Building CESM 1.2.2.1 Tetralith - Revision history

Hamish Struthers (NSC) at 19:31, 6 May 2021

2021-05-06T19:31:39Z

Hamish Struthers (NSC) at 12:08, 4 December 2020

2020-12-04T12:08:46Z

Hamish Struthers (NSC) at 14:50, 21 March 2019

2019-03-21T14:50:47Z

Hamish Struthers (NSC): Created page with "This page describes the building the [http://www.cesm.ucar.edu/models/cesm1.2/ CESM 1.2.2.1] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system. Tetralith is NS..."

2019-03-20T13:02:53Z

Created page with "This page describes the building the [http://www.cesm.ucar.edu/models/cesm1.2/ CESM 1.2.2.1] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system. Tetralith is NS..."

New page

This page describes the building the [http://www.cesm.ucar.edu/models/cesm1.2/ CESM 1.2.2.1] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system. Tetralith is NSC's largest HPC cluster. It replaced NSC's previous HPC cluster Triolith in 2018. Tetralith is funded by SNIC and uses for research by Swedish research groups. Access to Tetralith is granted by SNIC.

;CESM1 unix group on triolith

If you are going to run one of the CESM models on Tetralith, you should join the 'cesm_input-data' storage project (snic2014-5-61). This is not absolutely necessary but being a member allows access to shared storage space (<tt>/proj/cesm_input-data</tt>) where pre-downloaded initial data and ancillary files are stored. To join the 'cesm_input-data' project, log into SUPR (https://supr.snic.se/) and click the 'View and Manage Projects' button, the request membership to the snic2014-5-61 project.

;Getting the source code

CESM is a free, open source model, but a short [http://www.cesm.ucar.edu/models/register/register.html registration] is required before access to the subversion repository is granted. The source code, build and run scripts can be downloaded as described in the CESM1.2 [http://www.cesm.ucar.edu/models/cesm1.2/cesm/doc/usersguide/book1.html user guide]. To list the available model versions, after CESM registration (on Tetralith):

:<code>svn list https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags</code>

It is recommended that the source files be downloaded into the <tt>/home</tt> file system. This ensures that your code, and configuration files are backed up.

;Copying the Tetralith configuration files

As an example, download the CESM distribution to some base folder <tt><cesm-base></tt>:

1. Change to the appropriate folder

:<code>cd <cesm-base></code>

2. Checkout version 1.2.2.1

:<code>svn co https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2_1 cesm1.2.2.1</code>

3. Files containing Tetralith specific machine environment variables have been created and are stored in the folder <tt>/proj/cesm_input-data/tetralith_config_cesm1.2.2.1</tt>. These files should be copied to the appropriate location in your local distribution. Based on the steps above:

:<code>cd <cesm-base>/cesm1.2.2.1/scripts/</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm1.2.2.1/create_newcase .</code>

:<code>cd <cesm-base>/cesm1.2.2.1/scripts/ccsm_utils/Case.template</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm1.2.2.1/config_definition.xml .</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm1.2.2.1/ConfigCase.pm .</code>

:<code>cd <cesm-base>/cesm1.2.2.1/scripts/ccsm_utils/Machines</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm1.2.2.1/config_compilers.xml .</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm1.2.2.1/config_machines.xml .</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm1.2.2.1/env_mach_specific.tetralith .</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm1.2.2.1/mkbatch.tetralith .</code>

;Creating a new case and building the model

1. Load modules:

:<code>module load buildenv-intel/2018.u1-bare module load netCDF/4.4.1.1-HDF5-1.8.19-nsc1-intel-2018a-eb HDF5/1.8.19-nsc1-intel-2018a-eb PnetCDF/1.8.1-nsc1-intel-2018a-eb</code>

2. Create a new case, for example, to create a new 'f19_g16' resolution case using the 'B' compset:

:<code>cd <cesm-base>/cesm1.2.2.1/scripts/</code>
:<code>./create_newcase -case ../cases/lbtest-f19_g16-B -res f19_g16 -compset B -mach tetralith -ccsm_out /proj/bolinc/users/${USER}/cesm1.2.2.1</code>

3. Configure and build your model:

:<code>cd <cesm-base>/cesm1.2.2.1/cases/lbtest-f19_g16-B</code>
:<code>./cesm_setup</code>
:<code>./lbtest-f19_g16-B.build</code>

4. Edit the env_run.xml and the $CASE.run files for the particular simulation you wish to make, then submit your job:

:<code>sbatch ./lbtest-f19_g16-B.run</code>

{{set category list|field|Climate research}}

← Older revision		Revision as of 19:31, 6 May 2021
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	;CESM1 unix group on triolith		;CESM1 unix group on triolith

−	If you are going to run one of the CESM models on Tetralith, you should join the 'cesm_input-data' storage project (~~snic2014-5~~-61). This is not absolutely necessary but being a member allows access to shared storage space (<tt>/proj/cesm_input-data</tt>) where pre-downloaded initial data and ancillary files are stored. To join the 'cesm_input-data' project, log into SUPR (https://supr.snic.se/) and click the 'View and Manage Projects' button, the request membership to the ~~snic2014-5~~-61 project.	+	If you are going to run one of the CESM models on Tetralith, you should join the 'cesm_input-data' storage project (SNIC 2020/14-98). This is not absolutely necessary but being a member allows access to shared storage space (<tt>/proj/cesm_input-data</tt>) where pre-downloaded initial data and ancillary files are stored. To join the 'cesm_input-data' project, log into SUPR (https://supr.snic.se/) and click the 'View and Manage Projects' button, the request membership to the SNIC 2020/14-98 project.

@@ Line 50: / Line 50: @@
 . Load modules:
-:<code>module load buildenv-intel/2018.u1-bare netCDF/4.4.1.1-HDF5-1.8.19-nsc1-intel-2018a-eb HDF5/1.8.19-nsc1-intel-2018a-eb PnetCDF/1.8.1-nsc1-intel-2018a-eb</code>
+:<code>module load buildenv-intel/2018.u1-bare netCDF-HDF5/4.6.2-nsc1-parallel-private_hdf5-intel20018a-eb</code>
 . Create a new case, for example, to create a new 'f19_g16' resolution case using the 'B' compset: