Merge pull request #28 from jme52/schools/2023/sessions

SIESTA School 2023: Sessions, MN4

_events/SIESTA_School-2023.md

@@ -21,10 +21,12 @@ post-processing tools will also be presented.
 
 The School will consist of lectures from senior SIESTA developers
 and hands-on sessions where SIESTA experts will be available for discussion and guidance.
+These sessions will take place between 12:30 CEST and 17:30 CEST.
 
-While autonomous work on the exercises will be possible throughout the day,
-lectures and most discussions will take place in the central hours of the day
-(Central European Summer Time).
+Autonomous work on the exercises will be possible throughout the day.
+
+**UPDATE: You may find detailed information on the planned sessions and tutorials
+[here](Sessions.html).**
 
 ### Course materials
 
@@ -72,6 +74,7 @@ including registration and a tentative program.
 * Emilio Artacho (Nanogune, Spain; and University of Cambridge, UK)
 * Antonio Cammarata (Czech Technical University in Prague, Czech Republic)
 * José Mª Escartín (ICN2, Spain)
+* Julio Gutiérrez (BSC, Spain)
 * Nick Papior (DTU, Denmark)
 * Federico Pedron (ICN2, Spain)
 * Miguel Pruneda (CSIC, Spain)

events/SIESTA_School-2023/MN4.md

@@ -0,0 +1,244 @@
+---
+layout: siesta-nav
+title: "SIESTA School 2023: MareNostrum 4"
+---
+
+# SIESTA School 2023: MareNostrum 4
+
+MareNostrum 4 is the largest operational supercomputer of the Barcelona Supercomputing Center.
+Each node contains 2 Intel Xeon Platinum processors (with 24 cores each) and 96 GB of RAM.
+They all run SUSE Linux 12.
+
+You should have received your BSC credentials in your institutional email account
+on September 30th. Your BSC account is already enabled.
+Please contact the organisers if you have not received this email.
+
+## Connecting to MN4
+From your computer terminal, use your SSH client to connect to a MN4 login node.
+There are three login nodes, `mn1.bsc.es`, `mn2.bsc.es`, and `mn3.bsc.es`.
+You can connect to any of them, they are used interchangeably in the examples below.
+
+### Via conventional SSH client (Mac, Linux, Windows with WSL/Cygwin)
+
+From a terminal, run
+
+{% highlight bash %}
+$ ssh <USERNAME>@mn1.bsc.es
+{% endhighlight%}
+
+where `<USERNAME>` is your BSC username (e.g., `ctn99999`).  You will be prompted
+for the corresponding password.
+
+If you want to enable visualization, you need to use the `-X` option:
+{% highlight bash %}
+$ ssh -X <USERNAME>@mn1.bsc.es
+{% endhighlight %}
+
+### Via PuTTY or mobaXterm
+
+If you don't have any SSH client installed in your computer,
+please download and install
+[mobaXterm](https://mobaxterm.mobatek.net/download.html)
+(recommended)
+or
+[PuTTY](https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html).
+
+When you open the graphical interface define the server/host name (`mn3.bsc.es`)
+and provide your username and password when prompted.
+For mobaXterm, there is a short
+generic demo video available [here](https://mobaxterm.mobatek.net/demo.html).
+
+For visualizations using PuTTY, please keep in mind the following:
+ * Under connection → SSH → X11, make sure that the "Enable X11 forwarding" option is checked.
+ * You also need to install [xMing](https://sourceforge.net/projects/xming/).
+
+In mobaXterm this is enabled by default.
+
+## Changing your password
+
+Please change your password as soon as possible.
+In order to do this, connect via ssh to `dt01.bsc.es` and execute the `passwd` command;
+the prompt will ask you for your existing password (once) and for your new password (twice).
+The new password takes about 10 minutes to be effective.
+A sample session for changing the password is:
+
+{% highlight bash %}
+$ ssh <USERNAME>@dt01.bsc.es
+
+username@dtransfer1:~> passwd
+Changing password for username.
+Old Password:
+New Password:
+Reenter New Password:
+Password changed.
+{% endhighlight %}
+
+
+## Submitting a job
+
+Calculations in MareNostrum 4 need to be submitted through the queing system. For that purpose,
+we will be using a job script, provided in `/gpfs/projects/nct00/nct00003/SCRIPTS/runmn.sh`.
+You will need to copy this script to each tutorial folder in which you intend to run `siesta`.
+
+The contents of the script are:
+
+{% highlight slurm %}
+#!/bin/bash
+#SBATCH -J tutorialXX
+#SBATCH -n 4
+#SBATCH -t 0:30:00
+#SBATCH -o %x-%j.out
+#SBATCH -e %x-%j.err
+#SBATCH -D .
+
+source /gpfs/projects/nct00/nct00003/siestarc.sh
+
+srun -n 4 siesta < input.fdf > output.out
+{% endhighlight %}
+
+Note that `input.fdf` and `output.out` are generic input and output
+file names, for each execution of `siesta` you will need to change them
+to the actual names of your input and output files.
+It is also convenient to change the name of the job (`#SBATCH -J` option)
+to something that allows you to identify (vs. your other submissions)
+when checking the status of the queue.
+
+The `-n` options in `#SBATCH` and `srun` indicate the
+number of computing cores used.
+Please **do not** needlessly increase these quantities,
+be mindful that resources are limited and must be shared between all of the students.
+
+You can submit this job script from a login node by executing:
+
+{% highlight bash %}
+$ sbatch runmn.sh
+{% endhighlight %}
+
+For more information on running jobs, visit and read
+[the MareNostrum guides](https://www.bsc.es/supportkc/docs/MareNostrum4/intro).
+
+### SLURM reservations
+BSC has enabled two daily reservations for us, for the duration of the school:
+* `SIESTA-DAY` (between 08:00 and 21:00 CEST): 9 MN4 nodes (48 cores each).
+* `SIESTA-NIGHT` (between 21:00 and 08:00 CEST): 3 MN4 nodes (48 cores each).
+
+In order to make use of these reservations, run sbatch with the reservation option:
+
+{% highlight bash %}
+$ sbatch runmn.sh --reservation=SIESTA-DAY
+{% endhighlight %}
+
+or
+
+{% highlight bash %}
+$ sbatch runmn.sh --reservation=SIESTA-NIGHT
+{% endhighlight %}
+
+## Directory with tutorials
+For every practical there is a folder in the shared directory
+`/gpfs/projects/nct00/nct00003/TUTORIALS/`
+that contains all the files you will need for said practical.
+At the start of every tutorial, please copy the required files from that shared directory
+to your scratch folder.  For example, for the practical of the first day,
+
+{% highlight bash %}
+$ cd /gpfs/scratch/nct01/<USERNAME>
+$ cp -pr /gpfs/projects/nct00/nct00003/TUTORIALS/day1 .
+{% endhighlight %}
+
+Please do NOT copy these files before the start of the practical, in case they are updated
+shortly before the practical starts.
+
+Note: We will be running everything in the scratch folder, since disk space is limited in `$HOME`.
+
+## Visualization
+
+We strongly encourage you do visualizations in your own
+computer. You will first need to copy the files to it (see instructions below).
+Visualizations can also be done in the reserved compute nodes,
+but this is not recommended.
+
+Visualizations done directly on the MareNostrum login nodes
+will result in **account banning**.
+
+### Tools used for visualization
+If you run visualizations in your own PC, you may want to install the following software,
+which will be used during the school:
+
+* [gnuplot]( http://www.gnuplot.info/ )
+* [xcrysden]( http://www.xcrysden.org/ )
+* [vesta]( https://jp-minerals.org/vesta/en/ )
+* [vmd]( https://www.ks.uiuc.edu/Research/vmd/ )
+* Python with matplotlib
+
+### Visualization on the BSC compute nodes
+
+In this case you will need to connect directly (interactively) to a compute node instead
+of submitting a job script.
+In order to do this, you need to execute the following command
+from one of the login nodes of MareNostrum 4:
+
+{% highlight bash %}
+$ salloc -t 4:00:00 -n 1 -c 1 --reservation=SIESTA-DAY -J siestaschool
+{% endhighlight %}
+
+This will create a 4-hour long reservation (`-t` option), with 1 task (`-n`) that uses 1 CPU core (`-c`).
+The `-J` option is again an identifier that you can change at will.
+If you try this overnight, remember to change the `SIESTA-DAY` to `SIESTA-NIGHT`.
+
+Again, please **do not** needlessly increase these quantities,
+be mindful that resources are limited and must be shared between all of the students.
+
+Once inside this interactive session, make sure that you load the Siesta school environment
+before doing anything:
+
+{% highlight bash %}
+$ source /gpfs/projects/nct00/nct00003/siestarc.sh
+{% endhighlight %}
+
+This will give you access to the siesta binary and to the rest of the tools of the school.
+
+Beware that the Siesta school environment will stay active as long as your interactive session is active.
+If you logout or otherwise lose conntection to the compute node, you will need to load the environment again when you reconnect.
+
+**We encourage you to run visualizations locally on your own computer.**
+
+## Copying and backing up files
+
+You can backup your files in case you want to keep them after the school is finished.
+You need to do this from your local machine (you cannot start outgoing
+connections from BSC machines).  It is recommended that you transfer your files from one
+of the data transfer nodes (`dt01.bsc.es`) rather than from one of the login nodes.
+
+You can transfer files in multiple ways:
+
+* Via `scp` or `rsync` (Mac, Linux, Windows with WSL/Cygwin).  For example,
+from your local computer:
+
+{% highlight bash %}
+$ scp -pr <USERNAME>@dt01.bsc.es:/path/to/files .
+{% endhighlight %}
+
+* Via `sshfs` (all platforms).
+This may be specially useful for those running exclusively Windows.
+Please check the `sshfs` documentation at
+[the BSC guides](https://www.bsc.es/supportkc/docs/dtmachines/).
+
+
+## Data preservation
+
+**You will lose access to your account on October 7th or shortly afterwards.
+We strongly recommend that you perform regular (at least daily)
+backups of your BSC files to prevent the loss of any
+data.**
+
+## Advanced (no support given)
+
+* If you want to try your own SIESTA compilation,
+have a look at
+[this SIESTA compilation how-to](https://docs.siesta-project.org/projects/siesta/en/latest/how-to/installation/build-manually.html).
+Be sure to have all dependencies beforehand. Note that we will not be answering questions
+regarding compilation or other installations during the school.
+
+* Perform your visualizations with [ovito](https://www.ovito.org/about/).
+