Software skeleton-page: Difference between revisions

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&#124; = Pipe-Zeichen
&#124; = Pipe-Zeichen

Interne Verlinkungen benutzen. Syntax: [[#Ueberschrift|Link-Text]]

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|-
|-
| Availability
| Availability
| [[bwUniCluster]] &#124; [[BwForCluster_Chemistry]]
| [[bwUniCluster]] &#124; [[BwForCluster_Chemistry]]
<!-- Verfuegbare Cluster (soweit bekannt):
<!-- List of all available Systems (so far): [[bwUniCluster]] [[bwForCluster ENM]], [[bwForCluster MLS/WISO]], [[BwForCluster_Chemistry]], [[bwForCluster BinAC]] -->
[[bwUniCluster]] [[bwForCluster ENM]], [[BwForCluster_Chemistry]], [[bwForCluster BinAC]] -->
|-
|-
| License
| License
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| Citing
| Citing
| <small><small><pre>Citing-informations here</pre></small></small>
| <small><small><pre>Citing-informations here</pre></small></small>
oder [link to citing-information or citing-description]
or [link to citing-information or citing-description]
|-
|-
| Links
| Links
| [https://some.homepage.edu SW-Homepage] &#124; [https://some.otherpage.TLD some other pages]
| [https://some.homepage.edu SW-Homepage] &#124; [https://some.otherpage.TLD some other pages] &#124; [https://some.homepage.edu SW-Documentation]
|-
|-
| Graphical Interface
| Graphical Interface
| No &#124; Yes <!-- Yes could link to some x11-forwarding/vnc instructions -->
| No &#124; Yes <!-- Links zur Hardcopy, Beschreibung (X-forwardung, ssh -X ... -->
|-
|-
| Included in module
| Included in module
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<!-- e.g.: mpi/openmpi/1.6.5-gnu-4.8
<!-- e.g.: mpi/openmpi/1.6.5-gnu-4.8
mention if there is more than one software in the module, i.e. icc, ifort and debugger -->
mention if there is more than one software in the module, i.e. icc, ifort and debugger -->
|-
| <font color=red>Updates/News</font>
| Any other infos.... What's new!
|}
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'''Softwarename''' is used for worbeling the worbels. It makes use of advanced flubberdiflaps .
'''Softwarename''' is used for worbeling the worbels. It makes use of advanced flubberdiflaps .
<br>
<br>

This paragraph should give a short description of what the software does and should enable potential new users to decide if this is the software that might help them with their project.
This paragraph should give a short description of what the software does and should enable potential new users to decide if this is the software that might help them with their project.
<br>
<br>
<br>
<br>

= Versions and Availability =
= Versions and Availability =
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
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e.g.: |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/category/softwarename
e.g.: |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/category/softwarename
e.g.: |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/orca
e.g.: |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/orca
Adjust 'height=nnn' to fit the contents without scrolling!
-->
-->
<br>
<br>
Include a direct link to the description in CIS here and remove this line!
Include a direct link to the description in CIS here and remove this line!
<br>EXAMPLE:
{{#widget:Iframe
{{#widget:Iframe
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/gromacs <!-- modify here -->
|url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/gromacs <!-- modify here -->
|width=90%
|width=90%
|height=300
|height=420
|border=1
|border=0
}}
}}
<big><p style="color: red;">Open the above links by using the right mouse button and select "open in a new window" or "open in a new tab".</p></big>
<br>
<br>
Show a list of available versions using 'module avail category/softwarename' on any HPC-C5 cluster.
Show a list of available versions using 'module avail category/softwarename' on any HPC-C5 cluster.
<pre>
<pre>
: EXAMPLE with Gromacs
: EXAMPLE with Gromacs on the bwUniCluster
$ module avail chem/gromacs
$ module avail chem/gromacs
------------------------ /opt/bwhpc/common/modulefiles -------------------------
------------------------ /opt/bwhpc/common/modulefiles -------------------------
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</pre>
</pre>
<br>
<br>

= License =
= License =
Anything specific to the licensing model goes here. If the Program is GPL or one of the over very common free software licenses, you can probably remove this section. Things that should be mentioned here (if they apply)
Anything specific to the licensing model goes here. If the Program is GPL or one of the over very common free software licenses, you can probably remove this section. Things that should be mentioned here (if they apply)
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<br>
<br>
<br>
<br>

= Usage =
= Usage =
== Loading the module ==
== Loading the module ==
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</pre>
</pre>
<br>
<br>

== Program Binaries ==
== Program Binaries ==
Show the location and contents of the installed binaries in the main folder of the software
Show the location and contents of the installed binaries in the main folder of the software
and show some informations, too.
and show some informations, too.
e.g.: After loading the SOFTWARENAME module (''module load category/softwarename/'version''') this path is also set to the local $PATH- and $SOFTWARENAME_BIN_DIR environments.
e.g.: After loading the SOFTWARENAME module (''module load category/softwarename/'version''') this path is also set to the local $PATH- and [[#Software-Specific Environments|$SOFTWARENAME_BIN_DIR]] environments.

<pre>
<pre>
$ls -F (or ls -x) $SOFTWARE_BIN_DIR
$ ls -F (or ls -x) $SOFTWARE_BIN_DIR
... list of content of software-bin-dir ...
... list of content of software-bin-dir ...
$
$
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<br>
<br>
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'.
<br>

<pre>
<pre>
$ cd $(ws_find calc_repo)
$ cd $(ws_find calc_repo)
'your-id'-calc_repo-0]$ pwd
['your-id'-calc_repo-0]$ pwd
/work/workspace/scratch/'your-id'-calc_repo-0
/work/workspace/scratch/'your-id'-calc_repo-0
'your-id'-calc_repo-0]$
['your-id'-calc_repo-0]$
</pre>
</pre>
<br>

In case of multi-node parallel jobs, you might need to create the directory on all nodes used.
In case of multi-node parallel jobs, you might need to create the directory on all nodes used.
<br>
<br>
<br>
<br>

= Moab Submit Examples =
= Moab Submit Examples =
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'
You can copy a simple interactive example to your '''workspace''' and run it, using 'msub'
<br>
<br>
Strictly use the <font color=red>$SOFTWARENAME_EXA_DIR</font> environment-variable!
Strictly use the [[#Software-Specific Environments|$SOFTWARENAME_EXA_DIR]] environment-variable!
<br>
<br>
<pre>
<pre>
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To see a list of all SOFTWARENAME environments set by the 'module load'-command use 'env | grep SOFTWARENAME'<br>
To see a list of all SOFTWARENAME environments set by the 'module load'-command use 'env | grep SOFTWARENAME'<br>
or the command 'module display category/softwarename/version' (you don't need to load the module before!).
or the command 'module display category/softwarename/version' (you don't need to load the module before!).

<pre>
<pre>
# EXAMPLE ONLY
# EXAMPLE ONLY
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ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3
$
</pre>
</pre>
<br>
<br>
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</pre>
</pre>
<br>
<br>

Example
<pre>
<pre>
# EXAMPLE ONLY !!!
: EXAMPLES ONLY !!!
$ module avail chem/orca
$ module avail chem/orca
------------------------------ /opt/bwhpc/common/modulefiles ---------------------------------------
------------------------------ /opt/bwhpc/common/modulefiles ---------------------------------------
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$ module help chem/orca/3.0.1
$ module help chem/orca/3.0.1
----------- Module Specific Help for 'chem/orca/3.0.1' ------------
----------- Module Specific Help for 'chem/orca/3.0.1' ------------

This module provides the quantum chemistry package ORCA version 3.0.1
This module provides the quantum chemistry package ORCA version 3.0.1
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca'
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca'

[...]
[...]

Documentation:
Documentation:
* Max-Planck-Institut fuer Chemische Energiekonversion
* Max-Planck-Institut fuer Chemische Energiekonversion
https://cec.mpg.de/forum/portal.php
https://cec.mpg.de/forum/portal.php

* New features for version 3.0.1
* New features for version 3.0.1
https://cec.mpg.de/forum/portal.php#a3
https://cec.mpg.de/forum/portal.php#a3

* Manuals in pdf format:
* Manuals in pdf format:
/opt/bwhpc/common/chem/orca/3.0.1/manual
/opt/bwhpc/common/chem/orca/3.0.1/manual

* Example data and a Moab example script can be found here:
* Example data and a Moab example script can be found here:
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples
/opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples

[...]
[...]

$
</pre>
</pre>
<br>

<!-- ====================================================
<!-- ====================================================
remove comment to put page in category
remove comment to put page in category

Latest revision as of 13:10, 25 August 2022

Description Content
module load category/name (e.g. chem/orca)
Availability bwUniCluster | BwForCluster_Chemistry
License Link to SW-license-page, GPL ... License
Citing 
Citing-informations here

or [link to citing-information or citing-description]

Links SW-Homepage | some other pages | SW-Documentation
Graphical Interface No | Yes
Included in module catetgory/module/name-dependance | some/more/modules-here
Updates/News Any other infos.... What's new!

Description

Softwarename is used for worbeling the worbels. It makes use of advanced flubberdiflaps .
This paragraph should give a short description of what the software does and should enable potential new users to decide if this is the software that might help them with their project.

Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS
Include a direct link to the description in CIS here and remove this line! {{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/gromacs |width=90% |height=420 |border=0 }}
Show a list of available versions using 'module avail category/softwarename' on any HPC-C5 cluster. 

: EXAMPLE with Gromacs on the bwUniCluster
$ module avail chem/gromacs
------------------------ /opt/bwhpc/common/modulefiles -------------------------
chem/gromacs/4.5.3_gridcount-1.4 chem/gromacs/5.0
chem/gromacs/4.6.2(default)      chem/gromacs/5.0.2
chem/gromacs/4.6.5               chem/gromacs/5.0.5


License

Anything specific to the licensing model goes here. If the Program is GPL or one of the over very common free software licenses, you can probably remove this section. Things that should be mentioned here (if they apply) - does the software use a license server - if yes, how many concurrent licenses can we use - are there other restrictions on the license (most proprietary software run on Universitiescan only be used for non-commercial research or teaching purposes) - Do any other restrictions apply

Usage

Loading the module

You can load the default version of software name with the command 'module load category/softwarename'. Example: 

$ module load category/softwarename

The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for software name. If you wish to load a specific (older) version, you can do so using e.g. $ module load category/softwarename/'version' to load the version you desires. 

# EXAMPLE!
$ module avail chem/orca
------------------------ /opt/bwhpc/common/modulefiles -------------------------
chem/orca/3.0.1 chem/orca/3.0.3
$ module load chem/orca/3.0.1


Program Binaries

Show the location and contents of the installed binaries in the main folder of the software and show some informations, too. e.g.: After loading the SOFTWARENAME module (module load category/softwarename/'version') this path is also set to the local $PATH- and $SOFTWARENAME_BIN_DIR environments. 

$ ls -F (or ls -x) $SOFTWARE_BIN_DIR
... list of content of software-bin-dir ... 
$

What-is-what? Some more explanations here...

Disk Usage / Workspaces

Scratch files are written to the current directory by default. Please change to a local directory before starting your calculations. For example 

$ mkdir -p /tmp/$USER/job_sub_dir 
$ cd /tmp/$USER/job_sub_dir


Better solution: Change to a local directory or to your local workspace (preferred) before starting your calculations.
'calc_repo' is an example name of a repository you created by using the command 'ws_allocate'. 

$ cd $(ws_find calc_repo)
['your-id'-calc_repo-0]$ pwd
/work/workspace/scratch/'your-id'-calc_repo-0
['your-id'-calc_repo-0]$


In case of multi-node parallel jobs, you might need to create the directory on all nodes used.

Moab Submit Examples

You can copy a simple interactive example to your workspace and run it, using 'msub'
Strictly use the $SOFTWARENAME_EXA_DIR environment-variable! 

$ cd $(ws_find 'your_repo_name')
$ cp $SOFTWARENAME_EXA_DIR/bwhpc-'softwarename'-example.moab .
$ cp bwhpc-'softwarename'-example.moab my'softwarename'job.moab 
§ vi my'softwarename'job.moab         # do your own modifications
$ msub my'softwarename'job.moab       # start job submission


Software-Specific Environments

To see a list of all SOFTWARENAME environments set by the 'module load'-command use 'env | grep SOFTWARENAME'
or the command 'module display category/softwarename/version' (you don't need to load the module before!). 

# EXAMPLE ONLY
$ module load chem/orca/3.0.3
$ env | grep ORCA
ORCA_VERSION=3.0.3
ORCA_MAN_DIR=/opt/bwhpc/common/chem/orca/3.0.3/manual
ORCA_EXA_DIR=/opt/bwhpc/common/chem/orca/3.0.3/bwhpc-examples
ORCA_BIN_DIR=/opt/bwhpc/common/chem/orca/3.0.3
ORCA_HOME=/opt/bwhpc/common/chem/orca/3.0.3


Version-Specific Information

For a more detailed information specific to a specific SOFTWARENAME version, see the information available via the module system with the command 

$ module help category/softwarename/'version'


For a small abstract what SOFTWARENAME is about use the command 

$ module whatis category/softwarename/'version'



: EXAMPLES ONLY !!!
$ module avail chem/orca
------------------------------ /opt/bwhpc/common/modulefiles ---------------------------------------
chem/orca/3.0.1 chem/orca/3.0.3

$ module whatis chem/orca/3.0.1
chem/orca/3.0.1      : Quantum chemistry package ORCA, version 3.0.1 
    (command '/opt/bwhpc/common/chem/orca/3.0.1/orca')

$ module help chem/orca/3.0.1
----------- Module Specific Help for 'chem/orca/3.0.1' ------------
This module provides the quantum chemistry package ORCA version 3.0.1
via command '/opt/bwhpc/common/chem/orca/3.0.1/orca' 
[...] 
Documentation: 
*  Max-Planck-Institut fuer Chemische Energiekonversion  
    https://cec.mpg.de/forum/portal.php
*  New features for version 3.0.1
    https://cec.mpg.de/forum/portal.php#a3
*  Manuals in pdf format:
    /opt/bwhpc/common/chem/orca/3.0.1/manual
*  Example data and a Moab example script can be found here:
    /opt/bwhpc/common/chem/orca/3.0.1/bwhpc-examples
[...]


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