From 64bbf9d19fc5fb4f2702f8ac35b1fbc618e0952c Mon Sep 17 00:00:00 2001
From: Martin Schroschk <martin.schroschk@tu-dresden.de>
Date: Thu, 29 Jul 2021 08:30:42 +0200
Subject: [PATCH] WIP: Review (layout done, commands untested)
---
.../docs/software/mathematics.md | 330 +++++++++---------
.../docs/software/misc}/Mathematica-Fonts.zip | Bin
doc.zih.tu-dresden.de/mkdocs.yml | 2 +-
3 files changed, 175 insertions(+), 157 deletions(-)
rename {Compendium_attachments/Mathematics => doc.zih.tu-dresden.de/docs/software/misc}/Mathematica-Fonts.zip (100%)
diff --git a/doc.zih.tu-dresden.de/docs/software/mathematics.md b/doc.zih.tu-dresden.de/docs/software/mathematics.md
index bd127067f..a348fbbc7 100644
--- a/doc.zih.tu-dresden.de/docs/software/mathematics.md
+++ b/doc.zih.tu-dresden.de/docs/software/mathematics.md
@@ -1,161 +1,185 @@
# Mathematics Applications
- The following applications are
-installed at ZIH:
+!!! cite
+
+ Nature is written in mathematical language.
-| | | | | |
-|-----------------|-----------|------------|------------|-------------|
-| | **Venus** | **Triton** | **Taurus** | **module** |
-| **Mathematica** | | | x | Mathematica |
-| **Matlab** | | x | x | MATLAB |
-| **Octave** | | | | |
-| **R** | | x | x | r |
+ (Galileo Galilei)
-*Please do not run expensive interactive sessions on the login nodes.
-Instead, use* `srun --pty ...` *to let the batch system place it on a
-compute node.*
+<!--*Please do not run expensive interactive sessions on the login nodes. Instead, use* `srun --pty-->
+<!--...` *to let the batch system place it on a compute node.*-->
## Mathematica
-Mathematica is a general computing environment, organizing many
-algorithmic, visualization, and user interface capabilities within a
-document-like user interface paradigm.
-
-To remotely use the graphical frontend one has to add the Mathematica
-fonts to the local fontmanager.
-
-For a Linux workstation:
-
- scp -r taurus.hrsk.tu-dresden.de:/sw/global/applications/mathematica/10.0/SystemFiles/Fonts/Type1/ ~/.fonts
- xset fp+ ~/.fonts/Type1
-
-For a Windows workstation:
-You have to add additional mathematica fonts at your local PC. At the
-end of this webpage you can find an archive with these fonts (.zip)
-
-If you use **Xming** as X-server at your PC (see also our Information
-about Remote access from Windos to Linux):
-1 Create a new folder "Mathematica" in the diretory "fonts" of the
-installation directory of Xming. (mostly: C:\\Programme\\Xming\\fonts\\)
-1 Extract the fonts archive into this new directory "Mathematica".
-In result you should have 2 directories "DBF" and "Type1".
-1 Add the path to these font files into the file "font-dirs".
-You can find it in C:\\Programme\\Xming\\.
-
- # font-dirs
- # comma-separated list of directories to add to the default font path
- # defaults are built-ins, misc, TTF, Type1, 75dpi, 100dpi
- # also allows entries on individual lines
- C:\Programme\Xming\fonts\dejavu,C:\Programme\Xming\fonts\cyrillic
- C:\Programme\Xming\fonts\Mathematica\DBF
- C:\Programme\Xming\fonts\Mathematica\Type1
- C:\WINDOWS\Fonts
-
-**Mathematica and SLURM:** \<br />Please use the Batchsystem SLURM for
-running calculations. This is a small example for a batch script, that
-you should prepair and start with command \<br />sbatch
-\<scriptname>\<br />File "mathtest.m" is your input script, that
-includes the calculation statements for mathematica. File
-"mathtest.output" will collect the results of your calculation.
-
- #!/bin/bash <br />#SBATCH --output=mathtest.out <br />#SBATCH --error=mathtest.err <br />#SBATCH --time=00:05:00 <br />#SBATCH --ntasks=1 <br /><br />module load Mathematica <br />math -run < mathtest.m > mathtest.output
-
-(also
-<https://rcc.uchicago.edu/docs/software/environments/mathematica/index.html>)
-
-**%RED%NOTE:%ENDCOLOR%** Mathematica licenses are limited. There exist
-two types, MathKernel and SubMathKernel licenses. Every sequential job
-you start will consume a MathKernel license of which we only have 39. We
-do have, however, 312 SubMathKernel licenses, so please, don't start
-many sequential jobs but try to parallelize your calculation, utilizing
-multiple Sub MathKernel licenses per job, in order to achieve a more
-reasonable license usage.
-
-## Matlab
-
-MATLAB is a numerical computing environment and programming language.
-Created by The MathWorks, MATLAB allows easy matrix manipulation,
-plotting of functions and data, implementation of algorithms, creation
-of user interfaces, and interfacing with programs in other languages.
-Although it specializes in numerical computing, an optional toolbox
-interfaces with the Maple symbolic engine, allowing it to be part of a
-full computer algebra system.
-
-Running MATLAB via the batch system could look like this (for 456 MB RAM
-per core and 12 cores reserved). Please adapt this to your needs!
-
-- SLURM (taurus, venus):
-
-<!-- -->
-
- module load MATLAB<br /> srun -t 8:00 -c 12 --mem-per-cpu=456 --pty --x11=first bash<br /> matlab
+Mathematica is a general computing environment, organizing many algorithmic, visualization, and user
+interface capabilities within a document-like user interface paradigm.
+
+### Fonts
+
+To remotely use the graphical frontend you have to add the Mathematica fonts to the local
+fontmanager.
+
+#### Linux Workstation
+
+You need to copy the fonts from ZIH systems to your local system and expand the font path
+
+```bash
+localhost$ scp -r taurus.hrsk.tu-dresden.de:/sw/global/applications/mathematica/10.0/SystemFiles/Fonts/Type1/ ~/.fonts
+localhost$ xset fp+ ~/.fonts/Type1
+```
+
+#### Windows Workstation
+
+You have to add additional Mathematica fonts at your local PC
+[download fonts archive](misc/Mathematica-Fonts.zip).
+
+If you use **Xming** as X-server at your PC (refer to
+[remote access from Windows](../access/ssh_mit_putty.md), follow these steps:
+
+1. Create a new folder `Mathematica` in the diretory `fonts` of the installation directory of Xming
+ (mostly: `C:\\Programme\\Xming\\fonts\\`)
+1. Extract the fonts archive into this new directory `Mathematica`. In result you should have the
+ two directories `DBF` and `Type1`.
+1. Add the path to these font files into the file `font-dirs`. You can find it in
+ `C:\\Programme\\Xming\\`.
+
+```shell-session
+# font-dirs
+# comma-separated list of directories to add to the default font path
+# defaults are built-ins, misc, TTF, Type1, 75dpi, 100dpi
+# also allows entries on individual lines
+C:\Programme\Xming\fonts\dejavu,C:\Programme\Xming\fonts\cyrillic
+C:\Programme\Xming\fonts\Mathematica\DBF
+C:\Programme\Xming\fonts\Mathematica\Type1
+C:\WINDOWS\Fonts
+```
+
+### Mathematica and Slurm
+
+Please use the batchsystem Slurm for running calculations. This is a small example for a batch
+script, that you should prepare and start with the command `sbatch <scriptname>`. The File
+`mathtest.m` is your input script that includes the calculation statements for Mathematica. The file
+`mathtest.output` will hold the results of your calculations.
+
+```bash
+#!/bin/bash
+#SBATCH --output=mathtest.out
+#SBATCH --error=mathtest.err
+#SBATCH --time=00:05:00
+#SBATCH --ntasks=1
+
+module load Mathematica
+math -run < mathtest.m > mathtest.output
+```
+
+(also [Link](https://rcc.uchicago.edu/docs/software/environments/mathematica/index.html)).
+
+!!! note
+
+ Mathematica licenses are limited.
+
+There exist two types, MathKernel and SubMathKernel licenses. Every sequential job you start will
+consume a MathKernel license of which we only have 39. We do have, however, 312 SubMathKernel
+licenses, so please, don't start many sequential jobs but try to parallelize your calculation,
+utilizing multiple SubMathKernel licenses per job, in order to achieve a more reasonable license
+usage.
+
+## MATLAB
+
+[MATLAB](https://de.mathworks.com/products/matlab.html) is a numerical computing environment and
+programming language. Created by The MathWorks, MATLAB allows easy matrix manipulation, plotting of
+functions and data, implementation of algorithms, creation of user interfaces, and interfacing with
+programs in other languages. Although it specializes in numerical computing, an optional toolbox
+interfaces with the Maple symbolic engine, allowing it to be part of a full computer algebra system.
+
+Running MATLAB via the batch system could look like this (for 456 MB RAM per core and 12 cores
+reserved). Please adapt this to your needs!
+
+```bash
+zih$ module load MATLAB
+zih$ srun -t 8:00 -c 12 --mem-per-cpu=456 --pty --x11=first bash
+zih$ matlab
+```
With following command you can see a list of installed software - also
the different versions of matlab.
- module avail
+```bash
+zih$ module avail
+```
-Please choose one of these, then load the chosen software with the
-command:
+Please choose one of these, then load the chosen software with the command:
- module load MATLAB/version
+```bash
+zih$ module load MATLAB/version
+```
Or use:
- module load MATLAB
+```bash
+zih$ module load MATLAB
+```
+
+(then you will get the most recent Matlab version.
+[Refer to the modules section for details.](../software/runtime_environment.md#modules))
+
+### Interactive
-(then you will get the most recent Matlab version. [Refer to the modules
-section for details.](../software/runtime_environment.md#Modules))
+If X-server is running and you logged in at ZIH systems, you should allocate a CPU for your work
+with command
-### matlab interactive
+```bash
+zih$ srun --pty --x11=first bash
+```
-\* if X-server is running and you logged in at the HPC systems, you
-should allocate a CPU for your work with command \<pre> srun --pty
---x11=first bash \</pre>
+- now you can call "matlab" (you have 8h time to work with the matlab-GUI)
-- now you can call "matlab" (you have 8h time to work with the
- matlab-GUI)
+### Non-interactive
-### matlab with script
+Using Scripts
-- you have to start matlab-calculation as a Batch-Job via command
+You have to start matlab-calculation as a Batch-Job via command
-<!-- -->
+```bash
+srun --pty matlab -nodisplay -r basename_of_your_matlab_script #NOTE: you must omit the file extension ".m" here, because -r expects a matlab command or function call, not a file-name.
+```
- srun --pty matlab -nodisplay -r basename_of_your_matlab_script #NOTE: you must omit the file extension ".m" here, because -r expects a matlab command or function call, not a file-name.
+!!! info "License occupying"
-**%RED%NOTE:%ENDCOLOR%** while running your calculations as a script
-this way is possible, it is generally frowned upon, because you are
-occupying Matlab licenses for the entire duration of your calculation
-when doing so. Since the available licenses are limited, it is highly
-recommended you first compile your script via the Matlab Compiler (mcc)
-before running it for a longer period of time on our systems. That way,
-you only need to check-out a license during compile time (which is
-relatively short) and can run as many instances of your calculation as
-you'd like, since it does not need a license during runtime when
-compiled to a binary.
+ While running your calculations as a script this way is possible, it is generally frowned upon,
+ because you are occupying Matlab licenses for the entire duration of your calculation when doing so.
+ Since the available licenses are limited, it is highly recommended you first compile your script via
+ the Matlab Compiler (mcc) before running it for a longer period of time on our systems. That way,
+ you only need to check-out a license during compile time (which is relatively short) and can run as
+ many instances of your calculation as you'd like, since it does not need a license during runtime
+ when compiled to a binary.
You can find detailled documentation on the Matlab compiler at
-Mathworks: <https://de.mathworks.com/help/compiler/>
+[Mathworks' help pages](https://de.mathworks.com/help/compiler/).
-### using the matlab compiler (mcc)
+### Using the MATLAB Compiler (mcc)
-- compile your .m script to a binary: \<pre>mcc -m
- name_of_your_matlab_script.m -o compiled_executable -R -nodisplay -R
- -nosplash\</pre>
+Compile your `.m` script into a binary:
-This will also generate a wrapper script called
-run_compiled_executable.sh which sets the required library path
-environment variables in order to make this work. It expects the path to
-the Matlab installation as an argument, you can use the environment
-variable $EBROOTMATLAB as set by the module file for that.
+```bash
+mcc -m name_of_your_matlab_script.m -o compiled_executable -R -nodisplay -R -nosplash
+```
-- then run the binary via the wrapper script in a job (just a simple
- example, you should be using an [sbatch
- script](../jobs_and_resources/slurm.md#Job_Submission) for that): \<pre>srun
- ./run_compiled_executable.sh $EBROOTMATLAB\</pre>
+This will also generate a wrapper script called `run_compiled_executable.sh` which sets the required
+library path environment variables in order to make this work. It expects the path to the MATLAB
+installation as an argument, you can use the environment variable `$EBROOTMATLAB` as set by the
+module file for that.
-### matlab parallel (with 'local' configuration)
+Then run the binary via the wrapper script in a job (just a simple example, you should be using an
+[sbatch script](../jobs_and_resources/slurm.md#job-submission) for that)
+
+```bash
+zih$ srun ./run_compiled_executable.sh $EBROOTMATLAB
+```
+
+### Parallel MATLAB
+
+#### With 'local' Configuration
- If you want to run your code in parallel, please request as many
cores as you need!
@@ -165,46 +189,40 @@ variable $EBROOTMATLAB as set by the module file for that.
- inside use \<pre>matlabpool open 4\</pre> to start parallel
processing
-<!-- -->
-
- example for 1000\*1000 matrixmutliplication
-<!-- -->
+!!! example
- R = distributed.rand(1000);
- D = R * R
+ ```bash
+ R = distributed.rand(1000);
+ D = R * R
+ ```
- to close parallel task:
+`matlabpool close`
-<!-- -->
+#### With Parfor
- matlabpool close
+- start a batch job with the number N of processes (e.g. N=12)
+- inside use `matlabpool open N` or
+ `matlabpool(N)` to start parallel processing. It will use
+ the 'local' configuration by default.
+- Use 'parfor' for a parallel loop, where the **independent** loop
+ iterations are processed by N threads
-### matlab parallel (with parfor)
+!!! example
-- start a batch job with the number N of processes (e.g. N=12)
-- inside use \<pre>matlabpool open N\</pre> or
- \<pre>matlabpool(N)\</pre> to start parallel processing. It will use
- the 'local' configuration by default.
-- Use 'parfor' for a parallel loop, where the **independent** loop
- iterations are processed by N threads
-- Example:
+ ```bash
+ parfor i = 1:3
+ c(:,i) = eig(rand(1000));
+ end
+ ```
-<!-- -->
-
- parfor i = 1:3
- c(:,i) = eig(rand(1000));
- end
-
-- see also \<pre>help parfor\</pre>
+Please refer to the documentation `help parfor` for further information.
## Octave
-GNU Octave is a high-level language, primarily intended for numerical
-computations. It provides a convenient command line interface for
-solving linear and nonlinear problems numerically, and for performing
-other numerical experiments using a language that is mostly compatible
-with Matlab. It may also be used as a batch-oriented language.
-
-- [Mathematica-Fonts.zip]**todo**(%ATTACHURL%/Mathematica-Fonts.zip):
- Mathematica-Fonts
+GNU [Octave](https://www.gnu.org/software/octave/index) is a high-level language, primarily intended
+for numerical computations. It provides a convenient command line interface for solving linear and
+nonlinear problems numerically, and for performing other numerical experiments using a language that
+is mostly compatible with Matlab. It may also be used as a batch-oriented language.
diff --git a/Compendium_attachments/Mathematics/Mathematica-Fonts.zip b/doc.zih.tu-dresden.de/docs/software/misc/Mathematica-Fonts.zip
similarity index 100%
rename from Compendium_attachments/Mathematics/Mathematica-Fonts.zip
rename to doc.zih.tu-dresden.de/docs/software/misc/Mathematica-Fonts.zip
diff --git a/doc.zih.tu-dresden.de/mkdocs.yml b/doc.zih.tu-dresden.de/mkdocs.yml
index 4fffe2650..13a7a1e8c 100644
--- a/doc.zih.tu-dresden.de/mkdocs.yml
+++ b/doc.zih.tu-dresden.de/mkdocs.yml
@@ -36,6 +36,7 @@ nav:
- Overview: software/applications_overview.md
- Bio Informatics: software/bioinformatics.md
- Computational Fluid Dynamics (CFD): software/cfd.md
+ - Mathematics: software/mathematics.md
- Nanoscale Simulations: software/nanoscale_simulations.md
- FEM Software: software/fem_software.md
- Visualization: software/visualization.md
@@ -70,7 +71,6 @@ nav:
- Perf Tools: software/perf_tools.md
- PIKA: software/pika.md
- Vampir: software/vampir.md
- - Mathematics: software/mathematics.md
- Data Life Cycle Management:
- Overview: data_lifecycle/overview.md
- Filesystems:
--
GitLab