data export error ------ "verdi archive create"

[Witty Yonng]

Hi all,

When I run this command "verdi archive create my-calculations-09-02.aiida --all". It raise the below error. How can I solve it?

Thanks,

Report:
Archive Parameters
--------------------  ---------------------------
Path                  my-calculations-09-02.aiida
Version               main_0001
Compression           6

Inclusion rules
----------------------------  -----
Computers/Nodes/Groups/Users  All
Computer Authinfos            False
Node Comments                 True
Node Logs                     True

Report: Validating Nodes                                                                                                                                        
Report: Creating archive with:
-----------  ----
users           1
computers       4
groups         11
nodes        4457
logs           32
links        1152
group_nodes   336
-----------  ----
Traceback (most recent call last):                                                                                                                              
  File "/home/witty/envs/aiida/bin/verdi", line 8, in <module>
    sys.exit(verdi())
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/aiida/cmdline/utils/decorators.py", line 73, in wrapper
    return wrapped(*args, **kwargs)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/aiida/cmdline/commands/cmd_archive.py", line 197, in create
    create_archive(entities, filename=output_file, archive_format=archive_format, **kwargs)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/aiida/tools/archive/create.py", line 341, in create_archive
    _stream_repo_files(archive_format.key_format, writer, entity_ids[EntityTypes.NODE], backend, batch_size)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/aiida/tools/archive/create.py", line 585, in _stream_repo_files
    writer.put_object(stream, key=key)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/aiida/tools/archive/implementations/sqlite_zip/writer.py", line 186, in put_object
    self._stream_binary(f'{utils.REPO_FOLDER}/{key}', stream, buffer_size=buffer_size)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/aiida/tools/archive/implementations/sqlite_zip/writer.py", line 171, in _stream_binary
    handle.seek(0, os.SEEK_END)
  File "/home/witty/envs/aiida/lib/python3.8/site-packages/disk_objectstore/utils.py", line 421, in seek
    raise NotImplementedError(
NotImplementedError: Invalid value for `whence`: only 0 and 1 are currently implemented.

[Sebastiaan Huber]

Hi,

I think this bug may have been fixed but not yet released (see this commit: https://github.com/aiidateam/aiida-core/commit/46d244e32ac5eca2e22a3d088314591ce064be57)
If you like, you can try checking out the `main` branch from the repository (https://github.com/aiidateam/aiida-core) and installing that:

    git checkout https://github.com/aiidateam/aiida-core
    pip install -e aiida-core

Then try to export again.

Hope that helps,

Sebastiaan

--
AiiDA is supported by the NCCR MARVEL (http://nccr-marvel.ch/), funded by the Swiss National Science Foundation, and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/).
 
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[Witty Yonng]

Hi, Sebastiaan

Thank you for your help. When I run "git checkout https://github.com/aiidateam/aiida-core".  It raise error: The path specifications 'aiida-core/' not matched any Git known file.

So I run "git clone https://github.com/aiidateam/aiida-core", and get the aiida-core directory. But when I run "pip install -e aiida-core/", it raise another error: 

ERROR: File "setup.py" not found. Directory cannot be installed in editable mode: /home/witty/git_dir/aiida-core (A "pyproject.toml" file was found, but editable mode currently requires a setup.py based build.)

Best,

Witty

[Sebastiaan Huber]

Hi Witty,

Apologies, that was a mistake, I meant to type clone indeed.
Regarding the second error, that is due to an outdated version of pip.
You should be able to upgrade it with

    pip install --upgrade pip

HTH,

Sebastiaan

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[Witty Yonng]

Hi Sebastiaan,

I have tried "pip install --upgrade pip", and it still raises error.

"""

Defaulting to user installation because normal site-packages is not writeable
Obtaining file:///home/witty/git_dir/aiida-core
ERROR: file:///home/witty/git_dir/aiida-core does not appear to be a Python project: neither 'setup.py' nor 'pyproject.toml' found.

"""

Best,

Witty

[Sebastiaan Huber]

Hi Witty,

What is the output of

    python --version
    pip --version

Regards,

Sebastiaan

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[Witty Yonng]

python 3.8.10

pip 22.2.2 

[Sebastiaan Huber]

Hi Witty,

That looks fine.
What is the content of the `aiida-core` directory though?
The error says that there is no pyproject.toml file, which is very unlikely if you checked out the repository correctly.

Regards,

Sebastiaan

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