Remeis-Wiki - Recent changes [en]

Welcome Newbies

Zalot — Thu, 06 Aug 2026 07:00:58 GMT

Carpool

Lab course manual

Zalot — Fri, 31 Jul 2026 07:09:18 GMT

GIT repository

Guided Tours and Public Outreach

Zalot — Thu, 30 Jul 2026 13:12:33 GMT

Tours looking for a guide

Geant4

Thalhammer — Thu, 30 Jul 2026 08:27:56 GMT

Guided Tours and Public Outreach

Zalot — Mon, 27 Jul 2026 05:39:16 GMT

Tours looking for a guide

Geant4

Thalhammer — Fri, 24 Jul 2026 13:30:01 GMT

Geant4

Thalhammer — Thu, 23 Jul 2026 13:59:17 GMT

Create documentation for Geant4

New page

= Running Geant4 simulations on the Remeis cluster =

This page describes a practical workflow for building and running
[https://geant4.web.cern.ch/ Geant4] Monte-Carlo simulations on the Remeis
compute cluster, using SLURM for parameter scans and conda to provide the
Geant4 toolkit. The examples are taken from ''Cu67'' simulations,
but the mechanics apply to any Geant4 application.

== Overview ==

A Geant4 simulation on the cluster involves three steps, although the last step is optional:

* the compiled Geant4 application (a C++ executable, here <code>cu67_sim</code>);
* one or more macro files (<code>.mac</code>) that configure geometry, beam and run size;
* a Python wrapper that renders macros from a template, launches the executable, merges the output, and produces summary tables and plots.

For parameter scans the Python wrapper is submitted to a SLURM array job,
so that each grid point runs as an independent task.

== Geant4 via conda ==

Geant4 (including its data libraries) is available from
[https://conda-forge.org/ conda-forge]; there is no need to compile the toolkit
by hand. Create the environment once:

<syntaxhighlight lang="bash">
module load conda
conda create -n geant4 -c geant4 numpy scipy matplotlib
</syntaxhighlight>

and load it in every subsequent session (interactive shell or batch script):

<syntaxhighlight lang="bash">
module load conda
conda activate geant4
</syntaxhighlight>

Activating the environment sets the Geant4 data-library variables
(<code>G4NEUTRONHPDATA</code>, <code>G4PARTICLEXSDATA</code>, …), so — unlike a
manual install — there is no <code>geant4.sh</code> to source. Version 11.4 is the version used so far.

== Building the application ==

CMake locates the conda-provided Geant4 through <code>CMAKE_PREFIX_PATH</code>,
which is pointed at the active environment via <code>$CONDA_PREFIX</code>:

<syntaxhighlight lang="bash">
module load conda
conda activate geant4

mkdir -p build && cd build
cmake -DCMAKE_PREFIX_PATH=$CONDA_PREFIX ..
make -j$(nproc)
</syntaxhighlight>

It can be use full to contain this in e.g. a <code>build.sh</code>, scripts, which builds the simulation and copies the resulting <code>cu67_sim</code> executable to the
project root.

== Macros and templates ==

What is simulated is set by macro files:

<syntaxhighlight lang="bash">
./cu67_sim run.mac
</syntaxhighlight>

or interactively (with visualisation) by passing no argument.

Two points to keep in mind are:

* Commands that alter the geometry (e.g. <code>/det/converter/halfThickness</code>) must appear before <code>/run/initialize</code>, because the geometry is built when the run is initialised. Beam and run commands (<code>/gun/…</code>, <code>/run/beamOn</code>) come after.
* Multithreaded runs are requested with <code>/run/numberOfThreads N</code>. Note that high-precision (HP) physics data can cost ~1–2 GB per worker thread, which matters for the memory requested via SLURM.

For parameter scans the macro is kept as a template (<code>run.mac.tpl</code>)
with Python <code>str.format</code> placeholders, which the driver substitutes at
run time:

<syntaxhighlight lang="text">
/det/converter/halfThickness {HALF_THICKNESS_MM} mm
/analysis/setFileName {OUTPUT_BASE}

/run/initialize

/gun/particle e-
/gun/energy {BEAM_ENERGY_MEV} MeV
/gun/position 0 0 -5 cm
/gun/direction 0 0 1

/tracking/verbose 0
/run/beamOn {N_EVENTS}
</syntaxhighlight>

Caveat: <code>/analysis/setFileName</code> treats text after the last dot
as a file extension, so output base names must not contain dots (e.g. encode
"1.0 mm" as a tag like <code>t1000um</code>).

== Python drivers ==

Python can be used to run everything together. For a single-machine scan
(<code>scan_thickness.py</code>) each grid point:

# renders <code>run.mac.tpl</code> into a concrete macro with the point's parameters;
# runs the executable and captures stdout;
# merges the per-thread CSV output and moves it into the output directory;
# parses the result from stdout with a regex.

At the end it writes a summary CSV and the plots.

== Running scans with SLURM ==

Parameter scans are submitted as job arrays: the driver
(<code>scan_thickness_slurm.py</code>) runs one grid point per array task,
indexed by <code>$SLURM_ARRAY_TASK_ID</code>, with each task using
<code>$SLURM_CPUS_PER_TASK</code> Geant4 worker threads. The batch script:

<syntaxhighlight lang="bash">
#!/bin/bash
#SBATCH --job-name cu67_scan
#SBATCH --partition meggie
#SBATCH --account meggie
#SBATCH --time 12:00:00
#SBATCH --output log/scan_%A_%a.out
#SBATCH --error log/scan_%A_%a.err
#SBATCH --array 0-39
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 4
#SBATCH --mem-per-cpu 1G
#SBATCH --mail-type END,FAIL
#SBATCH --mail-user user@mail.de

module load conda
conda activate geant4

cd /path/to/project

srun /usr/bin/nice -n +19 \
python3 scan_thickness_slurm.py \
--task-id ${SLURM_ARRAY_TASK_ID} \
--threads ${SLURM_CPUS_PER_TASK}
</syntaxhighlight>

Submit it (creating the log directory first) with:

<syntaxhighlight lang="bash">
mkdir -p log && sbatch scan_thickness.slurm
</syntaxhighlight>

A few points are relevant for running simulations on the cluster:

* The <code>--array</code> range must span the number of grid points (0–39 here = 40 points). Keep it in sync with the grid defined in the driver.
* Isolated working directories. Each task runs in its own work directory, so the flat per-thread CSVs of concurrently running tasks never collide.
* Rather than 40 tasks appending to one summary file, each task writes its single result row atomically to <code>rows/<tag>.csv</code>.
* A point whose row file already exists is skipped, so a partially failed array can simply be resubmitted.
* <code>nice -n +19</code> keeps the jobs from crowding out interactive use of the node.

== Collecting and plotting ==

After the array finishes, a single collect step merges the per-task row
files into the summary table and draws the plots (this is the step that needs
matplotlib):

<syntaxhighlight lang="bash">
python3 scan_thickness_slurm.py --collect
</syntaxhighlight>

It can also be chained as a dependent job so it runs automatically once the
array completes:

<syntaxhighlight lang="bash">
sbatch --dependency=afterany:<jobid> --ntasks 1 \
--wrap "python3 scan_thickness_slurm.py --collect"
</syntaxhighlight>

If interest lies not in exploring the parameter but to maximize statistics for a single simulation, the parameters just need to be kept constant and the results of identical simulations merged in the end.

== Summary ==

{| class="wikitable"
! Step !! Command
|-
| Load Geant4 || <code>module load conda && conda activate geant4</code>
|-
| Build || <code>cmake -DCMAKE_PREFIX_PATH=$CONDA_PREFIX .. && make -j</code>
|-
| Single run || <code>./cu67_sim run.mac</code>
|-
| Submit scan || <code>mkdir -p log && sbatch scan_thickness.slurm</code>
|-
| Collect + plot || <code>python3 scan_thickness_slurm.py --collect</code>
|}

[[Category:Software]]

Sun (Observations)

Prucker — Tue, 14 Jul 2026 12:18:15 GMT

With the ASI1600MM PRO camera (this is a work done in progress)

Sun (Observations)

Canal — Tue, 14 Jul 2026 08:36:54 GMT

With the ASI1600MM PRO camera (this is a work done in progress)

Guided Tours and Public Outreach

Zalot — Wed, 08 Jul 2026 05:43:06 GMT

Tours looking for a guide

@@ Line 94: / Line 94: @@
 Contact person: Max, Nico
-We coordinate commuting for the carpool via the app [https://www.michael-obach.de MyCarpoolApp], which is available on Android and iOS. We use a group account with the name "Remeis Reloaded". The access password is Sternwartstr. 7 . By using "change user" in the menu you can create your user account. The fuel costs are shared equally by everybody in the car. In addition to the fuel costs there is a rate of 2.50€ per car per ride, which is also shared equally by everybody. This is used to reduce the driver's additional costs, like maintenance and such.
+We coordinate commuting for the carpool via the app [https://www.michael-obach.de MyCarpoolApp], which is available on Android and iOS. We use a group account with the name "Remeis Reloaded". The access password is "Sternwartstr. 7". By using "change user" in the menu you can create your user account. The fuel costs are shared equally by everybody in the car. In addition to the fuel costs there is a rate of 2.50€ per car per ride, which is also shared equally by everybody. This is used to reduce the driver's additional costs, like maintenance and such.
 =Lunch=

@@ Line 1: / Line 1: @@
 == GIT repository ==
-   git clone phoenix.sternwarte.uni-erlangen.de:/data/git/Praktikumsanleitung.git
+   git clone serpens.sternwarte.uni-erlangen.de:/data/git/Praktikumsanleitung.git
    cd Praktikumsanleitung
    cd anleitung

← Older revision	Revision as of 13:12, 30 July 2026
(One intermediate revision by the same user not shown)
(No difference)

@@ Line 160: / Line 160: @@
 ! Observing
 ! Deadline for guides
 |-

@@ Line 90: / Line 90: @@
 * LS60Ha telescope obviously
 * Eyepiece (8-21mm I believe) found inside the case of the telescope.
-* Tripod + EQ mount.
+* Tripod + EQ6 Pro mount.
-* "Black mount" (CELESTRON CGEM DX) as an alternative to the tripod.
+* "Black mount" (CELESTRON CGEM DX) and concrete pillar as an alternative to the tripod.
 * Weights and extensions for balancing.
 * Cables and electricity box for connecting to the mount.
@@ Line 113: / Line 113: @@
 * ASI1600MM PRO camera
 * LS60T Ha telescope
-* Mount or tripod
+* Mount and/or tripod
 * M42 connector
 * T2 connector (We managed with the Nikon T2 connector)
-* Cables and electricity box
+* Cables and electricity box (2 Usb cables and 2 power cables for the mount and the camera)
-* Laptop with ... program
+* Laptop with '''[https://kstars-docs.kde.org/en/ kstars]''' and '''[https://www.firecapture.de/ FireCapture]''' available
 To attach the camera to the telescope first take out the ocular adapter from the diagonal. What we found that worked is to attach the T2 to the diagonal and the M42 attachment between the T2 and the camera.
@@ Line 126: / Line 126: @@
 '''This entry now needs to be completed with a bit of info about the program used for taking the images :)'''

@@ Line 3: / Line 3: @@
 This page describes a practical workflow for building and running
 [https://geant4.web.cern.ch/ Geant4] Monte-Carlo simulations on the Remeis
-compute cluster, using SLURM for parameter scans and conda to provide the
+cluster, using SLURM for longer runs and conda to provide the
-Geant4 toolkit. The examples are taken from ''Cu67'' simulations,
+Geant4 package itself. The examples are taken from ''Cu67'' simulations,
 but the mechanics apply to any Geant4 application.
 == Overview ==
-A Geant4 simulation on the cluster involves three steps, although the last step is optional:
+A Geant4 simulation involves three steps, although the last step is optional:
 * the compiled Geant4 application (a C++ executable, here <code>cu67_sim</code>);
@@ Line 183: / Line 183: @@
 If interest lies not in exploring the parameter but to maximize statistics for a single simulation, the parameters just need to be kept constant and the results of identical simulations merged in the end.

@@ Line 1: / Line 1: @@
-	= Running Geant4 simulations on the Remeis cluster =
+= Running Geant4 simulations on the Remeis cluster =
 This page describes a practical workflow for building and running
@@ Line 26: / Line 26: @@
 <syntaxhighlight lang="bash">
 module load conda
-conda create -n geant4 -c geant4 numpy scipy matplotlib
+conda create -n geant4 -c conda-forge geant4 numpy scipy matplotlib
 </syntaxhighlight>
-and load it in every subsequent session (interactive shell or batch script):
+This might take a while. Afterwards, you can load it in every subsequent session (interactive shell or batch script) -- you might also place the following into you .bashrc /.cshrc:
 <syntaxhighlight lang="bash">
@@ Line 41: / Line 41: @@
 == Building the application ==
 CMake locates the conda-provided Geant4 through <code>CMAKE_PREFIX_PATH</code>,
-which is pointed at the active environment via <code>$CONDA_PREFIX</code>:
+which is pointed at the active environment via <code>$CONDA_PREFIX</code>:´. And the application can be compiled via:
 <syntaxhighlight lang="bash">
@@ Line 54: / Line 66: @@
 </syntaxhighlight>
-It can be use full to contain this in e.g. a <code>build.sh</code>, scripts, which builds the simulation and copies the resulting <code>cu67_sim</code> executable to the
+It can be usefull to package these, e.g. in a <code>build.sh</code>, scripts, which builds the simulation and copies the resulting <code>cu67_sim</code> executable to the
-project root.
+project root - or use a makefile.
 == Macros and templates ==
@@ Line 95: / Line 107: @@
 "1.0 mm" as a tag like <code>t1000um</code>).
-== Python drivers ==
+== Python Wrapper ==
-Python can be used to run everything together. For a single-machine scan
+Python can be useful to run everything together. To can e.g. several simulations on a grid of parameters. A script can be used that:
 # renders <code>run.mac.tpl</code> into a concrete macro with the point's parameters;
@@ Line 109: / Line 120: @@
 == Running scans with SLURM ==
-Parameter scans are submitted as job arrays: the driver
+For longer simulations it is best to use SLURM. Parameter scans are submitted as job arrays: the python script called by srun runs the simulation for one grid point per array task,
 indexed by <code>$SLURM_ARRAY_TASK_ID</code>, with each task using
-<code>$SLURM_CPUS_PER_TASK</code> Geant4 worker threads. The batch script:
+<code>$SLURM_CPUS_PER_TASK</code> Geant4 worker threads. The batch script. More CPUS per task can be used but as they all need to be available simultaneously, SLURM might delay the scheduling of the job:
 <syntaxhighlight lang="bash">
@@ Line 140: / Line 150: @@
 </syntaxhighlight>
-Submit it (creating the log directory first) with:
+Submit it with:
 <syntaxhighlight lang="bash">
-mkdir -p log && sbatch scan_thickness.slurm
+ sbatch scan_thickness.slurm
 </syntaxhighlight>
@@ Line 150: / Line 160: @@
 * The <code>--array</code> range must span the number of grid points (0–39 here = 40 points). Keep it in sync with the grid defined in the driver.
 * Isolated working directories. Each task runs in its own work directory, so the flat per-thread CSVs of concurrently running tasks never collide.
-* Rather than 40 tasks appending to one summary file, each task writes its single result row atomically to <code>rows/&lt;tag&gt;.csv</code>.
+* Rather than 40 tasks appending to one summary file, each task writes its single result to <code>rows/&lt;tag&gt;.csv</code>.
 * <code>nice -n +19</code> keeps the jobs from crowding out interactive use of the node.

← Older revision		Revision as of 08:36, 14 July 2026
(5 intermediate revisions by the same user not shown)
Line 80:		Line 80:
	\|sunny		\|sunny
	\|}		\|}
		+
		+	== Setup using the Lunt LS60T Ha ==
		+	This is a summary of the setup for solar observations using the LS60T telescope. It would be nice to eventually update it with images of the parts/setups as a visual reference, as some of the descriptions can be a bit weird to understand.
		+
		+	'''Note:''' The telescope has two filters, one on the tube and a second one in the diagonal, so always make sure you are using both!
		+
		+	===Eye observations ===
		+	Items you will need:
		+	* LS60Ha telescope obviously
		+	* Eyepiece (8-21mm I believe) found inside the case of the telescope.
		+	* Tripod + EQ mount.
		+	* "Black mount" (CELESTRON CGEM DX) as an alternative to the tripod.
		+	* Weights and extensions for balancing.
		+	* Cables and electricity box for connecting to the mount.
		+	With all of these you are now ready to start :)
		+
		+	If you chose to use the "black mount", congratulations, you chose easy setup difficulty! The mount can be put up on top of the pillar next to the barbecue place. The screws are put in a way that the mount is already polar aligned once put correctly. Attach the telescope with the eyepiece. For balancing with the CGEM, a small extension (also used in the labs) is enough for the telescope + ocular.
		+
		+	To align, chose the '''Solar System Align''' option. Then, the SELECT OBJECT message will appear on the top row of the control. Use the up and down scroll keys to select the daytime object: choose Sun and press ENTER. Use the direction arrow buttons to carefully center the object in the finderscope (the sun light circle should be roughly on the upper right of the finder). Press ENTER once centered. Finally, center the Sun in the eyepiece and press ALIGN. Detailed information can be found in the '''mount [https://www.fhsu.edu/physics/documents/CGEM-DX-Instruction-Manual.pdf manual]'''.
		+
		+	Once the alignment is completed we can focus. To be able to focus the telescope you have to pull out the focusing length by half. You will notice the diagonal tube is especially long. That is because you have to attach it pulling it out roughly 3.5 cm from it's innermost position. Once you have this setup you can start looking through the ocular and use the wheels to adjust the focusing position until the Sun looks like a sharp circle.
		+
		+	Once the Sun is sharp, you can start playing around with the lateral screw, which changes the pressure of the filter, and change it until you are able to discern the different substructures of the Sun (rough surface, filaments, light spots, black spots, flares). You can find more information about the telescope and focusing setup in the '''telescope [https://cdn.shopify.com/s/files/1/0615/8273/7521/files/LS60THaPT_Solar_Telescope_Manual_vMAY-2016.pdf?v=1748274315 manual]'''
		+
		+	And you are ready! Have fun observing the Sun!
		+
		+	PS: If you change the focal length of the ocular you will have to adjust the focus slightly, but it is worth to see better the surface elements!
		+
		+	=== With the ASI1600MM PRO camera (this is a work done in progress) ===
		+
		+	You will need the following:
		+	* ASI1600MM PRO camera
		+	* LS60T Ha telescope
		+	* Mount or tripod
		+	* M42 connector
		+	* T2 connector (We managed with the Nikon T2 connector)
		+	* Cables and electricity box
		+	* Laptop with ... program
		+
		+	To attach the camera to the telescope first take out the ocular adapter from the diagonal. What we found that worked is to attach the T2 to the diagonal and the M42 attachment between the T2 and the camera.
		+
		+	I will assume you have read the previous part and have balanced and aligned the telescope + camera setup (in this case for minor adjustments in the alignment use the camera view instead of your eye).
		+
		+	For focusing, we achieved focus having the diagonal taken out roughly 2 cm from the innermost position and starting with the focus at the middle point. From there you can play around with the screws until you achieve a sharp edge of the Sun.
		+
		+	'''This entry now needs to be completed with a bit of info about the program used for taking the images :)'''