ioos / Cloud-Sandbox

IOOS' Coastal Modeling Cloud Sandbox provides a framework for developing, modifying and running models in the cloud. It provides repeatable configurations, model code and required libraries, input data and analysis of model outputs. The Sandbox supports not only the development of services and models, but also Cloud HPC to run and validate models.

https://www-sandbox.ioos.us/

BSD 3-Clause "New" or "Revised" License

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Document requirements and Implement model run(s) for ADCIRC (ADvanced CIRCulation) #58

Open ZacharyWills opened 1 year ago

ZacharyWills commented 1 year ago

Welcome to the IOOS Cloud-Sandbox!

Expected Behavior

A ADCIRC (ADvanced CIRCulation) model version should be selected, compiled and made available to users of the Cloud-Sandbox.

Current Behavior

ADCIRC (ADvanced CIRCulation) is not available.

Possible Solution

The Source should be compiled periodically, a set of static configuration examples made available, and documentation should be written to describe not only how this is done but also the lifecycle of this model.

Steps to Reproduce or Implement:

[ ] ADCIRC source code acquired
[ ] Compilation and test-runs automated for availability
[ ] Available Data acquired, and it's location documented for community use
[ ] Documentation of full ADCIRC usage, necessary inputs, output location, etc. made available

Context

The National Ocean Service has adopted four different community code packages for use in the operational Coastal Ocean Modeling Framework (COMF):

Your Environment

Version used: To be updated upon Selection
Software Name and version: ADCIRC (ADvanced CIRCulation) model
Operating System and version (desktop or mobile): Amazon Linux 2
Link to your project/sponsor: tiffany.c.vance@noaa.gov

janahaddad commented 5 months ago

Hello, I'm getting familiar with the sandbox and was trying to compile ADCIRC using cmake in the NOAA EC2 instance (for eventually testing ADCIRC+SWAN model runs for CO-OPS CORA)

Cmake is not finding a fortran compiler on the system, and I'm wondering if I'm going about this the wrong way. Should I be cloning cloud-sandbox repo first? or can you provide a path for a fortran compiler? or should I install gfortran in my user directory?

Here's the full output from the Cmake GUI configuration:

thanks for your help!

cc @Michael-Lalime, @greg-dusek

Michael-Lalime commented 5 months ago

@ZacharyWills @KatherinePowell-NOAA @patrick-tripp I thought we had a Fortran compiler in the sandbox? Can any of you help @janahaddad and @greg-dusek with this problem with cmake and Fortran?

patrick-tripp commented 5 months ago

Hi Jana,

You need to load the appropriate modules that contain the libraries and compilers you want to use. 'spack load' might also work also. 'module avail' 'spack find'

I am assuming you ran the setup-instance script when your sandbox was deployed? That will install everything you need.

ZacharyWills commented 5 months ago

Here's the fortran install/version: https://github.com/ioos/Cloud-Sandbox/blob/7ecc756d85b9b9ea92be0e062331738536e45649/scripts/funcs-setup-instance.sh#L379

patrick-tripp commented 5 months ago

The above is for an older version and should be removed. When the sandbox is deployed it will automatically setup all of the software and libraries you need using the setup-instance.sh script. If it didn't run, you can manually run the scripts/setup-instance.sh script which will use Spack to install everything you need with the proper dependencies.

Michael-Lalime commented 5 months ago

I think Jana is using the currently deployed version of the sandbox and not deploying a new instance.

On Wed, Apr 3, 2024 at 1:00 PM Patrick Tripp @.***> wrote:

The above is for an older version and should be removed. When the sandbox is deployed it will automatically setup all of the software and libraries you need using the setup-instance.sh script. If it didn't run, you can manually run the scripts/setup-instance.sh script which will use Spack to install everything you need with the proper dependencies.

— Reply to this email directly, view it on GitHub https://github.com/ioos/Cloud-Sandbox/issues/58#issuecomment-2035121795, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR7UUIHFZBOBVQ3FSXRTIVLY3QYSVAVCNFSM6AAAAAAZ2BESN6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZVGEZDCNZZGU . You are receiving this because you were mentioned.Message ID: @.***>

janahaddad commented 5 months ago

I am assuming you ran the setup-instance script when your sandbox was deployed? That will install everything you need.

@patrick-tripp No, where is setup-instance? I believe that I'm working in an environment that already has the latest cloud-sandbox deployed, right @Michael-Lalime?

Thought I tried module load but I guess I didn't! Will give that a try. If that doesn't work, I'll try the spack option with the setup-instance.sh script. Thanks y'all

patrick-tripp commented 5 months ago

OK, In that case don't need to run the setup-instance.sh script. You only need to specify the modules you need to use in your build and run scripts. You can see the LiveOcean or nosofs models as a reference. This will enable all of the Intel compilers, MPI, ESMF, HDF, netCDF, etc.

Michael-Lalime commented 5 months ago

@Jana Haddad - NOAA Affiliate @.***> Yes you are using the version that was deployed in December. There might be updates since then that haven't been incorporated but Patrick's suggestions should help you get going.

On Wed, Apr 3, 2024 at 1:08 PM Patrick Tripp @.***> wrote:

OK, you need to specify the modules you need to use in your build and run scripts. You can see the LiveOcean or nosofs models as a reference.

— Reply to this email directly, view it on GitHub https://github.com/ioos/Cloud-Sandbox/issues/58#issuecomment-2035136443, or unsubscribe https://github.com/notifications/unsubscribe-auth/AR7UUIE5DPAECAC7Q7HLEMTY3QZQXAVCNFSM6AAAAAAZ2BESN6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZVGEZTMNBUGM . You are receiving this because you were mentioned.Message ID: @.***>