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Conda is hanging #250

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hmaarrfk opened this issue Dec 28, 2024 · 10 comments
Closed
1 task done

Conda is hanging #250

hmaarrfk opened this issue Dec 28, 2024 · 10 comments
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@hmaarrfk
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Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

For the last few days, I've noticed conda hangs upon (reactivation????)

$ mamba install "liblief<0.16.0"

Looking for: ["liblief[version='<0.16.0']"]

conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache

Pinned packages:
  - python 3.12.*


Transaction

  Prefix: /home/mark/miniforge3

  Updating specs:

   - liblief[version='<0.16.0']
   - ca-certificates
   - certifi
   - openssl


  Package    Version  Build            Channel           Size
───────────────────────────────────────────────────────────────
  Downgrade:
───────────────────────────────────────────────────────────────

  - liblief   0.16.0  h5888daf_1       conda-forge     Cached
  + liblief   0.15.1  h5888daf_0       conda-forge     Cached
  - py-lief   0.16.0  py312h2ec8cdc_1  conda-forge     Cached
  + py-lief   0.15.1  py312h2ec8cdc_0  conda-forge     Cached

  Summary:

  Downgrade: 2 packages

  Total download: 0 B

───────────────────────────────────────────────────────────────


Confirm changes: [Y/n] y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

just seems to hang...

Installed packages

# packages in environment at /home/mark/miniforge3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
anaconda-client           1.12.3             pyhd8ed1ab_1    conda-forge
anyio                     3.7.1              pyhd8ed1ab_0    conda-forge
archspec                  0.2.3              pyhd8ed1ab_0    conda-forge
attrs                     24.3.0             pyh71513ae_0    conda-forge
backports                 1.0                pyhd8ed1ab_5    conda-forge
backports.strenum         1.2.8              pyhd8ed1ab_0    conda-forge
backports.tarfile         1.2.0              pyhd8ed1ab_1    conda-forge
beautifulsoup4            4.12.3             pyha770c72_1    conda-forge
blinker                   1.9.0              pyhff2d567_0    conda-forge
boa                       0.17.0             pyhd8ed1ab_3    conda-forge
boltons                   24.0.0             pyhd8ed1ab_1    conda-forge
boolean.py                4.0                pyhd8ed1ab_1    conda-forge
brotli-python             1.1.0           py312h2ec8cdc_2    conda-forge
bzip2                     1.0.8                h4bc722e_7    conda-forge
c-ares                    1.34.4               hb9d3cd8_0    conda-forge
ca-certificates           2024.12.14           hbcca054_0    conda-forge
certifi                   2024.12.14         pyhd8ed1ab_0    conda-forge
cffi                      1.17.1          py312h06ac9bb_0    conda-forge
chardet                   5.2.0           py312h7900ff3_2    conda-forge
charset-normalizer        3.4.0              pyhd8ed1ab_1    conda-forge
cirun                     0.30               pyhd8ed1ab_0    conda-forge
click                     8.1.8              pyh707e725_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_1    conda-forge
conda                     24.11.2         py312h7900ff3_0    conda-forge
conda-build               24.5.1          py312h7900ff3_0    conda-forge
conda-forge-pinning       2024.12.27.18.01.51      hd8ed1ab_0    conda-forge
conda-index               0.5.0              pyhd8ed1ab_0    conda-forge
conda-libmamba-solver     24.9.0             pyhd8ed1ab_0    conda-forge
conda-package-handling    2.4.0              pyha770c72_1    conda-forge
conda-package-streaming   0.11.0             pyhd8ed1ab_0    conda-forge
conda-smithy              3.45.1          unix_pyhd81877a_0    conda-forge
cryptography              44.0.0          py312hda17c39_0    conda-forge
dbus                      1.13.6               h5008d03_3    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
deprecated                1.2.15             pyhd8ed1ab_1    conda-forge
distlib                   0.3.9              pyhd8ed1ab_1    conda-forge
distro                    1.9.0              pyhd8ed1ab_1    conda-forge
editables                 0.5                pyhd8ed1ab_1    conda-forge
exceptiongroup            1.2.2              pyhd8ed1ab_1    conda-forge
expat                     2.6.4                h5888daf_0    conda-forge
filelock                  3.16.1             pyhd8ed1ab_1    conda-forge
fmt                       11.0.2               h434a139_0    conda-forge
frozendict                2.4.6           py312h66e93f0_0    conda-forge
git                       2.47.1          pl5321h59d505e_0    conda-forge
gitdb                     4.0.11             pyhd8ed1ab_1    conda-forge
gitpython                 3.1.43             pyhff2d567_1    conda-forge
gmp                       6.3.0                hac33072_2    conda-forge
h11                       0.14.0             pyhd8ed1ab_1    conda-forge
h2                        4.1.0              pyhd8ed1ab_1    conda-forge
hatch                     1.14.0             pyhd8ed1ab_1    conda-forge
hatchling                 1.27.0           pypyhd8ed1ab_0    conda-forge
hpack                     4.0.0              pyhd8ed1ab_1    conda-forge
httpcore                  1.0.7              pyh29332c3_1    conda-forge
httpx                     0.28.1             pyhd8ed1ab_0    conda-forge
hyperframe                6.0.1              pyhd8ed1ab_1    conda-forge
hyperlink                 21.0.0             pyh29332c3_1    conda-forge
icu                       75.1                 he02047a_0    conda-forge
idna                      3.10               pyhd8ed1ab_1    conda-forge
importlib-metadata        8.5.0              pyha770c72_1    conda-forge
importlib_resources       6.4.5              pyhd8ed1ab_1    conda-forge
isodate                   0.7.2              pyhd8ed1ab_1    conda-forge
jaraco.classes            3.4.0              pyhd8ed1ab_2    conda-forge
jaraco.context            6.0.1              pyhd8ed1ab_0    conda-forge
jaraco.functools          4.1.0              pyhd8ed1ab_0    conda-forge
jeepney                   0.8.0              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.5              pyhd8ed1ab_0    conda-forge
joblib                    1.4.2              pyhd8ed1ab_1    conda-forge
json5                     0.10.0             pyhd8ed1ab_1    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_1    conda-forge
jsonpointer               3.0.0           py312h7900ff3_1    conda-forge
jsonschema                4.23.0             pyhd8ed1ab_1    conda-forge
jsonschema-specifications 2024.10.1          pyhd8ed1ab_1    conda-forge
jupyter_core              5.7.2              pyh31011fe_1    conda-forge
keyring                   25.6.0             pyha804496_0    conda-forge
keyutils                  1.6.1                h166bdaf_0    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
libarchive                3.7.7                h4585015_3    conda-forge
libcurl                   8.11.1               h332b0f4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 hd590300_2    conda-forge
libexpat                  2.6.4                h5888daf_0    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgit2                   1.8.4                hd24f944_1    conda-forge
libglib                   2.82.2               h2ff4ddf_0    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
liblief                   0.15.1               h5888daf_0    conda-forge
liblzma                   5.6.3                hb9d3cd8_1    conda-forge
liblzma-devel             5.6.3                hb9d3cd8_1    conda-forge
libmamba                  1.5.11               hf72d635_0    conda-forge
libmambapy                1.5.11          py312hf3f0a4e_0    conda-forge
libnghttp2                1.64.0               h161d5f1_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsodium                 1.0.20               h4ab18f5_0    conda-forge
libsolv                   0.7.30               h3509ff9_0    conda-forge
libsqlite                 3.47.2               hee588c1_0    conda-forge
libssh2                   1.11.1               hf672d98_0    conda-forge
libstdcxx                 14.2.0               hc0a3c3a_1    conda-forge
libstdcxx-ng              14.2.0               h4852527_1    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.13.5               h8d12d68_1    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
license-expression        30.3.1             pyhd8ed1ab_0    conda-forge
lz4-c                     1.10.0               h5888daf_1    conda-forge
lzo                       2.10              hd590300_1001    conda-forge
mamba                     1.5.11          py312h9460a1c_0    conda-forge
markdown-it-py            3.0.0              pyhd8ed1ab_1    conda-forge
markupsafe                3.0.2           py312h178313f_1    conda-forge
mbedtls                   3.5.1                h5888daf_1    conda-forge
mdurl                     0.1.2              pyhd8ed1ab_1    conda-forge
menuinst                  2.2.0           py312h7900ff3_0    conda-forge
more-itertools            10.5.0             pyhd8ed1ab_1    conda-forge
msrest                    0.6.21             pyh44b312d_0    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_1    conda-forge
ncurses                   6.5                  he02047a_1    conda-forge
oauthlib                  3.2.2              pyhd8ed1ab_1    conda-forge
openssl                   3.4.0                hb9d3cd8_0    conda-forge
packaging                 24.2               pyhd8ed1ab_2    conda-forge
patch                     2.7.6             h7f98852_1002    conda-forge
patchelf                  0.17.2               h58526e2_0    conda-forge
pathspec                  0.12.1             pyhd8ed1ab_1    conda-forge
pcre2                     10.44                hba22ea6_2    conda-forge
perl                      5.32.1          7_hd590300_perl5    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_1    conda-forge
pip                       24.3.1             pyh8b19718_2    conda-forge
pkginfo                   1.12.0             pyhd8ed1ab_1    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_2    conda-forge
platformdirs              4.3.6              pyhd8ed1ab_1    conda-forge
pluggy                    1.5.0              pyhd8ed1ab_1    conda-forge
prompt-toolkit            3.0.48             pyha770c72_1    conda-forge
prompt_toolkit            3.0.48               hd8ed1ab_1    conda-forge
psutil                    6.1.1           py312h66e93f0_0    conda-forge
ptyprocess                0.7.0              pyhd8ed1ab_1    conda-forge
py-lief                   0.15.1          py312h2ec8cdc_0    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py312h66e93f0_2    conda-forge
pycparser                 2.22               pyh29332c3_1    conda-forge
pycryptodome              3.21.0          py312h6368725_0    conda-forge
pygit2                    1.16.0          py312h66e93f0_0    conda-forge
pygithub                  2.5.0              pyhd8ed1ab_0    conda-forge
pygments                  2.18.0             pyhd8ed1ab_1    conda-forge
pyjwt                     2.10.1             pyhd8ed1ab_0    conda-forge
pynacl                    1.5.0           py312h66e93f0_4    conda-forge
pysocks                   1.7.1              pyha55dd90_7    conda-forge
python                    3.12.8          h9e4cc4f_1_cpython    conda-forge
python-dateutil           2.9.0.post0        pyhff2d567_1    conda-forge
python-fastjsonschema     2.21.1             pyhd8ed1ab_0    conda-forge
python-libarchive-c       5.1             py312h7900ff3_1    conda-forge
python_abi                3.12                    5_cp312    conda-forge
pytz                      2024.2             pyhd8ed1ab_1    conda-forge
pyyaml                    6.0.2           py312h66e93f0_1    conda-forge
rattler-build             0.33.1               hbcf9e9b_0    conda-forge
rattler-build-conda-compat 1.2.2              pyhd8ed1ab_0    conda-forge
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1             pyhd8ed1ab_1    conda-forge
reproc                    14.2.5.post0         hb9d3cd8_0    conda-forge
reproc-cpp                14.2.5.post0         h5888daf_0    conda-forge
requests                  2.32.3             pyhd8ed1ab_1    conda-forge
requests-oauthlib         2.0.0              pyhd8ed1ab_1    conda-forge
requests-toolbelt         1.0.0              pyhd8ed1ab_1    conda-forge
rich                      13.9.4             pyhd8ed1ab_1    conda-forge
ripgrep                   14.1.1               h8fae777_0    conda-forge
rpds-py                   0.22.3          py312h12e396e_0    conda-forge
ruamel.yaml               0.18.6          py312h66e93f0_1    conda-forge
ruamel.yaml.clib          0.2.8           py312h66e93f0_1    conda-forge
scrypt                    0.8.27          py312h2214df5_0    conda-forge
secretstorage             3.3.3           py312h7900ff3_3    conda-forge
setuptools                75.6.0             pyhff2d567_1    conda-forge
shellingham               1.5.4              pyhd8ed1ab_1    conda-forge
six                       1.17.0             pyhd8ed1ab_0    conda-forge
smmap                     5.0.0              pyhd8ed1ab_0    conda-forge
sniffio                   1.3.1              pyhd8ed1ab_1    conda-forge
soupsieve                 2.5                pyhd8ed1ab_1    conda-forge
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.2.1              pyhd8ed1ab_1    conda-forge
tomli-w                   1.1.0              pyhd8ed1ab_1    conda-forge
tomlkit                   0.13.2             pyha770c72_1    conda-forge
toolz                     1.0.0              pyhd8ed1ab_1    conda-forge
tqdm                      4.67.1             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.3             pyhd8ed1ab_1    conda-forge
trove-classifiers         2024.10.21.16      pyhd8ed1ab_1    conda-forge
truststore                0.10.0             pyhd8ed1ab_0    conda-forge
typer                     0.15.1             pyhd8ed1ab_0    conda-forge
typer-slim                0.15.1             pyhd8ed1ab_0    conda-forge
typer-slim-standard       0.15.1               hd8ed1ab_0    conda-forge
typing-extensions         4.12.2               hd8ed1ab_1    conda-forge
typing_extensions         4.12.2             pyha770c72_1    conda-forge
tzdata                    2024b                hc8b5060_0    conda-forge
urllib3                   2.3.0              pyhd8ed1ab_0    conda-forge
userpath                  1.7.0              pyhd8ed1ab_0    conda-forge
uv                        0.5.13               h0f3a69f_0    conda-forge
virtualenv                20.28.0            pyhd8ed1ab_0    conda-forge
vsts-python-api           0.1.25             pyhd8ed1ab_1    conda-forge
watchgod                  0.8.2              pyhd8ed1ab_1    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_1    conda-forge
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
wrapt                     1.17.0          py312h66e93f0_0    conda-forge
xz                        5.6.3                hbcc6ac9_1    conda-forge
xz-gpl-tools              5.6.3                hbcc6ac9_1    conda-forge
xz-tools                  5.6.3                hb9d3cd8_1    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge
yaml-cpp                  0.8.0                h59595ed_0    conda-forge
zipp                      3.21.0             pyhd8ed1ab_1    conda-forge
zstandard                 0.23.0          py312hef9b889_1    conda-forge
zstd                      1.5.6                ha6fb4c9_0    conda-forge

Environment info

active environment : base
    active env location : /home/mark/miniforge3
            shell level : 2
       user config file : /home/mark/.condarc
 populated config files : /home/mark/miniforge3/.condarc
                          /home/mark/.condarc
          conda version : 24.11.2
    conda-build version : 24.5.1
         python version : 3.12.8.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=skylake
                          __conda=24.11.2=0
                          __glibc=2.40=0
                          __linux=6.11.0=0
                          __unix=0=0
       base environment : /home/mark/miniforge3  (writable)
      conda av data dir : /home/mark/miniforge3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /home/mark/miniforge3/pkgs
                          /home/mark/.conda/pkgs
       envs directories : /home/mark/miniforge3/envs
                          /home/mark/.conda/envs
               platform : linux-64
             user-agent : conda/24.11.2 requests/2.32.3 CPython/3.12.8 Linux/6.11.0-9-generic ubuntu/24.10 glibc/2.40 solver/libmamba conda-libmamba-solver/24.9.0 libmambapy/1.5.11
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False
@hmaarrfk hmaarrfk added the bug label Dec 28, 2024
@hmaarrfk
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maybe it is mamba that is hanging and not conda??? feel free to move the issue and rename it.

hmaarrfk added a commit to hmaarrfk/mamba-feedstock that referenced this issue Dec 29, 2024
@hmaarrfk
Use __conda_activate reactivate
67ffb0c 
Backport of mamba-org/mamba#3702

Honestly, I've been having alot of trouble with the latest conda version

- Conda hanging: conda-forge/conda-feedstock#250
- Can't release conda build 24.11.2 -- conda-forge/miniforge#701
- I think we should just release this small backport in an attempt to
  help: conda-forge/miniforge#700
@hmaarrfk hmaarrfk mentioned this issue Dec 29, 2024
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@jjerphan
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jjerphan commented Jan 2, 2025

Hi Mark,

I cannot reproduce the issue with conda, mamba and micromamba.

Can you provide an environment export so that we can try to reproduce the issue?

@hmaarrfk
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hmaarrfk commented Jan 2, 2025

See conda-forge/miniforge#700 (comment) for an other user experiencing this

@hmaarrfk hmaarrfk mentioned this issue Jan 2, 2025
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@nwalters512
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nwalters512 commented Jan 2, 2025 •
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👋 it's me, the other user. I included reproduction instructions that can be run in a Docker image in the other thread. That uses miniforge to install conda and mambda. Let me know if I can provide any more information.

One novel thing I experienced that isn't mentioned here is the repeated logging of the following lines after several minutes of hanging:

is deprecated and will be removed in 25.9. Use instead.

@nwalters512
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nwalters512 commented Jan 3, 2025 •
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I ultimately let mamba install lxml run for 20 minutes, and it finally finished! It pinned the CPU to 100% almost the whole time. Over the course of those 20 minutes, memory usage jumped to over 15GB and then steadily decreased. Here's a screenshot of the stats from Docker Desktop:

Image

@jjerphan
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jjerphan commented Jan 3, 2025 •
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@nwalters512: can you open an issue on mamba-org/mamba with a full reproducer (in particular with the version of mamba and the configuration you are using)?

@jaimergp jaimergp mentioned this issue Jan 3, 2025
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@nwalters512
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Should I wait to see if conda/conda#14468 fixes this first?

@hmaarrfk
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hmaarrfk commented Jan 3, 2025

@conda-forge-admin please rerender

@conda-forge-webservices
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Hi! This is the friendly automated conda-forge-webservice.

I just wanted to let you know that I started rerendering the recipe in #251.

@conda-forge-admin conda-forge-admin mentioned this issue Jan 3, 2025
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@hmaarrfk
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hmaarrfk commented Jan 3, 2025

For users experiencing this you can:

# edit
~/miniforge3/etc/profile.d/conda.sh

delete the "echo" line below __conda_reactivate

profit

@hmaarrfk hmaarrfk closed this as completed Jan 4, 2025
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@hmaarrfk @nwalters512 @jjerphan