Hi,
I am following the instruction to install the instruction Getting the plugin — yambo-aiida 1.1.2 documentation
Both two methods failed. The same system works well for aiida-quantumespresso and aiida-vasp. Any idea what the problem is?
(aiida_QE_VASP_YAMBO) yang@yang-Inspiron-3670:~/AiiDA/plugin/aiida_quantum_espresso/03_aiida_YAMBO/git$ git clone https://github.com/yambo-code/yambo-aiida.git
正克隆到 'yambo-aiida'...
error: RPC 失败。curl 16 Error in the HTTP2 framing layer
fatal: 在引用列表之后应该有一个 flush 包
(aiida_QE_VASP_YAMBO) yang@yang-Inspiron-3670:~/AiiDA/plugin/aiida_quantum_espresso/03_aiida_YAMBO/git$ git config --global http.version HTTP/1.1
(aiida_QE_VASP_YAMBO) yang@yang-Inspiron-3670:~/AiiDA/plugin/aiida_quantum_espresso/03_aiida_YAMBO/git$ git clone https://github.com/yambo-code/yambo-aiida.git
正克隆到 'yambo-aiida'...
fatal: 无法访问 'https://github.com/yambo-code/yambo-aiida.git/'：GnuTLS recv error (-110): The TLS connection was non-properly terminated.
(aiida_QE_VASP_YAMBO) yang@yang-Inspiron-3670:~/AiiDA/plugin/aiida_quantum_espresso/03_aiida_YAMBO/git$ git config --global http.version HTTP/2
(aiida_QE_VASP_YAMBO) yang@yang-Inspiron-3670:~/AiiDA/plugin/aiida_quantum_espresso/03_aiida_YAMBO/git$ git clone https://github.com/yambo-code/yambo-aiida.git
正克隆到 'yambo-aiida'...
fatal: 无法访问 'https://github.com/yambo-code/yambo-aiida.git/'：GnuTLS recv error (-110): The TLS connection was non-properly terminated.
(aiida_QE_VASP_YAMBO) yang@y
(aiida_QE_VASP_YAMBO) yang@yang-Inspiron-3670:~/AiiDA/plugin/aiida_quantum_espresso/03_aiida_YAMBO$ date && sudo pip --default-timeout=1000000 install aiida-yambo
2024年 02月 26日 星期一 12:57:14 CST
[sudo] yang 的密码：
Collecting aiida-yambo
Using cached aiida_yambo-1.3.0-py3-none-any.whl (57 kB)
Collecting aiida-quantumespresso<4.0,>=3.0.0a6
Using cached aiida_quantumespresso-3.5.2-py3-none-any.whl (729 kB)
Collecting netcdf4
Using cached netCDF4-1.6.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (5.5 MB)
Collecting h5py
Using cached h5py-3.10.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.8 MB)
Collecting aiida-core[atomic_tools,docs]>=1.0.0a2
Using cached aiida_core-2.5.1-py3-none-any.whl (1.3 MB)
Collecting pytest
Using cached pytest-8.0.2-py3-none-any.whl (333 kB)
Requirement already satisfied: paramiko>=2.7.2,~=2.7 in /usr/lib/python3/dist-packages (from aiida-core[atomic_tools,docs]>=1.0.0a2->aiida-yambo) (2.9.3)
Collecting pgsu~=0.2.1
Using cached pgsu-0.2.4.tar.gz (9.9 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting docstring-parser
Using cached docstring_parser-0.15-py3-none-any.whl (36 kB)
Collecting plumpy~=0.21.6
Using cached plumpy-0.21.10-py3-none-any.whl (74 kB)
Collecting jedi<0.19
Using cached jedi-0.18.2-py2.py3-none-any.whl (1.6 MB)
Collecting psycopg2-binary~=2.8
Using cached psycopg2_binary-2.9.9-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.0 MB)
Collecting circus~=0.18.0
Using cached circus-0.18.0-py3-none-any.whl (200 kB)
Collecting jinja2~=3.0
Using cached Jinja2-3.1.3-py3-none-any.whl (133 kB)
Collecting archive-path~=0.4.2
Using cached archive_path-0.4.2-py3-none-any.whl (18 kB)
Collecting disk-objectstore~=1.0
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Collecting pyyaml~=6.0
Using cached PyYAML-6.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (705 kB)
Collecting tqdm~=4.45
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Using cached importlib_metadata-6.11.0-py3-none-any.whl (23 kB)
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Collecting tabulate~=0.8.5
Using cached tabulate-0.8.10-py3-none-any.whl (29 kB)
Collecting sqlalchemy~=2.0
Using cached SQLAlchemy-2.0.27-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
Collecting click-spinner~=0.1.8
Using cached click_spinner-0.1.10-py2.py3-none-any.whl (4.0 kB)
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Collecting kiwipy[rmq]~=0.7.7
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Using cached ipython-8.22.1-py3-none-any.whl (811 kB)
Requirement already satisfied: requests~=2.0 in /usr/lib/python3/dist-packages (from aiida-core[atomic_tools,docs]>=1.0.0a2->aiida-yambo) (2.25.1)
Collecting numpy~=1.21
Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Collecting pydantic~=2.4
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Collecting wrapt~=1.11
Using cached wrapt-1.16.0-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
Collecting click~=8.1
Using cached click-8.1.7-py3-none-any.whl (97 kB)
Collecting spglib<3.0,>=1.14
Using cached spglib-2.3.1-cp310-cp310-manylinux_2_17_x86_64.whl (807 kB)
Collecting matplotlib>=3.3.4,~=3.3
Using cached matplotlib-3.8.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
Collecting pymysql~=0.9.3
Using cached PyMySQL-0.9.3-py2.py3-none-any.whl (47 kB)
Collecting PyCifRW~=4.4
Using cached PyCifRW-4.4.6.tar.gz (1.1 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Collecting pymatgen>=2022.1.20
Using cached pymatgen-2024.2.23-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (10.0 MB)
Collecting seekpath>=1.9.3,~=1.9
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Collecting ase~=3.18
Using cached ase-3.22.1-py3-none-any.whl (2.2 MB)
Collecting sphinx-design~=0.5.0
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Collecting pydata-sphinx-theme~=0.13.3
Using cached pydata_sphinx_theme-0.13.3-py3-none-any.whl (2.0 MB)
Collecting sphinx-notfound-page~=1.0
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Using cached myst_nb-1.0.0-py3-none-any.whl (79 kB)
Collecting sphinxext-rediraffe~=0.2.4
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Collecting jsonschema
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Collecting packaging
Using cached packaging-23.2-py3-none-any.whl (53 kB)
Collecting aiida-pseudo~=0.6.1
Using cached aiida_pseudo-0.6.5-py3-none-any.whl (74 kB)
Collecting qe-tools~=2.0rc1
Using cached qe_tools-2.2.0-py3-none-any.whl (24 kB)
Collecting psycopg2-binary~=2.8
Using cached psycopg2-binary-2.8.6.tar.gz (384 kB)
Preparing metadata (setup.py) ... done
Collecting xmlschema>=1.2.5,~=1.2
Using cached xmlschema-1.11.3-py3-none-any.whl (356 kB)
Collecting aiida-quantumespresso<4.0,>=3.0.0a6
Using cached aiida_quantumespresso-3.5.1-py3-none-any.whl (783 kB)
Using cached aiida_quantumespresso-3.5.0-py3-none-any.whl (369 kB)
Using cached aiida_quantumespresso-3.4.2-py3-none-any.whl (354 kB)
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Using cached aiida_quantumespresso-3.3.0-py3-none-any.whl (337 kB)
Collecting aiida-pseudo~=0.4.0
Downloading aiida_pseudo-0.4.0-py3-none-any.whl (56 kB)
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Collecting aiida-quantumespresso<4.0,>=3.0.0a6
Using cached aiida_quantumespresso-3.2.1-py2.py3-none-any.whl (306 kB)
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Using cached aiida_quantumespresso-3.0.0-py2.py3-none-any.whl (283 kB)
Collecting xmlschema==1.0.13
Downloading xmlschema-1.0.13-py2.py3-none-any.whl (307 kB)
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Collecting qe-tools==1.1.3
Downloading qe-tools-1.1.3.tar.gz (15 kB)
Preparing metadata (setup.py) ... done
Collecting aiida-quantumespresso<4.0,>=3.0.0a6
Using cached aiida_quantumespresso-3.0.0a6-py3-none-any.whl (258 kB)
INFO: pip is looking at multiple versions of aiida-core[atomic-tools,docs] to determine which version is compatible with other requirements. This could take a while.
Collecting aiida-core[atomic_tools,docs]>=1.0.0a2
Using cached aiida_core-2.5.0-py3-none-any.whl (1.3 MB)
Collecting aiida_core[atomic_tools]>=1.4.4,~=1.4
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Collecting importlib_resources
Using cached importlib_resources-6.1.2-py3-none-any.whl (34 kB)
Collecting ete3~=3.1
Using cached ete3-3.1.3.tar.gz (4.8 MB)
Preparing metadata (setup.py) ... done
Collecting tzlocal~=2.0
Using cached tzlocal-2.1-py2.py3-none-any.whl (16 kB)
Collecting click-config-file~=0.6.0
Using cached click_config_file-0.6.0-py2.py3-none-any.whl (6.0 kB)
Collecting circus~=0.17.1
Using cached circus-0.17.2-py3-none-any.whl (204 kB)
Collecting click~=7.1
Using cached click-7.1.2-py2.py3-none-any.whl (82 kB)
Collecting sqlalchemy~=1.3.10
Using cached SQLAlchemy-1.3.24.tar.gz (6.4 MB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: markupsafe<2.1 in /usr/lib/python3/dist-packages (from aiida_core[atomic_tools]>=1.4.4,~=1.4->aiida-quantumespresso<4.0,>=3.0.0a6->aiida-yambo) (2.0.1)
Collecting django~=2.2
Using cached Django-2.2.28-py3-none-any.whl (7.5 MB)
Requirement already satisfied: python-dateutil~=2.8 in /usr/lib/python3/dist-packages (from aiida_core[atomic_tools]>=1.4.4,~=1.4->aiida-quantumespresso<4.0,>=3.0.0a6->aiida-yambo) (2.8.1)
Collecting wrapt~=1.11.1
Using cached wrapt-1.11.2.tar.gz (27 kB)
Preparing metadata (setup.py) ... done
Collecting simplejson~=3.16
Using cached simplejson-3.19.2-cp310-cp310-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (137 kB)
Collecting reentry~=1.3
Using cached reentry-1.3.3-py3-none-any.whl (17 kB)
Collecting sqlalchemy-utils~=0.36.0
Using cached SQLAlchemy-Utils-0.36.5.tar.gz (131 kB)
Preparing metadata (setup.py) ... done
Collecting jinja2~=2.10
Using cached Jinja2-2.11.3-py2.py3-none-any.whl (125 kB)
Collecting pamqp~=2.3
Using cached pamqp-2.3.0-py2.py3-none-any.whl (28 kB)
Collecting aldjemy~=0.9.1
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Collecting click-completion~=0.5.1
Using cached click-completion-0.5.2.tar.gz (10 kB)
Preparing metadata (setup.py) ... done
Collecting archive-path~=0.2.1
Using cached archive_path-0.2.1-py3-none-any.whl (17 kB)
Collecting pytz~=2019.3
Using cached pytz-2019.3-py2.py3-none-any.whl (509 kB)
Collecting plumpy~=0.20.0
Using cached plumpy-0.20.0-py3-none-any.whl (60 kB)
Collecting jsonschema
Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting ipython~=7.20
Using cached ipython-7.34.0-py3-none-any.whl (793 kB)
Requirement already satisfied: pyyaml~=5.4 in /usr/lib/python3/dist-packages (from aiida_core[atomic_tools]>=1.4.4,~=1.4->aiida-quantumespresso<4.0,>=3.0.0a6->aiida-yambo) (5.4.1)
Collecting spglib~=1.14
Downloading spglib-1.16.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (325 kB)
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Collecting pymatgen!=2019.9.7,<=2022.02.03,>=2019.7.2
Using cached pymatgen-2022.2.1.tar.gz (2.6 MB)
Installing build dependencies ... |
error
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 2
╰─> [90 lines of output]
Collecting oldest-supported-numpy
Using cached oldest_supported_numpy-2023.12.21-py3-none-any.whl (4.9 kB)
Collecting setuptools>=43.0.0
Using cached setuptools-69.1.1-py3-none-any.whl (819 kB)
Collecting Cython>=0.29.23
Downloading Cython-3.0.8-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)
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Collecting numpy==1.21.6
Downloading numpy-1.21.6-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.9 MB)
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ERROR: Exception:
Traceback (most recent call last):
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/urllib3/response.py", line 438, in _error_catcher
yield
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/urllib3/response.py", line 519, in read
data = self._fp.read(amt) if not fp_closed else b""
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/cachecontrol/filewrapper.py", line 90, in read
data = self.__fp.read(amt)
File "/usr/lib/python3.10/http/client.py", line 466, in read
s = self.fp.read(amt)
File "/usr/lib/python3.10/socket.py", line 705, in readinto
return self._sock.recv_into(b)
File "/usr/lib/python3.10/ssl.py", line 1303, in recv_into
return self.read(nbytes, buffer)
File "/usr/lib/python3.10/ssl.py", line 1159, in read
return self._sslobj.read(len, buffer)
TimeoutError: The read operation timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/cli/base_command.py", line 165, in exc_logging_wrapper
status = run_func(*args)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/cli/req_command.py", line 205, in wrapper
return func(self, options, args)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/commands/install.py", line 339, in run
requirement_set = resolver.resolve(
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/resolver.py", line 94, in resolve
result = self._result = resolver.resolve(
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/resolvelib/resolvers.py", line 481, in resolve
state = resolution.resolve(requirements, max_rounds=max_rounds)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/resolvelib/resolvers.py", line 373, in resolve
failure_causes = self._attempt_to_pin_criterion(name)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/resolvelib/resolvers.py", line 213, in _attempt_to_pin_criterion
criteria = self._get_updated_criteria(candidate)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/resolvelib/resolvers.py", line 204, in _get_updated_criteria
self._add_to_criteria(criteria, requirement, parent=candidate)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/resolvelib/resolvers.py", line 172, in _add_to_criteria
if not criterion.candidates:
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/resolvelib/structs.py", line 151, in __bool__
return bool(self._sequence)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__
return any(self)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in <genexpr>
return (c for c in iterator if id(c) not in self._incompatible_ids)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built
candidate = func()
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/factory.py", line 215, in _make_candidate_from_link
self._link_candidate_cache[link] = LinkCandidate(
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/candidates.py", line 288, in __init__
super().__init__(
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/candidates.py", line 158, in __init__
self.dist = self._prepare()
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/candidates.py", line 227, in _prepare
dist = self._prepare_distribution()
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/resolution/resolvelib/candidates.py", line 299, in _prepare_distribution
return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/operations/prepare.py", line 487, in prepare_linked_requirement
return self._prepare_linked_requirement(req, parallel_builds)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/operations/prepare.py", line 532, in _prepare_linked_requirement
local_file = unpack_url(
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/operations/prepare.py", line 214, in unpack_url
file = get_http_url(
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/operations/prepare.py", line 94, in get_http_url
from_path, content_type = download(link, temp_dir.path)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/network/download.py", line 146, in __call__
for chunk in chunks:
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/cli/progress_bars.py", line 304, in _rich_progress_bar
for chunk in iterable:
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_internal/network/utils.py", line 63, in response_chunks
for chunk in response.raw.stream(
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/urllib3/response.py", line 576, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/urllib3/response.py", line 512, in read
with self._error_catcher():
File "/usr/lib/python3.10/contextlib.py", line 153, in __exit__
self.gen.throw(typ, value, traceback)
File "/tmp/pip-standalone-pip-47u4wuwc/__env_pip__.zip/pip/_vendor/urllib3/response.py", line 443, in _error_catcher
raise ReadTimeoutError(self._pool, None, "Read timed out.")
pip._vendor.urllib3.exceptions.ReadTimeoutError: HTTPSConnectionPool(host='files.pythonhosted.org', port=443): Read timed out.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 2
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.
Many thanks!
Sincerely,
Dr. Guoyu Yang
Lecturer
Jimei Univ, School of Science, Digital Fujian Big Data Modeling and Intelligent Computing Institute
185 Yinjiang Rd.,
Jimei District, Xiamen,361021
Fujian, China
E-mail: 201961000100@jmu.edu.cn