Building CESM 2.1.0 Tetralith - Revision history

Hamish Struthers (NSC) at 19:32, 6 May 2021

2021-05-06T19:32:59Z

Hamish Struthers (NSC) at 12:23, 4 December 2020

2020-12-04T12:23:58Z

Hamish Struthers (NSC) at 14:54, 25 May 2020

2020-05-25T14:54:35Z

Hamish Struthers (NSC) at 07:55, 28 August 2019

2019-08-28T07:55:36Z

Hamish Struthers (NSC) at 07:55, 28 August 2019

2019-08-28T07:55:04Z

Hamish Struthers (NSC): Created page with "This page describes the building the [http://www.cesm.ucar.edu/models/cesm2/ CESM 2.1.0] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system. Tetralith is NSC's ..."

2019-08-26T13:35:24Z

Created page with "This page describes the building the [http://www.cesm.ucar.edu/models/cesm2/ CESM 2.1.0] on NSC's [http://www.nsc.liu.se/systems/tetralith/ Tetralith] system. Tetralith is NSC's ..."

New page

This page describes the building the [http://www.cesm.ucar.edu/models/cesm2/ CESM 2.1.0] 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. The source code, build and run scripts can be downloaded as described in the CESM 2.1.0 [https://escomp.github.io/cesm/release-cesm2 quick guide].

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.

Starting with CESM2, releases are available through a public GitHub repository, http://github.com/ESCOMP/cesm. The latest version of the release code can be downloaded by executing, e.g.:

:<code>git clone -b release-cesm2.1.0 https://github.com/ESCOMP/cesm.git cesm2.1.0</code>

;Copying the Tetralith configuration files

Files containing Tetralith specific machine environment variables have been created and are stored in the folder <tt>/proj/cesm_input-data/tetralith_config_cesm2.1.0</tt>. These files should be copied to the appropriate location in your local distribution. Based on the steps above:

:<code>cd <cesm-base>/cesm2.1.0/cime/config/cesm/machines/</code>
:<code>cp /proj/cesm_input-data/tetralith_config_cesm2.1.0/* .</code>

;Creating a new case and building the model

1. 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>

2. Create a new case, for example, to create a new 'f09_g17' resolution case using the 'BW1850' compset:

:<code>cd <cesm-base>/cesm2.1.0/cime/scripts/</code>
:<code>./create_newcase --case ../cases/BW1850 --walltime 24:00:00 --compset BW1850 --res f09_g17 --machine tetralith --project snic2019-1-2 --output-root /proj/bolinc/users/struthers/cesm2.1.0-out</code>

3. Configure and build your model:

:<code>cd <cesm-base>/cesm2.1.0/cime/cases/BW§1850</code>
:<code>./case.setup</code>
:<code>./case.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>./case.submit</code>

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

← Older revision		Revision as of 19:32, 6 May 2021
Line 4:		Line 4:
	;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 34: / Line 34: @@
 :<code>module purge</code>
-:<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 'f09_g17' resolution case using the 'BW1850' compset:

← Older revision		Revision as of 14:54, 25 May 2020
Line 16:		Line 16:

	:<code>git clone -b release-cesm2.1.0 https://github.com/ESCOMP/cesm.git cesm2.1.0</code>		:<code>git clone -b release-cesm2.1.0 https://github.com/ESCOMP/cesm.git cesm2.1.0</code>
		+	:<code>cd cesm2.1.0</code>
		+	:<code>./manage_externals/checkout_externals</code>
		+

← Older revision		Revision as of 07:55, 28 August 2019
Line 30:		Line 30:
	1. Load modules:		1. Load modules:

		+	:<code>module purge</code>
	:<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/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>

@@ Line 40: / Line 40: @@
 . Configure and build your model:
-:<code>cd <cesm-base>/cesm2.1.0/cime/cases/BW§1850</code>
+:<code>cd <cesm-base>/cesm2.1.0/cime/cases/BW1850</code>
 :<code>./case.setup</code>
 :<code>./case.build</code>