Recipes for daily eNATL60 at depth data #189

auraoupa · 2022-09-27T14:29:02Z

These recipes will create datasets containing some NEMO based runs outputs, more specifically temperature, salinity and vertical velocities at some depths (60m and 600m) + mixed layer depth. This datasets will be useful to M2LINES participants for spatial filtering testing, w’b’ computations, model training, etc …

The recipes have been successfully prune-tested on m2lines cloud with version 0.8.3 of pangeo_forge_recipes. The data are retrievable through opendap.

Two questions :

is it possible to define a compression rate for the resulting zarrs and if yes how ?
I will probably want to upload some more levels in the near future, will I have to set up a new contribution or could I amend this one later ?

andersy005 · 2022-09-28T19:02:35Z

pre-commit.ci autofix

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andersy005 · 2022-09-28T19:13:48Z

/run recipe-test recipe_run_id=1165

andersy005 · 2022-09-28T19:59:04Z

@cisaacstern,

/run recipe-test recipe_run_id=1165

is this the right way to test recipe runs?

cisaacstern · 2022-09-28T20:14:35Z

@andersy005, thanks for asking!

The syntax is now:

/run [RECIPE_ID]

where RECIPE_ID is one of the IDs listed in meta.yaml here. So possible commands for this PR would be:

/run eNATL60_wtides_1d_mld
/run eNATL60_wtides_1d_tsw60m
/run eNATL60_wtides_1d_tsw600m

The recipe is automatically run from the latest commit on the PR, and there is no way to run a test from any commit aside from the latest commit.

cisaacstern · 2022-09-28T20:18:09Z

@andersy005 for your reference, the "inversion" from RECIPE_ID to backend database object is done here:

https://github.com/pangeo-forge/pangeo-forge-orchestrator/blob/4b008d2eba4602dcc2681e7c538738c6b5ad79a9/pangeo_forge_orchestrator/routers/github_app.py#L335-L344

So you can see this is part of the general design trend we were discussing yesterday, to allow humans to request/query based on readable plain text identifiers, and then have the backend invert those values into the database index(es) that it needs. Similar to how you may want to add a /feedstocks/{spec} route, etc.

andersy005 · 2022-09-28T20:19:13Z

/run eNATL60_wtides_1d_mld

andersy005 · 2022-09-28T20:20:58Z

thank you for the clarification, @cisaacstern!

pangeo-forge · 2022-09-28T20:25:53Z

🎉 The test run of eNATL60_wtides_1d_mld at d69ab37 succeeded!

import xarray as xr

store = "https://ncsa.osn.xsede.org/Pangeo/pangeo-forge/test/pangeo-forge/staged-recipes/recipe-run-1163/eNATL60_wtides_1d_mld.zarr"
ds = xr.open_dataset(store, engine='zarr', chunks={})
ds

auraoupa · 2022-10-03T07:41:17Z

Thanks @andersy005 for running the first recipe !
Could you please run the other ones ?
/run eNATL60_wtides_1d_tsw60m
/run eNATL60_wtides_1d_tsw600m

andersy005 · 2022-10-04T00:34:22Z

/run eNATL60_wtides_1d_tsw60m

andersy005 · 2022-10-04T00:36:32Z

/run eNATL60_wtides_1d_tsw600m

pangeo-forge · 2022-10-04T00:56:31Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

pangeo-forge · 2022-10-04T00:58:12Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

auraoupa · 2022-10-04T07:55:37Z

I wonder what went wrong 😕 The logs look empty : https://pangeo-forge.org/dashboard/recipe-run/1164?feedstock_id=1 so it is difficult to know what to change ...

cisaacstern · 2022-10-04T18:23:53Z

@auraoupa thanks for raising this issue. The missing logs are a known issue, which is problematic for exactly the reasons you mention, and which I am working to resolve in pangeo-forge/pangeo-forge-orchestrator#150. It is possible, albeit rather cumbersome, for Pangeo Forge Cloud admins to manually locate these logs, using the methods linked in pangeo-forge/pangeo-forge-orchestrator#146 (comment). My hope is to have the above linked PR merged sometime today. If that does not happen, we can revisit manually searching for these logs. Thank you for your patience and engagement with Pangeo Forge at this crucial early stage of development. Your feedback is a great help to us in refining the platform in response to real user needs. 🙏

auraoupa · 2022-10-05T12:08:58Z

Thanks @cisaacstern for the explanations, I'll wait for your PR to merge then, good luck !

cisaacstern · 2022-10-06T02:44:44Z

@auraoupa, thank you for your understanding. The linked PR is not yet complete. In the meantime, I have manually pulled what appear to be the errors for the latest runs (unfortunately, I am not sure which goes with which recipe):

FileNotFoundError: https://ige-meom-opendap.univ-grenoble-alpes.fr/thredds/fileServer/meomopendap/extract/eNATL60/eNATL60-BLBT02/1d/eNATL60-BLBT02_y2009m07d01.1d_TSW_600m.nc

FileNotFoundError: https://ige-meom-opendap.univ-grenoble-alpes.fr/thredds/fileServer/meomopendap/extract/eNATL60/eNATL60-BLBT02/1d/eNATL60-BLBT02_y2009m07d02.1d_TSW_60m.nc

In both cases, it would seem that a file which the recipe expects to find was not accessible. Perhaps the server was down, or the file path has a small typo somewhere?

auraoupa · 2022-10-06T07:54:10Z

Ok, so the path is correct and the files are accessible today so our server must have been down at the time the recipe has been run, it can happen sometimes unfortunately ... Is it possible to test the recipes again ?

auraoupa · 2022-10-13T07:44:20Z

Hello @andersy005 ans @cisaacstern , sorry to be pushy, could you please launch again the two test recipes /run eNATL60_wtides_1d_tsw60m and /run eNATL60_wtides_1d_tsw600m ? Thanks !

andersy005 · 2022-10-19T01:55:44Z

/run eNATL60_wtides_1d_tsw600m

andersy005 · 2022-10-19T01:57:24Z

thank you for your patience, @auraoupa! i just launched new runs, and hopefully🤞🏽everything goes well

andersy005 · 2022-10-19T02:05:05Z

/run eNATL60_wtides_1d_tsw60m

pangeo-forge · 2022-10-19T02:17:22Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

pangeo-forge · 2022-10-19T02:33:48Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

auraoupa · 2022-10-19T07:09:45Z

Thanks @andersy005 for launching the tests again ! Unfortunately they still failed 😟 I really do not understand why, the opendap is doing fine and the links are good ...

andersy005 · 2022-10-19T20:43:08Z

/run eNATL60_wtides_1d_tsw600m

andersy005 · 2022-10-19T20:57:25Z

Thanks @andersy005 for launching the tests again ! Unfortunately they still failed worried I really do not understand why, the opendap is doing fine and the links are good ...

@auraoupa, i believe the failures have to do with connectivity issues within dataflow runner. These connectivity issues are similar to what i reported in #145 (comment). I'm currently investigating what's really going on, and will keep you posted.

 TimeoutError: [Errno 110] Connect call failed ('129.88.191.39', 443)

  The above exception was the direct cause of the following exception:

  Traceback (most recent call last):
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/implementations/http.py", line 391, in _info
      await _file_info(
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/implementations/http.py", line 768, in _file_info
      r = await session.get(url, allow_redirects=ar, **kwargs)
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/aiohttp/client.py", line 536, in _request
      conn = await self._connector.connect(
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/aiohttp/connector.py", line 540, in connect
      proto = await self._create_connection(req, traces, timeout)
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/aiohttp/connector.py", line 901, in _create_connection
      _, proto = await self._create_direct_connection(req, traces, timeout)
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/aiohttp/connector.py", line 1206, in _create_direct_connection
      raise last_exc
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/aiohttp/connector.py", line 1175, in _create_direct_connection
      transp, proto = await self._wrap_create_connection(
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/aiohttp/connector.py", line 988, in _wrap_create_connection
      raise client_error(req.connection_key, exc) from exc
  aiohttp.client_exceptions.ClientConnectorError: Cannot connect to host ige-meom-opendap.univ-grenoble-alpes.fr:443 ssl:default [Connect call failed ('129.88.191.39', 443)]

  The above exception was the direct cause of the following exception:

  Traceback (most recent call last):
    File "apache_beam/runners/common.py", line 1417, in apache_beam.runners.common.DoFnRunner.process
    File "apache_beam/runners/common.py", line 624, in apache_beam.runners.common.SimpleInvoker.invoke_process
    File "/usr/local/lib/python3.9/dist-packages/apache_beam/transforms/core.py", line 1956, in <lambda>
    File "/usr/local/lib/python3.9/dist-packages/pangeo_forge_recipes/executors/beam.py", line 40, in exec_stage
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/pangeo_forge_recipes/recipes/xarray_zarr.py", line 156, in cache_input
      config.storage_config.cache.cache_file(
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/pangeo_forge_recipes/storage.py", line 173, in cache_file
      _copy_btw_filesystems(input_opener, target_opener)
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/pangeo_forge_recipes/storage.py", line 37, in _copy_btw_filesystems
      with input_opener as source:
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/core.py", line 103, in __enter__
      f = self.fs.open(self.path, mode=mode)
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/spec.py", line 1034, in open
      f = self._open(
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/implementations/http.py", line 340, in _open
      size = size or self.info(path, **kwargs)["size"]
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/asyn.py", line 111, in wrapper
      return sync(self.loop, func, *args, **kwargs)
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/asyn.py", line 96, in sync
      raise return_result
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/asyn.py", line 53, in _runner
      result[0] = await coro
    File "/srv/conda/envs/notebook/lib/python3.9/site-packages/fsspec/implementations/http.py", line 404, in _info
      raise FileNotFoundError(url) from exc
  FileNotFoundError: https://ige-meom-opendap.univ-grenoble-alpes.fr/thredds/fileServer/meomopendap/extract/eNATL60/eNATL60-BLBT02/1d/eNATL60-BLBT02_y2009m07d02.1d_TSW_600m.nc

pangeo-forge · 2022-10-19T21:05:15Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

andersy005 · 2022-10-19T22:12:10Z

/run eNATL60_wtides_1d_mld

pangeo-forge · 2022-10-19T22:34:11Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

andersy005 · 2022-10-19T23:20:39Z

/run eNATL60_wtides_1d_mld

pangeo-forge · 2022-10-19T23:42:19Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

andersy005 · 2022-10-19T23:43:33Z

/run eNATL60_wtides_1d_tsw600m

pangeo-forge · 2022-10-20T00:05:34Z

The test failed, but I'm sure we can find out why!

Pangeo Forge maintainers are working diligently to provide public logs for contributors.
That feature is not quite ready yet, however, so please reach out on this thread to a
maintainer, and they'll help you diagnose the problem.

andersy005 · 2022-10-20T15:19:27Z

/run eNATL60_wtides_1d_tsw600m

pangeo-forge · 2022-10-20T15:29:16Z

🎉 The test run of eNATL60_wtides_1d_tsw600m at d69ab37 succeeded!

import xarray as xr

store = "https://ncsa.osn.xsede.org/Pangeo/pangeo-forge/test/pangeo-forge/staged-recipes/recipe-run-1165/eNATL60_wtides_1d_tsw600m.zarr"
ds = xr.open_dataset(store, engine='zarr', chunks={})
ds

andersy005 · 2022-10-20T15:30:34Z

/run eNATL60_wtides_1d_tsw600m

auraoupa · 2022-10-20T15:31:26Z

That looks promising ! Thanks @andersy005 for sorting that out !

andersy005 · 2022-10-20T15:32:36Z

/run eNATL60_wtides_1d_mld

andersy005 · 2022-10-20T15:33:38Z

That looks promising ! Thanks @andersy005 for sorting that out !

You are welcome! i'm going to try the other runs as well, and fingers crossed everything goes well :)

andersy005 · 2022-10-20T15:33:58Z

/run eNATL60_wtides_1d_tsw60m

pangeo-forge · 2022-10-20T15:36:11Z

🎉 The test run of eNATL60_wtides_1d_tsw600m at d69ab37 succeeded!

import xarray as xr

store = "https://ncsa.osn.xsede.org/Pangeo/pangeo-forge/test/pangeo-forge/staged-recipes/recipe-run-1165/eNATL60_wtides_1d_tsw600m.zarr"
ds = xr.open_dataset(store, engine='zarr', chunks={})
ds

pangeo-forge · 2022-10-20T15:38:00Z

🎉 The test run of eNATL60_wtides_1d_mld at d69ab37 succeeded!

import xarray as xr

store = "https://ncsa.osn.xsede.org/Pangeo/pangeo-forge/test/pangeo-forge/staged-recipes/recipe-run-1163/eNATL60_wtides_1d_mld.zarr"
ds = xr.open_dataset(store, engine='zarr', chunks={})
ds

pangeo-forge · 2022-10-20T15:40:45Z

🎉 The test run of eNATL60_wtides_1d_tsw60m at d69ab37 succeeded!

import xarray as xr

store = "https://ncsa.osn.xsede.org/Pangeo/pangeo-forge/test/pangeo-forge/staged-recipes/recipe-run-1164/eNATL60_wtides_1d_tsw60m.zarr"
ds = xr.open_dataset(store, engine='zarr', chunks={})
ds

andersy005 · 2022-10-20T15:42:29Z

@auraoupa, all test runs are passing. do you plan on making any changes? if not, we can go ahead and merge this PR.

auraoupa · 2022-10-20T16:12:57Z

Yay 👏 That's fine for me, we can go ahead !

andersy005 · 2022-10-20T17:59:08Z

Thank you for your patience, @auraoupa!

auraoupa · 2022-10-24T11:58:43Z

Hi @andersy005 , does this mean the recipes have failed ? The timestamps suggest it happened 15mn after the merge ...

auraoupa · 2022-10-31T07:54:01Z

Hi @andersy005, @cisaacstern ! So no datasets have been produced after the pull request has been merged, I do not know what went wrong : https://pangeo-forge.org/dashboard/feedstock/87, it only says that the status is failed ... Do you have any insights on this ? Is it possible to run it again ?

auraoupa added 5 commits September 16, 2022 11:35

Create recipe.py

f8cf750

Create meta.yaml

bd4aec2

fix typos

6074b6e

Update meta.yaml

19574ee

removes import of unused library

1a63b8b

[pre-commit.ci] auto fixes from pre-commit.com hooks

d69ab37

for more information, see https://pre-commit.ci

cisaacstern mentioned this pull request Oct 4, 2022

In test run failed comments, give recipe_id and head_sha pangeo-forge/pangeo-forge-orchestrator#108

Closed

derekocallaghan mentioned this pull request Oct 5, 2022

Adding EOOffshore CMEMS ASCAT REP and NRT recipes #183

Open

andersy005 merged commit 7ece666 into pangeo-forge:master Oct 20, 2022

auraoupa mentioned this pull request Oct 25, 2022

Draft for INALT60 recipe #26

Open

andersy005 mentioned this pull request Oct 31, 2022

No datasets have been produced after first feedstock run pangeo-forge/eNATL60-feedstock#2

Open

Recipes for daily eNATL60 at depth data #189

Recipes for daily eNATL60 at depth data #189

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auraoupa commented Sep 27, 2022

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