Tycho - User contributions [en]

First steps

2023-11-15T14:22:57Z

Jredondo:

To start using Tycho, please follow these steps

* Get a user account by contacting a sponsor and signing up at

https://hpc.ku.dk/account.html

You have to select "Astro" as your group. '''Remember to sign the rules-of-conduct-form'''

* '''BE AWARE THAT THE WELCOME E-MAIL IS NOT CORRECT'''. You should never login to fend0X.hpc.ku.dk, but instead use the Tycho-specific frontends called astro0X.hpc.ku.dk (see [[Hardware]] for an up to date list of available frontends / Analysis hardware).

* Set up an SSH key pair for secure passwordless login (see [[Accessing Tycho]])

* Add <code>module load astro</code> to you <code>$HOME/.bashrc</code> file to have access to all the custom installed software.
* Consider changing <code>umask 077</code> to <code>umask 027</code> in <code>$HOME/.bashrc</code> to allow collaborators and/or your supervisor read access to your files when logged in to the cluster.

* If you are going to travel, but want to continue working on Tycho while you are travelling, you need to set up a Dynamic Firewall '''before''' travelling. You can do so by following the detailed instructions [https://hpc.ku.dk/documentation/otp.html: here]

* Consider setting up Visual Studio Code for remote development for transparent editing of files on the cluster. See [[Visual Studio Remote Development]]

* Whenever you are going to be working with large amounts of data, considering using the <code>/lustre/astro/yourusername</code> directory. The scratch directory is a ZFS based high performance Lustre filesystem with dedicated hardware for our group. No quotas are enforced and the total space (disregarding the transparent compression) is 1300 TB.

Module system

2023-11-15T14:10:27Z

Jredondo: Created page with "Tycho makes use of the Module system to manage dependencies and load common compilers and software. Environment modules modify the users environment via modulefiles. They are typically used to manage different versions of applications, by e.g. modifying the PATH system variable, using one module file per application version. To ensure consistency, we recommend that you put relevant module commands in a file (e.g. ~/.modules), and source it from relevant startup files..."

Tycho makes use of the Module system to manage dependencies and load common compilers and software.

Environment modules modify the users environment via modulefiles. They are typically used to manage different versions of applications, by e.g. modifying the PATH system variable, using one module file per application version.

To ensure consistency, we recommend that you put relevant module commands in a file (e.g. ~/.modules), and source it from relevant startup files. Note that, even if you use tcsh as login shell, your batch jobs may use bash, so be sure to add "source ~/.modules" to ~/.bashrc in all cases. If you do this there is no need to put source statements in your job scripts.

== Useful Commands ==

When you first log in, it is encouraged to write

<pre>
module load astro
</pre>

to your <code>source $HOME/.bashrc</code>. This will let you have access to all the available software.

If you want to see what software can you load, you can run

<pre>
module avail
</pre>

To check what software have you currently loaded, check

<pre>
module list
</pre>

To load a particular module, for example, the <code>intel</code> compilers, you can run

<pre>
module load intel
</pre>

or if you want a specific version

<pre>
module load intel/20.1
</pre>

To unload a loaded module do

<pre>
module unload "modulename"
</pre>

To switch to a different version, for example, from <code>intel/20.1</code> to <code>intel/18.0.3</code>, do

<pre>
module switch intel/20.1 intel/18.0.3
</pre>

You can find more documentation by checking the manual pages

<pre>
man module
</pre>

in [http://en.wikipedia.org/wiki/Environment_Modules_(software): this link], or in [https://modules.sourceforge.net/: this other link]

Tycho Technical Documentation

2023-11-15T14:01:52Z

Jredondo:

Welcome to the technical documentation for the Tycho high performance computing resources. See [https://nbi.ku.dk/english/research_infrastructure/tycho-supercomputer/ the Infrastructure page] at NBI for a non-technical overview of the cluster.

Tycho contain in total more 10,000 CPU cores and 13 data center class GPUs. The cluster is complemented by a 1,300 TB data storage archive and a number of powerful analysis machines used as frontends for the cluster and for pre- and post-prcessing. Current peak performance is 443 TFlops from the CPUs and 93 TFlops from the GPUs.

Tycho is hosted at the [http://www.dcsc.ku.dk/: High Performance Computing center] at the faculty of SCIENCE, University of Copenhagen.

===First steps===
Please visit the [[first steps]] page to get started

===Overview===
* [[Acknowledging the use of Tycho in articles and presentations]]
* [[Getting Help]]
* [[Mattermost discussion forum]]
* [[Being a good HPC user]]
* [[Accessing Tycho]]
* [[Using Jupyter notebooks on the frontends]]
* [[Visual Studio Remote Development]]
* [[Virtual Desktop]]
* [[Hardware]]
* [[Erda]]
* [[Using GPUs]]
* [[Compilers]]
* [[Debugging and Profiling]]
* [[MPI Libraries]]
* [[Examples of SLURM scripts]]
* [[Codes]]
* [[Adding a second IP Address]]
* [[Setting up One-Time-Password Access before travelling]]

===Scientific Software===

* [[Module system]]
* [[Running Mathematica on compute nodes]]
* [[GRChombo]]

*************************

Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]

First steps

2023-11-15T13:56:57Z

Jredondo:

Adding a second IP Address

2023-11-15T13:56:06Z

Jredondo: Created page with "Once you are logged in to the front-end, write: <pre> hpc-setup-firewall.sh </pre> There, you can add up to 3 total IP addresses. One useful tip is to add the ERDA IP address, so that you can always log in to the cluster even if you are travelling."

Once you are logged in to the front-end, write:

<pre>
hpc-setup-firewall.sh
</pre>

There, you can add up to 3 total IP addresses.

One useful tip is to add the ERDA IP address, so that you can always log in to the cluster even if you are travelling.

GRChombo

2023-11-15T13:51:58Z

Jredondo:

[https://www.grchombo.org/: GRChombo] is an open-source, AMR-based code for Numerical Relativity. Here are some instructions on how to set up GRChombo in Tycho.

=== Step 1. Compile Chombo ===

Go to [https://github.com/GRTLCollaboration/Chombo: Chombo] and clone the repository in the cluster:

<pre>
>>git clone https://github.com/GRTLCollaboration/Chombo.git
</pre>

Then we need to make a new file that will set up the compilation details, specifically tweaked for our cluster. Run these commands:

<pre>
>>cd Chombo/lib
>>touch mk/Make.defs.local
</pre>

Using your favourite editor (vim or nano) copy this into Make.defs.local:

<pre>
DIM = 3
DEBUG = FALSE
CXX = g++ -I${MKLROOT}/include
FC = gfortran -I${MKLROOT}/include
OPT = TRUE
MPI = TRUE
OPENMPCC = TRUE
OPT = TRUE
USE_64 = TRUE
USE_HDF = TRUE
MPICXX = mpicxx -I${MKLROOT}/include
HDFINCFLAGS = -I/software/astro/hdf5/hdf5-1.8.14-intel/include
HDFLIBFLAGS = -L/software/astro/hdf5/hdf5-1.8.14-intel/lib -lhdf5 -lz
HDFMPIINCFLAGS = -I/software/astro/hdf5/hdf5-1.8.14-intel/include
HDFMPILIBFLAGS = -L/software/astro/hdf5/hdf5-1.8.14-intel/lib -lhdf5 -lz
cxxdbgflags = -g -Wl,--eh-frame-hdr
cxxoptflags = -O3
fdbgflags = -g -Wl,--eh-frame-hdr
foptflags = -O3
syslibflags = -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl
</pre>

Notice that we are NOT compiling the Apparent Horizon finder. That requires some additional work.

Now, load the appropriate modules.

<pre>
>>module purge
>>module load astro
>>module load hdf5/inte/1.10.4
>>module load gcc/12.2-offload
>>module load intelmpi/18.0.3
>>module load intel/20.1
</pre>

It is recommended to add these to your <code>~/.bashrc</code> profile.

Now, do

<pre>
make all -j 8
</pre>

And it all should compile in a matter of minutes.

=== Step 2. Run a Binary BH ===

Go back to your home directory, and clone the GRChombo repository:

<pre>
>> cd ~
>> git clone https://github.com/GRTLCollaboration/GRChombo.git]
>> cd GRChombo
</pre>

Export the variable containing where is the Chombo library

<pre>
>>export CHOMBO_HOME=~/Chombo/lib/
</pre>

Let us go to the example of the Binary BH and compile the code:

<pre>
>>cd GRChombo/Examples/BinaryBH/
>>make all -j 8
</pre>

Now you can start the run with the following BASH script:

<pre>
#!/bin/sh
#SBATCH -J BBH # job name
#SBATCH -t 6:00:00 # walltime (dd:hh:mm:ss)
#SBATCH -p astro2_short

#SBATCH --nodes 8
#SBATCH --ntasks-per-node=24
#SBATCH --cpus-per-task=2
# Output files
#SBATCH -o std_output.txt
#SBATCH -e std_error.txt
#SBATCH -D ./
module load intelmpi/18.0.3

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
# Run the program
srun ./Main_BinaryBH3d.Linux.64.mpicxx.gfortran.OPT.MPI.OPENMPCC.ex params.txt
</pre>

You can check [https://github.com/GRTLCollaboration/GRChombo/wiki/Running-the-BinaryBH-example: the Wiki] for more information on the parameter file <code>params.txt</code>, and how to visualize the output data. Visit is a good option for this.

Accessing Tycho

2023-11-15T13:50:36Z

Jredondo:

After getting an account (following the instructions [https://hpc.ku.dk/account.html: here]), you can now log into Tycho using [https://en.wikipedia.org/wiki/Secure_Shell: ssh].

== SSH into the frontends ==

Open your terminal, and type:

<pre>
>>ssh username@astro06.hpc.ku.dk
</pre>

In "username", replace it with your username. You will be prompted to type your password. Do so, press enter, and then you will be in the frontend. You should see something like this:

<pre>
Last login: Mon Nov 6 09:33:04 2023 from 130.225.188.XX
[username@astro06 ~]$
</pre>

This way you logged into the astro06 frontend. You can also log in to the other frontends (astro01 and astro02).

== Quality of Life Improvements ==

=== Shortening the access prompt ===

You can shorten the command that you need to write to log into the cluster by adding this line to the <code> ~/.ssh/config </code> file:

<pre>
Host astro06 User username HostName astro06.hpc.ku.dk
</pre>

Once you have that, you can log in writing

<pre>
>>ssh astro06
</pre>

=== Aliasing the access prompt ===

If you will be using a bash command very often, it is sometimes useful to make an alias. You can do this by adding this line to your <code>~/.bashrc</code> file (using vim or nano):

<pre>
alias tycho='ssh astro06'
</pre>

Once you do this, write <code> source ~/.bashrc </code> in the Terminal, and then you can log in to the astro06 frontend by just typing <code> tycho </code>.

Do not use the ssh option -Y, which "enables trusted X11 forwarding". This means, basically, that you turn off some essential X security features and say "I trust the remote host completely".

=== Passwordless access ===

There is one more quality of life improvement to log into the cluster, which will let you log in without having to write your password every time.

First, we generate a key writing:

<pre>
ssh-keygen -t ed25519
</pre>

With the option t we specify the encryption type. You will be asked for the filename, you can just press enter and use the default. Then, you will be asked for a passphrase to protect your personal key.

You should NOT under any circumstances use an empty pass phrase; it is not necessary for convenience reasons (see below), and could endanger your access to remote supercomputers. Use instead really a "pass phrase"; a relatively long expression, which need not have the character of a password (such as "Carlsberg is probably the best beer in the world").

There will be stored two keys (id_rsa and id_rsa.pub) in the hidden folder <code>~/.ssh/</code> on your client. Note that if you specified a particular name for the key when generating it, the keys will appear with the file name you specified.

You need to copy your public key to the accepted key list of on your host machine (authorized_keys). We do this by writing:

<pre>
cat ~/.ssh/id_rsa.pub | ssh username@astro06.hpc.ku.dk 'cat >> .ssh/authorized_keys'
</pre>

Now if you try to log in, you will be prompted to write the passphrase. Instead of writing the passphrase, do

<pre>
ssh-add
</pre>

to add the passphrase once and for all. Once you do this, you will be able to log in without having to write your password.

If for some reason no ssh-agent is running on an intermediate host, then as an alternative you can forward your ssh-credentials from your laptop, by using <code>ssh -A</code> to login to astro0X, and continuing an ssh from there (having stored the id_rsa.pub from your laptop on the remote supercomputer).
Finally, if for some reason you start out from a place (such a just a command window) where no ssh-agent is running, you can just start one, by doing <code>ssh-agent bash</code>, this starts an ssh-agent, which starts bash (or tcsh) as a descendant. Then execute "ssh-add", and you're free from typing the pass phrase, for as long as you keep the ssh-agent running.

Setting up One-Time-Password Access before travelling

2023-11-15T13:49:44Z

Jredondo: Created page with "If you are going to travel, but want to continue working on Tycho while you are travelling, you need to set up a One Time Password access '''before''' travelling. You can do so by following the detailed instructions [https://hpc.ku.dk/documentation/otp.html: here]"

If you are going to travel, but want to continue working on Tycho while you are travelling, you need to set up a One Time Password access '''before''' travelling.

You can do so by following the detailed instructions [https://hpc.ku.dk/documentation/otp.html: here]

Tycho Technical Documentation

2023-11-15T13:46:35Z

Jredondo:

Welcome to the technical documentation for the Tycho high performance computing resources. See [https://nbi.ku.dk/english/research_infrastructure/tycho-supercomputer/ the Infrastructure page] at NBI for a non-technical overview of the cluster.

Tycho contain in total more 10,000 CPU cores and 13 data center class GPUs. The cluster is complemented by a 1,300 TB data storage archive and a number of powerful analysis machines used as frontends for the cluster and for pre- and post-prcessing. Current peak performance is 443 TFlops from the CPUs and 93 TFlops from the GPUs.

Tycho is hosted at the [http://www.dcsc.ku.dk/: High Performance Computing center] at the faculty of SCIENCE, University of Copenhagen.

Please visit the [[first steps]] page to get started

Overview:
* [[Getting Help]]
* [[Mattermost discussion forum]]
* [[Being a good HPC user]]
* [[Accessing Tycho]]
* [[Using Jupyter notebooks on the frontends]]
* [[Visual Studio Remote Development]]
* [[Virtual Desktop]]
* [[Hardware]]
* [[Erda]]
* [[Using GPUs]]
* [[Compilers]]
* [[Debugging and Profiling]]
* [[MPI Libraries]]
* [[Examples of SLURM scripts]]
* [[Codes]]
* [[Adding a second IP Address]]
* [[Setting up One-Time-Password Access before travelling]]
* Software:

* [[Running Mathematica on compute nodes]]
* [[GRChombo]]

*************************

Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]

GRChombo

2023-11-15T13:42:39Z

Jredondo: Created page with "[GRChombo](https://www.grchombo.org/) is an open-source, AMR-based code for Numerical Relativity. Here are some instructions on how to set up GRChombo in Tycho. === Step 1. Compile Chombo === Go to [Chombo](https://github.com/GRTLCollaboration/Chombo) and clone the repository in the cluster: <pre> >>git clone https://github.com/GRTLCollaboration/Chombo.git </pre> Then we need to make a new file that will set up the compilation details, specifically tweaked for our cl..."

[GRChombo](https://www.grchombo.org/) is an open-source, AMR-based code for Numerical Relativity. Here are some instructions on how to set up GRChombo in Tycho.

=== Step 1. Compile Chombo ===

Go to [Chombo](https://github.com/GRTLCollaboration/Chombo) and clone the repository in the cluster:

<pre>
>>git clone https://github.com/GRTLCollaboration/Chombo.git
</pre>

Then we need to make a new file that will set up the compilation details, specifically tweaked for our cluster. Run these commands:

<pre>
>>cd Chombo/lib
>>touch mk/Make.defs.local
</pre>

Using your favourite editor (vim or nano) copy this into Make.defs.local:

<pre>
DIM = 3
DEBUG = FALSE
CXX = g++ -I${MKLROOT}/include
FC = gfortran -I${MKLROOT}/include
OPT = TRUE
MPI = TRUE
OPENMPCC = TRUE
OPT = TRUE
USE_64 = TRUE
USE_HDF = TRUE
MPICXX = mpicxx -I${MKLROOT}/include
HDFINCFLAGS = -I/software/astro/hdf5/hdf5-1.8.14-intel/include
HDFLIBFLAGS = -L/software/astro/hdf5/hdf5-1.8.14-intel/lib -lhdf5 -lz
HDFMPIINCFLAGS = -I/software/astro/hdf5/hdf5-1.8.14-intel/include
HDFMPILIBFLAGS = -L/software/astro/hdf5/hdf5-1.8.14-intel/lib -lhdf5 -lz
cxxdbgflags = -g -Wl,--eh-frame-hdr
cxxoptflags = -O3
fdbgflags = -g -Wl,--eh-frame-hdr
foptflags = -O3
syslibflags = -L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl
</pre>

Notice that we are NOT compiling the Apparent Horizon finder. That requires some additional work.

Now, load the appropriate modules.

<pre>
>>module purge
>>module load astro
>>module load hdf5/inte/1.10.4
>>module load gcc/12.2-offload
>>module load intelmpi/18.0.3
>>module load intel/20.1
</pre>

It is recommended to add these to your <code>~/.bashrc</code> profile.

Now, do

<pre>
make all -j 8
</pre>

And it all should compile in a matter of minutes.

=== Step 2. Run a Binary BH ===

Go back to your home directory, and clone the GRChombo repository:

<pre>
>> cd ~
>> git clone https://github.com/GRTLCollaboration/GRChombo.git]
>> cd GRChombo
</pre>

Export the variable containing where is the Chombo library

<pre>
>>export CHOMBO_HOME=~/Chombo/lib/
</pre>

Let us go to the example of the Binary BH and compile the code:

<pre>
>>cd GRChombo/Examples/BinaryBH/
>>make all -j 8
</pre>

Now you can start the run with the following BASH script:

<pre>
#!/bin/sh
#SBATCH -J BBH # job name
#SBATCH -t 6:00:00 # walltime (dd:hh:mm:ss)
#SBATCH -p astro2_short

#SBATCH --nodes 8
#SBATCH --ntasks-per-node=24
#SBATCH --cpus-per-task=2
# Output files
#SBATCH -o std_output.txt
#SBATCH -e std_error.txt
#SBATCH -D ./
module load intelmpi/18.0.3

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
# Run the program
srun ./Main_BinaryBH3d.Linux.64.mpicxx.gfortran.OPT.MPI.OPENMPCC.ex params.txt
</pre>

You can check [the Wiki](https://github.com/GRTLCollaboration/GRChombo/wiki/Running-the-BinaryBH-example) for more information on the parameter file <code>params.txt</code>, and how to visualize the output data. Visit is a good option for this.

Tycho Technical Documentation

2023-11-15T13:40:11Z

Jredondo:

Welcome to the technical documentation for the Tycho high performance computing resources. See [https://nbi.ku.dk/english/research_infrastructure/tycho-supercomputer/ the Infrastructure page] at NBI for a non-technical overview of the cluster.

Tycho contain in total more 10,000 CPU cores and 13 data center class GPUs. The cluster is complemented by a 1,300 TB data storage archive and a number of powerful analysis machines used as frontends for the cluster and for pre- and post-prcessing. Current peak performance is 443 TFlops from the CPUs and 93 TFlops from the GPUs.

Tycho is hosted at the [http://www.dcsc.ku.dk/: High Performance Computing center] at the faculty of SCIENCE, University of Copenhagen.

Please visit the [[first steps]] page to get started

Overview:
* [[Getting Help]]
* [[Mattermost discussion forum]]
* [[Being a good HPC user]]
* [[Accessing Tycho]]
* [[Using Jupyter notebooks on the frontends]]
* [[Visual Studio Remote Development]]
* [[Virtual Desktop]]
* [[Hardware]]
* [[Erda]]
* [[Using GPUs]]
* [[Compilers]]
* [[Debugging and Profiling]]
* [[MPI Libraries]]
* [[Examples of SLURM scripts]]
* [[Codes]]
* Software:

* [[Running Mathematica on compute nodes]]
* [[GRChombo]]

*************************

Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.

== Getting started ==
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/postorius/lists/mediawiki-announce.lists.wikimedia.org/ MediaWiki release mailing list]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]

Running Mathematica on compute nodes

2023-11-15T13:38:25Z

Jredondo: Created page with "Here are some instructions on how to run Mathematica on the cluster. === Step 1. === Load the mathematica module: <pre> >>module load astro >>module load mathematica </pre> === Step 2. === Prepare our test script. You can make mathematica scripts in different ways, but .wls files are good option. Here is an example script, you can make it into a file called <code>test.wls</code>: <pre> #!/usr/bin/env wolframscript outdir = "Data/"; fn1 = outdir<>"test.dat"; values..."

Here are some instructions on how to run Mathematica on the cluster.

=== Step 1. ===

Load the mathematica module:

<pre>
>>module load astro
>>module load mathematica
</pre>

=== Step 2. ===

Prepare our test script. You can make mathematica scripts in different ways, but .wls files are good option. Here is an example script, you can make it into a file called <code>test.wls</code>:

<pre>
#!/usr/bin/env wolframscript
outdir = "Data/";
fn1 = outdir<>"test.dat";
values = Table[{x, x^2},{x,0,1,0.1}];
Export[fn1, values, "Table"];
</pre>

=== Step 3. ===

Now prepare your bash script to submit the job. Here's a template:

<pre>
#!/bin/bash
#SBATCH --job-name=math_test # shows up in the output of squeue
#SBATCH --time=00:59:00 # specify the requested wall-time
#SBATCH --partition=astro3_devel # specify the partition to run on
#SBATCH --ntasks=1 # number of tasks
#SBATCH --cpus-per-task=1 # number of OpenMP threads per MPI rank
#SBATCH --threads-per-core=1 # number of threads active per CPU core (=1: Hyperthreading off)
# Make sure that Mathematica is loaded

module load astro
module load math

# Set up port forwarding so that Mathematica finds the license

ssh astro01.hpc.ku.dk -L16286:mathlm.nbi.dk:16286 -L16287:mathlm.nbi.dk:16287 -Nf

# Execute the code

wolframscript stupid_test.wls

# Make sure that the ssh tunnel is killed

pkill -fu $USER astro01
</pre>

Now you are ready to submit your job and have fun. Before submitting, make sure you create the directory <code>>>mkdir Data</code>. If it runs successfully, you will see a <code>Data/test.dat</code> file.

Accessing Tycho

2023-11-15T13:28:26Z

Jredondo:

After getting an account (following the instructions [https://hpc.ku.dk/account.html](here)), you can now log into Tycho using [https://en.wikipedia.org/wiki/Secure_Shell](ssh).

== SSH into the frontends ==

Open your terminal, and type:

<pre>
>>ssh username@astro06.hpc.ku.dk
</pre>

In "username", replace it with your username. You will be prompted to type your password. Do so, press enter, and then you will be in the frontend. You should see something like this:

<pre>
Last login: Mon Nov 6 09:33:04 2023 from 130.225.188.XX
[username@astro06 ~]$
</pre>

This way you logged into the astro06 frontend. You can also log in to the other frontends (astro01 and astro02).

== Quality of Life Improvements ==

=== Shortening the access prompt ===

You can shorten the command that you need to write to log into the cluster by adding this line to the <code> ~/.ssh/config </code> file:

<pre>
Host astro06 User username HostName astro06.hpc.ku.dk
</pre>

Once you have that, you can log in writing

<pre>
>>ssh astro06
</pre>

=== Aliasing the access prompt ===

If you will be using a bash command very often, it is sometimes useful to make an alias. You can do this by adding this line to your <code>~/.bashrc</code> file (using vim or nano):

<pre>
alias tycho='ssh astro06'
</pre>

Once you do this, write <code> source ~/.bashrc </code> in the Terminal, and then you can log in to the astro06 frontend by just typing <code> tycho </code>.

Do not use the ssh option -Y, which "enables trusted X11 forwarding". This means, basically, that you turn off some essential X security features and say "I trust the remote host completely".

=== Passwordless access ===

There is one more quality of life improvement to log into the cluster, which will let you log in without having to write your password every time.

First, we generate a key writing:

<pre>
ssh-keygen -t ed25519
</pre>

With the option t we specify the encryption type. You will be asked for the filename, you can just press enter and use the default. Then, you will be asked for a passphrase to protect your personal key.

You should NOT under any circumstances use an empty pass phrase; it is not necessary for convenience reasons (see below), and could endanger your access to remote supercomputers. Use instead really a "pass phrase"; a relatively long expression, which need not have the character of a password (such as "Carlsberg is probably the best beer in the world").

There will be stored two keys (id_rsa and id_rsa.pub) in the hidden folder <code>~/.ssh/</code> on your client. Note that if you specified a particular name for the key when generating it, the keys will appear with the file name you specified.

You need to copy your public key to the accepted key list of on your host machine (authorized_keys). We do this by writing:

<pre>
cat ~/.ssh/id_rsa.pub | ssh username@astro06.hpc.ku.dk 'cat >> .ssh/authorized_keys'
</pre>

Now if you try to log in, you will be prompted to write the passphrase. Instead of writing the passphrase, do

<pre>
ssh-add
</pre>

to add the passphrase once and for all. Once you do this, you will be able to log in without having to write your password.

If for some reason no ssh-agent is running on an intermediate host, then as an alternative you can forward your ssh-credentials from your laptop, by using <code>ssh -A</code> to login to astro0X, and continuing an ssh from there (having stored the id_rsa.pub from your laptop on the remote supercomputer).
Finally, if for some reason you start out from a place (such a just a command window) where no ssh-agent is running, you can just start one, by doing <code>ssh-agent bash</code>, this starts an ssh-agent, which starts bash (or tcsh) as a descendant. Then execute "ssh-add", and you're free from typing the pass phrase, for as long as you keep the ssh-agent running.

Accessing Tycho

2023-11-15T13:28:00Z

Jredondo:

After getting an account (following the instructions [https://hpc.ku.dk/account.html](here)), you can now log into Tycho using [https://en.wikipedia.org/wiki/Secure_Shell](ssh).

== SSH into the frontends ==

Open your terminal, and type:

<pre>
>>ssh username@astro06.hpc.ku.dk
</pre>

In "username", replace it with your username. You will be prompted to type your password. Do so, press enter, and then you will be in the frontend. You should see something like this:

<pre>
Last login: Mon Nov 6 09:33:04 2023 from 130.225.188.XX
[username@astro06 ~]$
</pre>

This way you logged into the astro06 frontend. You can also log in to the other frontends (astro01 and astro02).

== Quality of Life Improvements ==

=== Shortening the access prompt ===

You can shorten the command that you need to write to log into the cluster by adding this line to the <code> ~/.ssh/config <\code> file:

<pre>
Host astro06 User username HostName astro06.hpc.ku.dk
</pre>

Once you have that, you can log in writing

<pre>
>>ssh astro06
</pre>

=== Aliasing the access prompt ===

If you will be using a bash command very often, it is sometimes useful to make an alias. You can do this by adding this line to your <code>~/.bashrc</code> file (using vim or nano):

<pre>
alias tycho='ssh astro06'
</pre>

Once you do this, write <code> source ~/.bashrc </code> in the Terminal, and then you can log in to the astro06 frontend by just typing <code> tycho </code>.

Do not use the ssh option -Y, which "enables trusted X11 forwarding". This means, basically, that you turn off some essential X security features and say "I trust the remote host completely".

=== Passwordless access ===

There is one more quality of life improvement to log into the cluster, which will let you log in without having to write your password every time.

First, we generate a key writing:

<pre>
ssh-keygen -t ed25519
</pre>

With the option t we specify the encryption type. You will be asked for the filename, you can just press enter and use the default. Then, you will be asked for a passphrase to protect your personal key.

You should NOT under any circumstances use an empty pass phrase; it is not necessary for convenience reasons (see below), and could endanger your access to remote supercomputers. Use instead really a "pass phrase"; a relatively long expression, which need not have the character of a password (such as "Carlsberg is probably the best beer in the world").

There will be stored two keys (id_rsa and id_rsa.pub) in the hidden folder <code>~/.ssh/</code> on your client. Note that if you specified a particular name for the key when generating it, the keys will appear with the file name you specified.

You need to copy your public key to the accepted key list of on your host machine (authorized_keys). We do this by writing:

<pre>
cat ~/.ssh/id_rsa.pub | ssh username@astro06.hpc.ku.dk 'cat >> .ssh/authorized_keys'
</pre>

Now if you try to log in, you will be prompted to write the passphrase. Instead of writing the passphrase, do

<pre>
ssh-add
</pre>

to add the passphrase once and for all. Once you do this, you will be able to log in without having to write your password.

If for some reason no ssh-agent is running on an intermediate host, then as an alternative you can forward your ssh-credentials from your laptop, by using <code>ssh -A</code> to login to astro0X, and continuing an ssh from there (having stored the id_rsa.pub from your laptop on the remote supercomputer).
Finally, if for some reason you start out from a place (such a just a command window) where no ssh-agent is running, you can just start one, by doing <code>ssh-agent bash</code>, this starts an ssh-agent, which starts bash (or tcsh) as a descendant. Then execute "ssh-add", and you're free from typing the pass phrase, for as long as you keep the ssh-agent running.

Accessing Tycho

2023-11-15T12:33:22Z

Jredondo: Created page with "After getting an account (following the instructions [https://hpc.ku.dk/account.html](here)), you can now log into Tycho using [https://en.wikipedia.org/wiki/Secure_Shell](ssh). == SSH into the frontends == Open your terminal, and type: <pre> >>ssh username@astro06.hpc.ku.dk </pre> In "username", replace it with your username. You will be prompted to type your password. Do so, press enter, and then you will be in the frontend. You should see something like this: <p..."