Working on the MTRI cluster computers
The Michigan Tech Research Institute (MTRI) in Ann Arbor, MI maintains a computing cluster made up of Linux servers similar to CTM. GEOS-Chem and supporting files have been installed on the server for use by our research group. However, IDL is NOT available on this server, so GC data files must be transferred back to the CTM server for processing.
A note on the cluster: While the MTRI cluster has several nodes, GEOS-Chem can only run on the main host. The GC code is written with OpenMP parallel directives which support execution of code across multiple processors, but not across multiple physical computers. Thus, it will make use of all eight processors in a single computer with two quad core processors (host node), but will not run on other nodes. Performance is similar to that on the CTM server. GC developers are working on a version that uses MPI directives, but it is not yet ready.
Connect to the MTRI server in the same way as the CTM server by using the PuTTy terminal software. The server name is 'poweredger900a.mtri.org'. See the GEOS-Chem system administrator for log in information.
Once connected to the server, you will find your user directory under 'data/users'. This is where your GEOS-Chem models should be stored.
Other relevant information:
- GC Met Data Directory: /data/users/rwpage/ctm_data/ctm/
- GC v822 Source Code: /data/users/rwpage/ctm_tools/geos_code/GEOS-Chem.v8-02-02.stdrun/code
The following lines in your input.geos file must be updated to reflect the different directory structure:
- Root Data Directory : /data/users/rwpage/ctm_data/ctm/GEOS_4x5
- Dir w/ 1x1 emissions etc: /data/users/rwpage/ctm_data/ctm/GEOS_1x1/
- Temporary directory : /data/users/(your username)/geos-temp/
- Dir w/ archived OH files: /data/users/rwpage/ctm_data/ctm/GEOS_MEAN/OHmerge/v5-07-08/
- Dir w/ O3 P/L rate files: /data/users/rwpage/ctm_data/ctm/GEOS_MEAN/O3_PROD_LOSS/2003.v6-01-05/
Copying Files to and from the MTRI Server
To copy files and directories between the CTM and MTRI servers, the Linux 'scp' command is the best and fastest method. scp stands for 'secure copy' and uses the SSH protocol for communation between servers. While it is possible to recursively copy files and directories, it is recommended that the model files be packaged into a 'tarball' before being transferred. This packages all model directories and files into a single, compressed file which can be transferred to the server with a single command.
The format of the command is scp <source> <destination>, where <source> is the path of the file on the server which you currently logged into.
Creating a tarball file of a model directory
As an example, if the model directory 'practice_20100826' is being readied for transfer, the tarball file is created with the command:
ctm> tar -czvf model.tgz ./practice_20100826
Transferring the File from CTM to the MTRI Server
In the directory where the tarball is located, use the following command to copy the file to the MTRI server. The destination directory MUST already exist.
ctm> scp model.tgz <username>@poweredger900a.mtri.org:/path/to/model/dir/
Expanding the tarball on the MTRI Server
Log into the MTRI server and go to the directory where the tarball is located, then use the following command to 'untar' or expand the file/directory:
ctm> tar -xzvf model.tgz
Transferring BPCH files from MTRI to CTM Server
Log into the MTRI server and go to the directory where the BPCH file is located, then use the following command to transfer it to the CTM server:
mtri> scp file.bpch <username>@ctm.geo.mtu.edu:/path/to/model/dir/
Once the BPCH file is saved to the CTM server, exit from the MTRI server and log on to CTM. Then, go to the directory where you saved the BPCH file and process with IDL, as usual.