Trouble shooting

This chapter contains a collection of common errors and their solutions.

• snakemake: command not found:

  • Did you install the cd2es environment and activated it before executing snakemake?

• sh: 1: cdo: not found:

  • The setup of the climate data processing tool cdo did not work correctly. Did you correctly execute all installation scripts?

  • If you did and the error persists, look into Installation to install cdo manually.

• ValueError: unrecognized chunk manager dask - must be one of: []

  • the python package dask, which is used to handle large amounts of climate data is not installed correctly

  • that happens sometimes, it often can be fixed by reinstalling dask via pip install dask (when the cd2es environment is activated)

• Exception: No climate data available with the given parameters. Check model name and the cordex parameter in the config.

  • The combination of climate variable, climate model and RCP does not exist. Compare the parameters given in the config (under scenario and cordexParameters) and check whether the combination exisits on https://esgf-data.dkrz.de/search/cordex-dkrz/

• requests.exceptions.SSLError in the downloadEra5 rule

  • error in the authentification at the copernicus climate data store

  • Did you register at https://cds.climate.copernicus.eu/?

  • Did you make a mistake when typing in your credentials?

  • Is loginDataAsParams activated in the config? Then you must give your credentials via the command line (see The config file for more infos).

• Snakemake terminates without giving an indication for the type of error:

  • often memory related, try diminishing mem_mb or enlarging numberOfChunks in the config

• Unable to allocate memory, process died with <Signals.SIGKILL: 9>:

  • not enough RAM, try diminishing mem_mb to execute less processes at the same time or enlarging numberOfChunks in the config

• time-out, to allocate more time, change maxTime parameter in config or process returned non-zero exit status 50:

  • execution of rule exceeded time limits

  • sometimes, the parallelized computations within the tool with dask get stuck, therefore, there is a time limit on all complicated rules

  • if a rule exceeds the time limit, it gets killed and restarted - therefore this error might exist but the tool can still successfully complete (if the restarted process does not get stuck)

  • the error code for a rule killed by the time out is 50 (sometimes the display of the written warning does not work)

  • the time limit is given by the maxTime in the config

  • if all retries of a rule are killed with the out of time error, enlarge the time limit to make sure it is only activated in case of a stuck process

• Error in rule downloadEra5 without information on the error:

  • Did you register with the copernicus climate data store?

  • See Prerequisites for more information.

  • If you have problems with setting up the .cdsapirc in the home folder, you can also give your copernicus climate data store credentials directly in the config (giveCdsCredentialsInConfig).

• Downloads of era5 or cordex data fail (e.g. with Gateway Time-out, Read timed out. or 500 Server Error)

  • This is often not related to the tool or your execution but the download server which has down times or failures from time to time. Wait a little and try again later and contact either the Copernicus data store (for era5 data) or the ESGF (for cordex data) if the problem persists.

• No rule to produce {filename}:

  • The file you are trying to produce cannot be created by snakemake workflow.

  • If you have specified a filename, check whether there is a rule that produces your desired file and check your spelling. Check the wildcards you inserted by checking wildcard_constraints in line 12 of the snakefile.

  • If you run the tool without a specified filename, check the information in the section scenario of the config and whether they are correct (either by checking the comments in the config or by checking wildcard_constraints in line 12 of the snakefile).

  • If you are on Windows and having a snakemake version < 8, you need to add --keep-target-files to your command line to resolve this problem.

• Permission denied

  • Is any of the output files still open in another programme?