Building and running MIMICAv4 on Tetralith

2020-03-19T14:37:54Z

Hamish Struthers (NSC): Created page with "This page describes the building the [https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2013MS000292 MIMICAv4] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith..."

This page describes the building the [https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2013MS000292 MIMICAv4] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system.

MIMICA is a 3D high-resolution model designed for atmospheric applications and written entirely in fortran. The code has been originally developed by Chien Wang at MIT, and later updated and transformed into a true LES model by Julien Savre at Stockholm University. Today, MIMICA is developed under the git version control system and is hosted on the [https://bitbucket.org/matthiasbrakebusch/mimicav4/src/master/ Bitbucket] web-page

;Getting the source code

Once you have a Bitbucket account with the correct permissions to access the MIMICA repository, the MIMICAv4 distribution can be cloned by executing, e.g.:

:<code>git clone --branch tetralith_version https://my-username@bitbucket.org/matthiasbrakebusch/mimicav4.git</code>

Note: choose the tetralith_version branch. If you want to use the master branch, instructions given below.

If space permits, it is recommended that the source files be downloaded into the <tt>/home</tt> file system on Tetralith. This ensures that your code, and configuration files are backed up.

Category:Climate research

2020-03-19T14:17:24Z

Hamish Struthers (NSC): /* How to's: NCS's Tetralith system */

{{research area info
|description=application of computer science methods to study the Earth's climate
}}
{{PAGENAME}} is {{#show: Category:{{PAGENAME}}|?description}}.

== Experts ==
{{list general experts}}

== Software ==
{{list software for category}}

== PRACE Projects ==
:[[Petascaling enabling and support for EC-EARTH3]], (not active)
:[[Performance Benchmark of NEMO Oceanography Code]], (not active)

== SNIC Projects ==
:[[Porting Earth system models to triolith]], (not active)
:[[Develop multi-category LIM3 sea-ice capabilities in EC-Earth 3]], (not active)
:[[NorESM code analysis]], (not active)
:[[EC-Earth compilation and performance analysis: Beskow]], (not active)
:[[Optimization of a lagrangian cloud parcel model for use in the global climate model ECHAM6.1-HAM2.2]], (not active)
:[[Integration of OpenIFS into EC-Earth3]], (not active)
:[[Technical development of the EC-Earth3 Single Column Model (SCM)]], (not active)
:[[Implementation of parallel NetCDF output and COSP in OpenIFS]], (not active)
:[[Configuration of CAM5.3 nudged to ERA-Interim reanalysis and related post-processing software]], (not active)
:[[MIMICA code analysis]], (not active)
:[[EC-Earth/COSP code analysis]], (not active)
:[[Bolin Centre software management through local modules - trial evaluation.]], (active)

== Other Projects ==
:[[HYPE Code Parallelisation]], (not active)
:[[Portability performance analysis and improvement of ESM]], (not active)
:[[Infrastructure for the European Network for Earth System modelling - Phase 2]], (not active)
:[[Nordic collaboration on e-infrastructures for Earth System Modeling]], (active)

== How to's: NCS's Tetralith system ==

:Tetralith [https://www.nsc.liu.se/support/systems/tetralith-getting-started/ getting started]
:[https://www.nsc.liu.se/support/systems/tetralith-dcs-topics/ Tetralith DCS large-scale storage and analysis nodes]
:Applying for SNIC allocations on Tetralith: [http://www.snic.se/resources/ apply for resources].
:Job submission and monitoring, SLURM commands: [http://www.schedmd.com/slurmdocs/quickstart.html quick start user guide]
:[https://dev.ec-earth.org/projects/ecearth3/wiki/Building_EC-Earth_3_on_the_NSC_tetralith_system Building EC-Earth3 on the NSC Tetralith system]
:[[Building CESM 1.2.2.1 Tetralith]]
:[[Building NorESM 1 Tetralith]]
:[[Building CESM 2.1.0 Tetralith]]
:[[Building and running MIMICAv5 on Tetralith]]
:[[Building and running MIMICAv4 on Tetralith]]

== How to's: NCS's Triolith system ==

:Triolith [http://www.nsc.liu.se/systems/triolith/ user guide].
:Applying for SNIC allocations on triolith: [http://www.snic.vr.se/apply-for-resources apply for resources].
:Job submission and monitoring, SLURM commands: [http://www.schedmd.com/slurmdocs/quickstart.html quick start user guide]
:[[Building CESM models on the NSC triolith system]]
:[[Building NorESM (CMIP5) on the NSC triolith system]]
:[https://dev.ec-earth.org/projects/ecearth3/wiki/Building_EC-Earth_3_on_the_NSC_triolith_system Building EC-Earth3 on the NSC triolith system]
:[[EC-Earth and CESM model timings]]
:[[Building interpinic tool for interpolation of land initial conditions for the CESM1.1 model]]
:[[Building and running the COAMPS model on triolith]]
:[[Building mom5.0.2 (modular ocean model) on triolith]]
:[https://www.nsc.liu.se/systems/triolith/software/triolith-software-apps-NCARdiag.html NCAR diagnostics packages on the NSC Triolith system]
:[[CESM & NorESM users on Triolith: changing to the new centre storage (/proj/) system]]
:[[NorESM fix for change to buildenv system (2015-02-16)]]
:[https://redmine.hammoz.ethz.ch/projects/hammoz/wiki/Triolith_NSC Building HAMMOZ on the NSC triolith system]
:[[Building the PORT (Parallel Offline Radiative Transfer) configuration of CESM on Triolith]]
:[[Building and testing WRF on Triolith]]

== How to's: PDC's Beskow system ==

:[https://dev.ec-earth.org/projects/ecearth3/wiki/Building_EC-Earth_3_on_the_PDC_beskow_system Building EC-Earth3 on the PDC Beskow system]
:[[Media:IFS-Beskow.pdf|IFS scaling on Beskow - EC-Earth version 3.1]]
:[[Building CESM models on the PDC Beskow system]]
:[[Media:Beskow3.2beta-report-V2.pdf|EC-Earth 3.2beta scaling and performance analysis report]]
:[[Building MOM (Modular Ocean Model) on the PDC Beskow system]]

Building and running MIMICAv5 on Tetralith

2020-03-09T13:54:41Z

Hamish Struthers (NSC):

This page describes the building the [https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2013MS000292 MIMICAv5] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system.

MIMICA is a 3D high-resolution model designed for atmospheric applications and written entirely in fortran. The code has been originally developed by Chien Wang at MIT, and later updated and transformed into a true LES model by Julien Savre at Stockholm University. Today, MIMICA is developed under the git version control system and is hosted on the [https://bitbucket.org/matthiasbrakebusch/mimicav5 Bitbucket] web-page

;Getting the source code

Once you have a Bitbucket account with the correct permissions to access the MIMICA repository, the MIMICAv5 distribution can be cloned by executing, e.g.:

:<code>git clone https://my-username@bitbucket.org/matthiasbrakebusch/mimicav5.git mimicav5</code>

If space permits, it is recommended that the source files be downloaded into the <tt>/home</tt> file system on Tetralith. This ensures that your code, and configuration files are backed up.

;MIMICA modules

A set of software modules have been installed on Tetralith specifically to try to match as closely as possible the environment used in the model development by Julien. It is recommended that these modules are used for building and running MIMICA on Tetralith to reduce porting problems.

:<code>$ module purge</code>
:<code>$ module load buildenv-intel/2017.u7-bare</code>
:<code>$ module use /proj/bolinc/shared/software/modules</code>
:<code>$ module load netCDF/4.4.1-intel-2017.u7-bare</code>
:<code>$ module load fftw/3.3.8-intel-2017.u7-bare</code>

;Environment variables and Makefile

Loading the modules above sets a number of environment variables (incl. <tt>NETCDF_DIR, FFTW_LIB, FFTW_INC</tt>). The <tt>MIMICA</tt> environment variable must be set to the root path of the MIMICAv5 download (see 'Getting the source code' above), e.g.

:<code>$ export MIMICA=/home/my-tetralith-username/models/mimicav5</code>

A Tetralith specific <tt>Makefile</tt> associated with the above modules can be copied on Tetralith from (<tt>/proj/nsc/users/struthers/Public/MIMICA/Makefile-v5</tt>) to your working folder.

This <tt>Makefile</tt> uses the 'centrally' installed fftw (module fftw/3.3.8-intel-2017.u7-bare).

;The start file

Two environment variables have to be set in the 'start' file specifically for Tetralith + MIMICA modules/environment.

:<code>setenv NETCDF ${NETCDF_DIR}</code>

and

:<code>setenv CMPLER INTEL</code>

;Run file/SLURM settings

The resource request to Tetralith's SLURM batch system should match the domain decomposition defined in the 'start' file. Simply the number of cores (-n in SLURM) should = NPX*NPY from the start file, e.g. if the definitions of NPX and NPY in your start file are:

:<code>setenv NPX 4</code>
:<code>setenv NPY 2</code>

then the number of cores requested in your run script should be:

:<code>#SBATCH -n 8</code>

Building and running MIMICAv5 on Tetralith

2020-03-09T13:28:42Z

Hamish Struthers (NSC):

This page describes the building the [https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2013MS000292 MIMICAv5] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system.

MIMICA is a 3D high-resolution model designed for atmospheric applications and written entirely in fortran. The code has been originally developed by Chien Wang at MIT, and later updated and transformed into a true LES model by Julien Savre at Stockholm University. Today, MIMICA is developed under the git version control system and is hosted on the [https://bitbucket.org/matthiasbrakebusch/mimicav5 Bitbucket] web-page

;Getting the source code

Once you have a Bitbucket account with the correct permissions to access the MIMICA repository, the MIMICAv5 distribution can be cloned by executing, e.g.:

:<code>git clone https://my-username@bitbucket.org/matthiasbrakebusch/mimicav5.git mimicav5</code>

If space permits, it is recommended that the source files be downloaded into the <tt>/home</tt> file system on Tetralith. This ensures that your code, and configuration files are backed up.

;MIMICA modules

A set of software modules have been installed on Tetralith specifically to try to mimic as closely as possible the environment used in the model development by Julien. It is recommended that these modules are used for building and running MIMICA on Tetralith to reduce porting problems.

:<code>$ module purge</code>
:<code>$ module load buildenv-intel/2017.u7-bare</code>
:<code>$ module use /proj/bolinc/shared/software/modules</code>
:<code>$ module load netCDF/4.4.1-intel-2017.u7-bare</code>
:<code>$ module load fftw/3.3.8-intel-2017.u7-bare</code>

;Environment variables, Makefile and start file

Loading the modules above sets a number of environment variables (incl. <tt>NETCDF_DIR, FFTW_LIB, FFTW_INC</tt>). The <tt>MIMICA</tt> environment variable must be set to the root path of the MIMICAv5 download (see 'Getting the source code' above), e.g.

:<code>$ export MIMICA=/home/my-tetralith-username/models/mimicav5</code>

A Tetralith specific Makefile associated with the above modules can be downloaded here or the same file can be copied on Tetralith from (<tt>/proj/nsc/users/struthers/Public/MIMICA/makefile-v5</tt>).

Building and running MIMICAv5 on Tetralith

2020-03-09T09:54:33Z

Hamish Struthers (NSC): Created page with "This page describes the building the [https://agupubs.onlinelibrary.wiley.com/doi/full/10.1002/2013MS000292 MIMICAv5] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith..."

Category:Climate research

2020-03-09T09:15:16Z

Hamish Struthers (NSC): /* How to's: NCS's Tetralith system */

{{research area info
|description=application of computer science methods to study the Earth's climate
}}
{{PAGENAME}} is {{#show: Category:{{PAGENAME}}|?description}}.

== Experts ==
{{list general experts}}

== Software ==
{{list software for category}}

== PRACE Projects ==
:[[Petascaling enabling and support for EC-EARTH3]], (not active)
:[[Performance Benchmark of NEMO Oceanography Code]], (not active)

== SNIC Projects ==
:[[Porting Earth system models to triolith]], (not active)
:[[Develop multi-category LIM3 sea-ice capabilities in EC-Earth 3]], (not active)
:[[NorESM code analysis]], (not active)
:[[EC-Earth compilation and performance analysis: Beskow]], (not active)
:[[Optimization of a lagrangian cloud parcel model for use in the global climate model ECHAM6.1-HAM2.2]], (not active)
:[[Integration of OpenIFS into EC-Earth3]], (not active)
:[[Technical development of the EC-Earth3 Single Column Model (SCM)]], (not active)
:[[Implementation of parallel NetCDF output and COSP in OpenIFS]], (not active)
:[[Configuration of CAM5.3 nudged to ERA-Interim reanalysis and related post-processing software]], (not active)
:[[MIMICA code analysis]], (not active)
:[[EC-Earth/COSP code analysis]], (not active)
:[[Bolin Centre software management through local modules - trial evaluation.]], (active)

== Other Projects ==
:[[HYPE Code Parallelisation]], (not active)
:[[Portability performance analysis and improvement of ESM]], (not active)
:[[Infrastructure for the European Network for Earth System modelling - Phase 2]], (not active)
:[[Nordic collaboration on e-infrastructures for Earth System Modeling]], (active)

== How to's: NCS's Tetralith system ==

:Tetralith [https://www.nsc.liu.se/support/systems/tetralith-getting-started/ getting started]
:[https://www.nsc.liu.se/support/systems/tetralith-dcs-topics/ Tetralith DCS large-scale storage and analysis nodes]
:Applying for SNIC allocations on Tetralith: [http://www.snic.se/resources/ apply for resources].
:Job submission and monitoring, SLURM commands: [http://www.schedmd.com/slurmdocs/quickstart.html quick start user guide]
:[https://dev.ec-earth.org/projects/ecearth3/wiki/Building_EC-Earth_3_on_the_NSC_tetralith_system Building EC-Earth3 on the NSC Tetralith system]
:[[Building CESM 1.2.2.1 Tetralith]]
:[[Building NorESM 1 Tetralith]]
:[[Building CESM 2.1.0 Tetralith]]
:[[Building and running MIMICAv5 on Tetralith]]

== How to's: NCS's Triolith system ==

:Triolith [http://www.nsc.liu.se/systems/triolith/ user guide].
:Applying for SNIC allocations on triolith: [http://www.snic.vr.se/apply-for-resources apply for resources].
:Job submission and monitoring, SLURM commands: [http://www.schedmd.com/slurmdocs/quickstart.html quick start user guide]
:[[Building CESM models on the NSC triolith system]]
:[[Building NorESM (CMIP5) on the NSC triolith system]]
:[https://dev.ec-earth.org/projects/ecearth3/wiki/Building_EC-Earth_3_on_the_NSC_triolith_system Building EC-Earth3 on the NSC triolith system]
:[[EC-Earth and CESM model timings]]
:[[Building interpinic tool for interpolation of land initial conditions for the CESM1.1 model]]
:[[Building and running the COAMPS model on triolith]]
:[[Building mom5.0.2 (modular ocean model) on triolith]]
:[https://www.nsc.liu.se/systems/triolith/software/triolith-software-apps-NCARdiag.html NCAR diagnostics packages on the NSC Triolith system]
:[[CESM & NorESM users on Triolith: changing to the new centre storage (/proj/) system]]
:[[NorESM fix for change to buildenv system (2015-02-16)]]
:[https://redmine.hammoz.ethz.ch/projects/hammoz/wiki/Triolith_NSC Building HAMMOZ on the NSC triolith system]
:[[Building the PORT (Parallel Offline Radiative Transfer) configuration of CESM on Triolith]]
:[[Building and testing WRF on Triolith]]

== How to's: PDC's Beskow system ==

:[https://dev.ec-earth.org/projects/ecearth3/wiki/Building_EC-Earth_3_on_the_PDC_beskow_system Building EC-Earth3 on the PDC Beskow system]
:[[Media:IFS-Beskow.pdf|IFS scaling on Beskow - EC-Earth version 3.1]]
:[[Building CESM models on the PDC Beskow system]]
:[[Media:Beskow3.2beta-report-V2.pdf|EC-Earth 3.2beta scaling and performance analysis report]]
:[[Building MOM (Modular Ocean Model) on the PDC Beskow system]]

User:Hamish Struthers (NSC)

2020-02-25T08:34:55Z

Hamish Struthers (NSC):

{{application expert info
|first name=Hamish
|last name=Struthers
|centre=NSC
|fields=Climate research
|fte=80
|financing=SeRC
|general activities=Users support focused on weather and climate codes.
|other activities=ESGF data node collaboration with SMHI; Collaborative projects with SMHI and the Bolin Centre.
|image=Hamish_Struthers.jpg
|office=Room A2:138; Campus Valla; Linköping University.
|phone=013 281072 (office).
}}

== Quick facts ==
* PhD. in Chemistry.
* Started at NSC 1 January, 2013.

== Expertise ==
* [[expertise::EC-Earth]]
* [[expertise::CESM1]]
* [[expertise::NorESM]]
* [[expertise::NCL]]
* [[expertise::MIMICA]]

== Projects ==
* [[project::Develop multi-category LIM3 sea-ice capabilities in EC-Earth 3]]
* [[project::Porting Earth system models to triolith]]
* [[project::Infrastructure for the European Network for Earth System modelling - Phase 2]]
* [[project::Integration of OpenIFS into EC-Earth3]]
* [[Project::Technical development of the EC-Earth3 Single Column Model (SCM)]]
* [[Project::Implementation of parallel NetCDF output and COSP in OpenIFS]]
* [[Project::Configuration of CAM5.3 nudged to ERA-Interim reanalysis and related post-processing software]]
* [[project::EC-Earth/COSP code analysis]]
* [[project::Bolin Centre software management through local modules - trial evaluation.]]
* [[project::Nordic collaboration on e-infrastructures for Earth System Modeling]]

File:Hamish Struthers.jpg

2020-02-25T08:34:34Z

Hamish Struthers (NSC):

User:Hamish Struthers (NSC)

2020-02-25T08:33:31Z

Hamish Struthers (NSC):

{{application expert info
|first name=Hamish
|last name=Struthers
|centre=NSC
|fields=Climate research
|fte=80
|financing=SeRC
|general activities=Users support focused on weather and climate codes.
|other activities=ESGF data node collaboration with SMHI; Collaborative projects with SMHI and the Bolin Centre.
|image=Hamish_Struthers_crop.jpg
|office=Room A2:138; Campus Valla; Linköping University.
|phone=013 281072 (office).
}}

== Quick facts ==
* PhD. in Chemistry.
* Started at NSC 1 January, 2013.

== Expertise ==
* [[expertise::EC-Earth]]
* [[expertise::CESM1]]
* [[expertise::NorESM]]
* [[expertise::NCL]]
* [[expertise::MIMICA]]

== Projects ==
* [[project::Develop multi-category LIM3 sea-ice capabilities in EC-Earth 3]]
* [[project::Porting Earth system models to triolith]]
* [[project::Infrastructure for the European Network for Earth System modelling - Phase 2]]
* [[project::Integration of OpenIFS into EC-Earth3]]
* [[Project::Technical development of the EC-Earth3 Single Column Model (SCM)]]
* [[Project::Implementation of parallel NetCDF output and COSP in OpenIFS]]
* [[Project::Configuration of CAM5.3 nudged to ERA-Interim reanalysis and related post-processing software]]
* [[project::EC-Earth/COSP code analysis]]
* [[project::Bolin Centre software management through local modules - trial evaluation.]]
* [[project::Nordic collaboration on e-infrastructures for Earth System Modeling]]

2018-03-19T15:59:53Z

Hamish Struthers (NSC):

{{application expert info
|first name=Hamish
|last name=Struthers
|centre=NSC
|fields=Climate research
|fte=100
|financing=SeRC
|general activities=Users support focused on weather and climate codes.
|other activities=ESGF data node collaboration with SMHI.; Collaborative projects with SMHI and [http://www.bolin.su.se/ BBCC].
|image=Hamish.jpg
|office=Room A2:138; Campus Valla; Linköping University.
|phone=013 281072 (office).
}}

== Quick facts ==
* PhD. in Chemistry.
* Started at NSC 1 January, 2013.

== Expertise ==
* [[expertise::EC-Earth]]
* [[expertise::CESM1]]
* [[expertise::NorESM]]
* [[expertise::NCL]]

== Projects ==
* [[project::Develop multi-category LIM3 sea-ice capabilities in EC-Earth 3]]
* [[project::Porting Earth system models to triolith]]
* [[project::Infrastructure for the European Network for Earth System modelling - Phase 2]]
* [[project::Integration of OpenIFS into EC-Earth3]]
* [[Project::Technical development of the EC-Earth3 Single Column Model (SCM)]]
* [[Project::Implementation of parallel NetCDF output and COSP in OpenIFS]]
* [[Project::Configuration of CAM5.3 nudged to ERA-Interim reanalysis and related post-processing software]]
* [[project::EC-Earth/COSP code analysis]]
* [[project::Bolin Centre software management through local modules - trial evaluation.]]
* [[project::Nordic collaboration on e-infrastructures for Earth System Modeling]]

Main Page

2018-01-23T13:04:18Z

Implementation of parallel NetCDF output and COSP in OpenIFS

2017-08-31T12:25:24Z

Hamish Struthers (NSC):

{{project info
|description=Assist researchers from Göteborg in including parallel NetCDF IO support and the COSP module in the OpenIFS model
|fields=Climate research
|financing=SNIC
|active=No
|start date=2016-06-01
|end date=2016-12-31
}}

This [[Media:EC-Earth-PIO.pdf|project]] is a technical development of OpenIFS that aims to enable the simulation of satellite products using the COSP simulator incorporated into the OpenIFS global atmospheric model. One requirement for efficient running of such a simulator is support for parallel NetCDF IO.

== Members ==
{{#ask: [[Category:Person]] [[project::{{PAGENAME}}]]
|?centre
|?role
|?field
}}