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H5Fopen failed during fast_check #3

Closed happysky19 closed 5 years ago

happysky19 commented 5 years ago

Hi,

I got following error message when I run fast_check

Running 417 test cases...

0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| **unknown location(0): fatal error: in "forward_model_spectral_grid/low_resolution_grid": FullPhysics::Exception: Lua error: std::exception: 'While trying to open file '/groups/algorithm/l2_fp/absco/v3.3.0/lowres/co2_v3.3.0-lowres.hdf' a HDF 5 Exception thrown: H5Fopen failed'

lib/Interface/forward_model_spectral_grid_test.cc(68): last checkpoint: "low_resolution_grid" fixture entry. unknown location(0): fatal error: in "forward_model_spectral_grid/high_resolution_grid": FullPhysics::Exception: Lua error: std::exception: 'While trying to open file '/groups/algorithm/l2_fp/absco/v3.3.0/lowres/co2_v3.3.0-lowres.hdf' a HDF 5 Exception thrown: H5Fopen failed'

What may cause this error? Thanks, Tianhao

mikesmyth commented 5 years ago

Tianhao,

The unit tests depend on a set of files referred to as ABSCO (see http://nasa.github.io/RtRetrievalFrameworkDoc/testing.html). The normal production runs use version 5.0.0 of these files, but our unit tests use older versions of these tables. We just froze the unit tests at one point in development, we didn't want to update these each time we updated the ABSCO data. The unit tests depend on the older v3.3.0 version of these files.

The ABSCO tables are available at https://oco2.gesdisc.eosdis.nasa.gov/data/.A4ft5bK203Mc2nXI/OCO2_DATA, with the version v3.3.0 absco data one level lower at OCO2_L2_ABSCO.3.3.0/. Note that you will need to get a free Earthdata Login account, there are directions on the download page for getting this account.

When you have the data installed on your system, you'll need to specify the directory location you have using the "--with-absco" option in the configuration. We have this default to the directory /groups/algorithm/l2_fp/absco which is where the data is on our system, but presumably you'll have them installed in a different directory. There is an assumed directory structure here, the V3.3.0 data should go in the directory $(abscodir)/v3.3.0/lowres. The production v5.0.0 data should go into $(abscodir)/v5.0.0.

We don't include the ABSCO data with the source because of the size. Each of the data sets is about 2GB which is too large to put into github.

Mike

mcduffie commented 5 years ago

Additionally, this software has been forked and is actively worked on here: https://github.com/ReFRACtor/framework

Depending on your work this might be better for you going forward since that is the version of this code base that will be actively maintained going forward.

happysky19 commented 5 years ago

Many thanks! I will try this.

Also, seems the link for the ReFRACtor documentation doesn't work now(https://github.jpl.nasa.gov/pages/refractor/documentation/). Could you update the link?

Thanks, Tianhao

mcduffie commented 5 years ago

Use this link for the public ReFRACtor documentation: https://refractor.github.io/documentation/