBM2)
• skylakesp2: Intel Xeon “Skylake” Gold 6148 CPU (2x 20 cores + SMT) @ 2.40GHz, 96 GiB RAM
• summitridge1: AMD Ryzen 7 1700X CPU (8 cores + SMT), 32 GiB RAM
• teramem: Dual Intel Xeon Platinum “Icelake” 8360Y CPU (2x 36 cores + SMT) @ 2.40GHz, 2.048 GiB RAM, 30 TB of local NVMe storage – will later be moved to the new Cluster2021 cluster or TinyFat
• warmup: Dual Cavium/Marvell “ThunderX2” (ARMv8) CN9980 (2x 32 cores + 4-way SMT) @ 2.20 GHz, 128 GiB RAM

Technical specifications of all more or less recent GPUs available at RRZE (either in the Testcluster or in TinyGPU):

This website shows information regarding the following topics:

• Access, User Environment, File Systems
  • Access to the machine
  • File systems
  • Batch processing

Access, User Environment, and File Systems

Access to the machine

Note that access to the test cluster is restricted: If you want access to it, you will need to contact hpc@rrze. In order to get access to the NDA machines you have to provide a short (!) description of what you want to do there.

From within the FAU network, users can connect via SSH to the frontend
testfront.rrze.fau.de
If you need access from outside of FAU, you usually have to connect for example to the dialog server cshpc.rrze.fau.de first and then ssh to testfront from there.

While it is possible to ssh directly to a compute node, a user is only allowed to do this while they have a batch job running there. When all batch jobs of a user on a node have ended, all of their processes, including any open shells, will be killed automatically.

The login nodes and most of the compute nodes run Ubuntu 18.04. As on most other RRZE HPC systems, a modules environment is provided to facilitate access to software packages. Type “module avail” to get a list of available packages. Note that, depending on the node, the modules may be different due to the wide variety of architectures. Expect inconsistencies. In case of questions, contact  hpc@rrze.

File Systems

The nodes have local hard disks of very different capacities and speeds. These are not production systems, so do not expect a production environment.

When connecting to the front end node, you’ll find yourself in your regular RRZE $HOME directory (/home/hpc/...). There are relatively tight quotas there, so it will most probably be too small for the inputs/outputs of your jobs. It however does offer a lot of nice features, like fine grained snapshots, so use it for “important” stuff, e.g. your job scripts, or the source code of the program you’re working on. See the HPC file system page for a more detailed description of the features and the other available file systems including, e.g., $WORK.

Batch processing

As with all production clusters at RRZE, resources are controlled through a batch system, SLURM in this case. Due to the broad spectrum of architectures in the test cluster, it is usually advisable to compile on the target node using an interactive SLURM job (see below).

There is a “work” queue and an “nda” queue, both with up to 24 hours of runtime.  Access to the “nda” queue is restricted because the machines tied to this queue are pre-production hardware or otherwise special so that benchmark results must not be published without further consideration.

Batch jobs can be submitted on the frontend. The default job runtime is 10 minutes.

The currently available nodes can be listed using:

sinfo -o "%.14N %.9P %.11T %.4c %.8z %.6m %.35f"

To select a node, you can either use the host name or a feature name from sinfo:

• sbatch --nodes=1 --constraint=featurename --time=hh:mm:ss --export=NONE jobskript
• sbatch --nodes=1 --nodelist=hostname --time=hh:mm:ss --export=NONE jobskript

Submitting an interactive job:

srun --nodes=1 --nodelist=hostname --time=hh:mm:ss --export=NONE --pty /bin/bash -l

For getting access to performance counter registers and other restricted parts of the hardware (so that lkwid-perfctr works as intended), use the option -C hwperf.

By default, SLURM exports the environment of the shell where the job was submitted. If this is not desired, use   --export=NONE and  unset SLURM_EXPORT_ENV. Otherwise, problems may arise on nodes that do not run Ubuntu.

Please see the batch system description for further details.

VASP

Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modeling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.

Availability / Target HPC systems

VASP requires an individual license.

Notes

• Parallelization and optimal performance:
  • (try to) always use full nodes (ppn=20 for Emmy/Meggie)
  • NCORE=5/10 & PPN=20 results in optimal performance in almost all cases, in general NCORE should be a divisor of PPN
  • OpenMP parallelization is supposed to supersede NCORE
  • use kpar if possible
  • do not use hyperthreads on Emmy!
• Compilation:
  • use -Davoidalloc
  • use Intel toolchain and MKL
  • in case of very large jobs with high memory requirements add ‘ -heap-arrays 64’ to Fortran flags before compilation (only possible for Intel ifort)
• Filesystems:
  • Occasionally VASP user reported failing I/O on Meggie’s $FASTTMP (/lxfs), this might be a problem with Lustre and Fortran I/O. Please try to use the fix described here: https://github.com/RRZE-HPC/getcwd-autoretry-preload
  • Since VASP does not do parallel MPI I/O, $WOODYHOME, /home/vault or purchaseable NFS storage (/home/titan /home/saturn) is more appropriate than /lxfs
  • For medium sized jobs, even node local /dev/shm/ might be an option
• Walltime limit:
  • VASP can only be gracefully stopped by creating the file “STOPCAR” https://www.vasp.at/wiki/index.php/STOPCAR automatic creation is shown in the example scripts below

Sample job scripts

#!/bin/bash -l
#PBS -lnodes=1:ppn=40,walltime=10:00:00
#PBS -N my-VASP
#PBS -j eo

#enter submit directory
cd $PBS_O_WORKDIR

#define executeable:
VASP=/path-to-your-vasp-installation/vasp

#load modules
module load intel64

#set PPN and pinning
export PPN=20
export I_MPI_PIN=enable

#set stacksize to unlimited
ulimit -s unlimited

#create STOPCAR with LSTOP 1800s before reaching walltimelimit
lstop=1800

#create STOPCAR with LABORT 600s before reaching walltimelimit
labort=600

#timer for STOP = .TRUE.
let SLEEPTIME1=$PBS_WALLTIME-$lstop

#timer for LABORT = .TRUE.
let SLEEPTIME2=$PBS_WALLTIME-$labort

echo "lstop in $SLEEPTIME1 seconds"
echo "labort in $SLEEPTIME2 seconds"

(sleep ${SLEEPTIME1} ; echo "LSTOP = .TRUE." > STOPCAR) &
lstoppid=!$
(sleep ${SLEEPTIME2} ; echo "LABORT = .TRUE." > STOPCAR) &
labortpid=!$

mpirun -ppn $PPN $VASP

pkill -p $lstoppid
pkill -p $labortpid

#! /bin/bash -l
#
#SBATCH --nodes=4
#SBATCH --tasks-per-node=20
#SBATCH --time=24:00:00
#SBATCH --job-name=my-vasp
#SBATCH --mail-user=my.mail
#SBATCH --mail-type=ALL
#SBATCH --export=NONE
unset SLURM_EXPORT_ENV

#enter submit directory
cd $SLURM_SUBMIT_DIR

#load modules
module load intel64

#set PPN and pinning
export PPN=20
export I_MPI_PIN=enable

#define executable:
VASP=/path-to-your-vasp-installation/vasp

#create STOPCAR with LSTOP 1800s before reaching walltimelimit
lstop=1800

#create STOPCAR with LABORT 600s before reaching walltimelimit
labort=600

#automatically detect how much time this batch job requested and adjust the 
# sleep accordingly 
TIMELEFT=$(squeue -j $SLURM_JOBID -o %L -h)
HHMMSS=${TIMELEFT#*-}
[ $HHMMSS != $TIMELEFT ] && DAYS=${TIMELEFT%-*} 
IFS=: read -r HH MM SS <<< $TIMELEFT
[ -z $SS ] && { SS=$MM; MM=$HH; HH=0 ; }
[ -z $SS ] && { SS=$MM; MM=0; }
#timer for STOP = .TRUE.
SLEEPTIME1=$(( ( ( ${DAYS:-0} * 24 + 10#${HH} ) * 60 + 10#${MM} ) * 60 + 10#$SS - $lstop ))
echo "Avilable runtime: ${DAYS:-0}-${HH:-0}:${MM:-0}:${SS}, sleeping for up to $SLEEPTIME1, thus reserving $lstop for clean stopping/saving results"

#timer for LABORT = .TRUE.
SLEEPTIME2=$(( ( ( ${DAYS:-0} * 24 + 10#${HH} ) * 60 + 10#${MM} ) * 60 + 10#$SS - $labort ))
echo "Avilable runtime: ${DAYS:-0}-${HH:-0}:${MM:-0}:${SS}, sleeping for up to $SLEEPTIME2, thus reserving $labort for clean stopping/saving results"

(sleep ${SLEEPTIME1} ; echo "LSTOP = .TRUE." > STOPCAR) &
lstoppid=!$
(sleep ${SLEEPTIME2} ; echo "LABORT = .TRUE." > STOPCAR) &
labortpid=!$

mpirun -ppn $PPN $VASP 

pkill -p $lstoppid
pkill -p $labortpid

Further information

• https://www.vasp.at/

Mentors

• T. Klöffel, RRZE, hpc-support@fau.de
• AG A. Görling (Chair of Theoretical Chemistry)

ANSYS Mechanical

ANSYS Mechanical is a computational structural mechanics software which makes it possible to solve structural engineering problems. It is available in two different software environments – ANSYS Workbench (the newer GUI-oriented environment) and ANSYS Mechanical APDL (sometimes called ANSYS Classic, the older MAPDL scripted environment).

Please note that the clusters do not come with any license. If you want to use ANSYS products on the HPC clusters, you have to have access to suitable licenses. These can be purchased directly from RRZE. To efficiently use the HPC resources, ANSYS HPC licenses are necessary.

Availability / Target HPC systems

Production jobs should be run on the parallel HPC systems in batch mode. For simulations with high memory requirements, a single-node job on TinyFAT can be used.

ANSYS Mechanical can also be used in interactive GUI mode via Workbench for serial pre- and/or post-processing on the login nodes. This should only be used to make quick simulation setup changes.  It is NOT permitted to run computationally/memory intensive ANSYS Mechanical simulations on login nodes.

Different versions of all ANSYS products are available via the modules system, which can be listed by module avail ansys. A special version can be loaded, e.g. by module load ansys/2019R1.

We mostly install the current versions automatically, but if something is missing, please contact hpc-support@fau.de.

Notes

• Two different parallelization methods are available: shared-memory and distributed-memory parallelization.
• Shared-memory parallelization: uses multiple cores on a single node; specify via ansys191 -smp -np N, default: N=2
• Distributed-memory parallelization: uses multiple nodes; specify via ansys191 -dis -b -machines machine1:np:machine2:np:...

Sample job scripts

All job scripts have to contain the following information:

• Resource definition for the queuing system (more details here)
• Load ANSYS environment module
• Generate a variable with names of hosts of the current simulation run and specify the number of processes per host
• Execute Mechanical with appropriate command line parameters (distributed memory run in batch mode)
• Specify input and output file

#!/bin/bash -l
#PBS -lnodes=2:ppn=40,walltime=24:00:00
#PBS -N mech
#PBS -j eo

# load environment module
module load ansys/XXXX
# generate machine list, uses 20 processes per node
machines=$(cat $PBS_NODEFILE | uniq | echo $(awk '{print $0":20"}') | sed 's/ /:/g')

# execute mechanical with command line parameters 
# Please insert here the correct version and your own input and output file with its correct name! 
ansys191 -dis -b -machines $machines < input.dat > output.out

Further information

• Documentation is available within the application help manual. Further information is provided through the ANSYS Customer Portal for registered users.
• More in-depth documentation is available at LRZ. Please note: not everything is directly applicable to HPC systems at RRZE!

Mentors

• Dr.-Ing. Katrin Nusser, RRZE, hpc-support@fau.de
• please volunteer!

IMD

IMD is a software package for classical molecular dynamics simulations. Several types of interactions are supported, such as central pair potentials, EAM potentials for metals, Stillinger-Weber and Tersoff potentials for covalent systems, and Gay-Berne potentials for liquid crystals. A rich choice of simulation options is available: different integrators for the simulation of the various thermodynamic ensembles, options that allow to shear and deform the sample during the simulation, and many more. There is no restriction on the number of particle types. (http://imd.itap.physik.uni-stuttgart.de/)

The latest versions of IMD are released under GPL-3.0.

Availability / Target HPC systems

IMD is currently not centrally installed, but can be installed locally in users’ home folder. Follow the instruction on http://imd.itap.physik.uni-stuttgart.de/userguide/compiling.html. While compiling at RRZE, first load “intel64” module. It is recommended to clean the compilation before initiating a new compiling process, i.e. gmake clean. SpecifyIMDSYS=lima on any of RRZE’s cluster; however, only use the resulting binary on the cluster where you produced it, i.e. recompile again with IMDSYS=lima when moving to a different cluster.

If there is enough demand, RRZE might also provide a module for IMD.

Sample job scripts

#!/bin/bash -l
#PBS -l nodes=2:ppn=40,walltime=01:00:00
#PBS -N myJobName
#PBS -M myEmailAdress@fau.de
#PBS -j oe

module load intel64

# specify the full path of the IMD excutable
IMDCMD=$HOME/bin/imd_mpi_eam4point_fire_fnorm_homdef_stress_nbl_mono_hpo

# input parameter file name
PARAM=myJob.param

# run your job
/apps/rrze/bin/mpirun_rrze-intelmpd -pinexpr S0:0-9@S1:0-9  $IMDCMD -p $PARAM

Further information

• http://imd.itap.physik.uni-stuttgart.de/
• https://github.com/itapmd/imd

Mentors

• hpc-support@fau.de
• AG Bitzek (WW1 – I: General Materials Properties)

Quantum Espresso

Quantum Espresso is an integrated suite of open-source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.

Availability / Target HPC systems

• parallel computers: try to stick to one k-point / node, main target machines
• throughput cluster Woody: might be useful for small systems, manually distributed phonon calculations

Notes on parallelization in general

• do not use Hyperthreading
  • e.g. Emmy, OpenMPI (3.1): mpirun –report-bindings –bind-to core –map-by ppr:1:core
• use image parallelization .e.g. for NEB / phonon calculation
• ask for help with parallelization of phonon calculation
• use gamma point version (KPOINTS GAMMA) instead of KPOINTS AUTOMATIC
• k-point parallelization
  • 1 k-point per  node .e.g. -npools #nnodes
  • -npools must be a divisor of #MPI tasks
• -ndiag for  #bands > 500 (use ELPA version, will be provided soon)
• -ntg 2,5,10 as a last resort only, and if nr3 < #MPI tasks

Sample job scripts

TBD

Further information

• https://www.quantum-espresso.org/

Mentors

• T. Klöffel, RRZE, hpc-support@fau.de
• AG B. Meyer (Interdisciplinary Center for Molecular Materials)