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Permission Error when making filemarker for top of experiment

  • ESM Analysis version: 0.3.0
  • Python version: 3.6
  • Operating System: mistral

Description

It turns out that there is a permission error when you try to mark an experiment that isn't yours (duh).

What I Did

Enter the top-level directory of your experiment: /work/ba0989/a270077/CMIP6_PMIP4/a270073/CMIP6/CMIP_PMIP/dynveg_true/1percCO2/
Making marker file .top_of_exp_tree in /work/ba0989/a270077/CMIP6_PMIP4/a270073/CMIP6/CMIP_PMIP/dynveg_true/1percCO2
Press Enter to continue, Ctrl-C to canel...
Traceback (most recent call last):
  File "/pf/a/a270077/.local/bin/esm_analysis", line 11, in <module>
    load_entry_point('esm-analysis', 'console_scripts', 'esm_analysis')()
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/mnt/lustre01/pf/a/a270077/Code/esm_analysis/esm_analysis/cli.py", line 44, in fldmean
    analyzer = EsmAnalysis(preferred_analysis_dir=preferred_analysis_dir)
  File "/mnt/lustre01/pf/a/a270077/Code/esm_analysis/esm_analysis/esm_analysis.py", line 109, in __init__
    with open(self.EXP_BASE + "/.top_of_exp_tree", "w") as f:
PermissionError: [Errno 13] Permission denied: '/work/ba0989/a270077/CMIP6_PMIP4/a270073/CMIP6/CMIP_PMIP/dynveg_true/1percCO2//.top_of_exp_tree'

File Lists in ECHAM still being used

  • ESM Analysis version: 0.4.2
  • Python version: 3.6 (probably)
  • Operating System: Mistral

Description

Lars was following the example for fldmean temp2 on Mistral. There seems to be a problem with the echam fldmean function call, it still wants file lists.

What I Did

This will generate a fldmean for: temp2
You passed in preferred_analysis_dir: None
WARNING:root:Oops: Trouble initializing or no analysis class available for: oasis3mct
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: hdmodel
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: esm_analysis.dkrz.log.02
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: jsbach
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: pism
ERROR:root:Error was: <class 'ModuleNotFoundError'>
Load 2d part of the grid in 2 second(s)
Traceback (most recent call last):
  File "/pf/a/a270124/.local/bin/esm_analysis", line 8, in <module>
    sys.exit(main())
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/cli.py", line 71, in fldmean
    analyzer.fldmean(varname)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/esm_analysis.py", line 486, in fldmean
    return component.fldmean(varname)
TypeError: fldmean() missing 1 required positional argument: 'file_list'

The best way to get around this is to make sure file_list isn't used anywhere
in any of the calls from the EsmAnalysis instance. Everything should just work
with variable names; or ask questions if it gets stuck.

Problem on Ollie 

This will generate a fldmean for: temp2
You passed in preferred_analysis_dir: None
Traceback (most recent call last):
  File "/home/ollie/lackerma/.local/bin/esm_analysis", line 8, in <module>
    sys.exit(main())
  File "/global/AWIsoft/intel/2019/intelpython3/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/global/AWIsoft/intel/2019/intelpython3/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/global/AWIsoft/intel/2019/intelpython3/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/global/AWIsoft/intel/2019/intelpython3/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/global/AWIsoft/intel/2019/intelpython3/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/home/ollie/lackerma/.local/lib/python3.6/site-packages/esm_analysis/cli.py", line 67, in fldmean
    analyzer = EsmAnalysis(preferred_analysis_dir=preferred_analysis_dir)
  File "/home/ollie/lackerma/.local/lib/python3.6/site-packages/esm_analysis/esm_analysis.py", line 151, in __init__
    self.CDO = cdo.Cdo()
  File "/home/ollie/lackerma/.local/lib/python3.6/site-packages/cdo.py", line 144, in __init__
    self.operators         = self.__getOperators()
  File "/home/ollie/lackerma/.local/lib/python3.6/site-packages/cdo.py", line 190, in __getOperators
    version = parse_version(getCdoVersion(self.CDO))
  File "/home/ollie/lackerma/.local/lib/python3.6/site-packages/cdo.py", line 73, in getCdoVersion
    return match.group(1)
AttributeError: 'NoneType' object has no attribute 'group'

Index out of range in comps[0]

  • ESM Analysis version: 0.4.2
  • Python version: 3.6
  • Operating System: Mistral

Description

Looks like there is a problem when on;y one particular component has a
variable, in this case so. Probably I need to do a check if the list is empty
or not and check if it only has one entry. This should ideally throw a more
useful error message...

What I Did

This will generate a fldmean for: so
You passed in preferred_analysis_dir: None
WARNING:root:Oops: Trouble initializing or no analysis class available for: oasis3mct
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: hdmodel
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: esm_analysis.dkrz.log.02
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: jsbach
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: pism
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: esm_analysis.dkrz.log.03
ERROR:root:Error was: <class 'ModuleNotFoundError'>
Load 2d part of the grid in 2 second(s)
Traceback (most recent call last):
  File "/pf/a/a270124/.local/bin/esm_analysis", line 8, in <module>
    sys.exit(main())
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/cli.py", line 71, in fldmean
    analyzer.fldmean(varname)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/esm_analysis.py", line 486, in fldmean
    return component.fldmean(varname)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/esm_analysis.py", line 485, in fldmean
    component = self.get_component_for_variable_short_name(varname)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/esm_analysis.py", line 476, in get_component_for_variable_short_name
    return multi_comps[0]
IndexError: list index out of range

Save file tag preference

Currently, if a requested variable is found in more than one file tag (e.g. temp2 in both echam6_echam and echam6_ma), the program asks each time which files should be taken. This preference could be stored (and, if needed, ignored)

Problem on MISTRAL 

This will generate a fldmean for: temp2
You passed in preferred_analysis_dir: None
WARNING:root:Oops: Trouble initializing or no analysis class available for: oasis3mct
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: hdmodel
ERROR:root:Error was: <class 'ModuleNotFoundError'>
WARNING:root:Oops: Trouble initializing or no analysis class available for: fesom
ERROR:root:Error was: <class 'AttributeError'>
Traceback (most recent call last):
  File "/pf/a/a270124/.local/bin/esm_analysis", line 8, in <module>
    sys.exit(main())
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/sw/rhel6-x64/conda/anaconda3-bleeding_edge/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/cli.py", line 69, in fldmean
    preferred_analysis_dir=preferred_analysis_dir
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/esm_analysis.py", line 202, in initialize_analysis_components
    )(exp_base=self.EXP_BASE, preferred_analysis_dir=preferred_analysis_dir)
  File "/pf/a/a270124/.local/lib/python3.6/site-packages/esm_analysis/components/fesom.py", line 49, in __init__
    self._config = self._config.get("fesom", {})
AttributeError: 'str' object has no attribute 'get'

FESOM Support

Before I give esm-analysis to the group, I'd like FESOM support.

Currently, I can easily load data into an xarray dataframe. However, there are
currently MemoryErrors occuring as soon as I try to use the multi-file
dataset to do anything. An example will follow.

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