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The Fast Cross-Platform Package Manager
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[micromamba] cannot delete environment #3298

Closed kdu4108 closed 1 month ago

kdu4108 commented 1 month ago

Troubleshooting docs

Anaconda default channels

How did you install Mamba?

Micromamba

Search tried in issue tracker

(1) critical libmamba could not load prefix data (2) critical libmamba An unexpected file-system separator was found in environment name: '/cluster/home/kevidu/micromamba/envs/mlm'

Latest version of Mamba

Tried in Conda?

I didn't try

Describe your issue

I have an env named mlm located at /cluster/home/kevidu/micromamba/envs/mlm, as seen in the below (partial) output of micromamba env list:

Name        Active  Path                                           
───────────────────────────────────────────────────────────────────────
  base                /cluster/home/kevidu/micromamba                
  mlm                 /cluster/home/kevidu/micromamba/envs/mlm

When I try to run micromamba env remove -n mlm, I get the error critical libmamba could not load prefix data.

When I try to run micromamba env remove -n /cluster/home/kevidu/micromamba/envs/mlm, I get the error:

info     libmamba ****************** Backtrace Start ******************
debug    libmamba Loading configuration
trace    libmamba Compute configurable 'create_base'
trace    libmamba Compute configurable 'no_env'
trace    libmamba Compute configurable 'no_rc'
trace    libmamba Compute configurable 'rc_files'
trace    libmamba Compute configurable 'root_prefix'
trace    libmamba Get RC files configuration from locations up to HomeDir
trace    libmamba Configuration not found at '/cluster/home/kevidu/.mambarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.mamba/mambarc.d'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.mamba/mambarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.mamba/.mambarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.config/mamba/mambarc.d'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.config/mamba/mambarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.config/mamba/.mambarc'
trace    libmamba Configuration found at '/cluster/home/kevidu/.condarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.conda/condarc.d'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.conda/condarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.conda/.condarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.config/mamba/../conda/condarc.d'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.config/mamba/../conda/condarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/.config/mamba/../conda/.condarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/micromamba/.mambarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/micromamba/condarc.d'
trace    libmamba Configuration not found at '/cluster/home/kevidu/micromamba/condarc'
trace    libmamba Configuration not found at '/cluster/home/kevidu/micromamba/.condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.mambarc'
trace    libmamba Configuration not found at '/var/lib/conda/condarc.d/'
trace    libmamba Configuration not found at '/var/lib/conda/condarc'
trace    libmamba Configuration not found at '/var/lib/conda/.condarc'
trace    libmamba Configuration not found at '/etc/conda/.mambarc'
trace    libmamba Configuration not found at '/etc/conda/condarc.d/'
trace    libmamba Configuration not found at '/etc/conda/condarc'
trace    libmamba Configuration not found at '/etc/conda/.condarc'
trace    libmamba Update configurable 'no_env'
trace    libmamba Compute configurable 'envs_dirs'
trace    libmamba Compute configurable 'file_specs'
trace    libmamba Compute configurable 'spec_file_env_name'
trace    libmamba Compute configurable 'env_name'
critical libmamba An unexpected file-system separator was found in environment name: '/cluster/home/kevidu/micromamba/envs/mlm'
info     libmamba ****************** Backtrace End ********************

Can you help me figure out how to delete the environment? (I would prefer not to do a clean re-install micromamba because I want to preserve some other environments, unless there's a way to clean re-install while preserving existing environments?)

Thanks!

mamba info / micromamba info

libmamba version : 1.5.8
     micromamba version : 1.5.8
           curl version : libcurl/8.6.0 OpenSSL/3.2.1 zlib/1.2.13 zstd/1.5.5 libssh2/1.11.0 nghttp2/1.58.0
     libarchive version : libarchive 3.7.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.5
       envs directories : /cluster/home/kevidu/micromamba/envs
          package cache : /cluster/home/kevidu/micromamba/pkgs
                          /cluster/home/kevidu/.mamba/pkgs
            environment : None (not found)
           env location : -
      user config files : /cluster/home/kevidu/.mambarc
 populated config files : /cluster/home/kevidu/.condarc
       virtual packages : __unix=0=0
                          __linux=3.10.0=0
                          __glibc=2.17=0
                          __archspec=1=x86_64-v3
               channels : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/nodefaults/linux-64
                          https://conda.anaconda.org/nodefaults/noarch
       base environment : /cluster/home/kevidu/micromamba
               platform : linux-64

Logs

[kevidu@eu-login-36 ~]$ micromamba env remove -n mlm -v
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/_libgcc_mutex-0.1-main.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/ld_impl_linux-64-2.38-h1181459_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/ca-certificates-2024.3.11-h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libstdcxx-ng-11.2.0-h1234567_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libgomp-11.2.0-h1234567_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/_openmp_mutex-5.1-1_gnu.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libgcc-ng-11.2.0-h1234567_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libffi-3.4.4-h6a678d5_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/bzip2-1.0.8-h5eee18b_5.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/zlib-1.2.13-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/xz-5.4.6-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/openssl-3.0.13-h7f8727e_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/ncurses-6.4-h6a678d5_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libuuid-1.41.5-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/tk-8.6.12-h1ccaba5_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/readline-8.2-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/sqlite-3.41.2-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/tzdata-2024a-h04d1e81_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/python-3.10.14-h955ad1f_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/wheel-0.41.2-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/setuptools-68.2.2-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/pip-23.3.1-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libcublas-12.1.0.26-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libcufft-11.0.2.4-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libcusolver-11.4.4.55-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libcusparse-12.0.2.55-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libnpp-12.0.2.50-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libnvjitlink-12.1.105-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/cuda-cudart-12.1.105-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/cuda-nvrtc-12.1.105-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/cuda-opencl-12.4.99-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libcufile-1.9.0.20-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libcurand-10.3.5.119-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libnvjpeg-12.1.1.14-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/cuda-cupti-12.1.105-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/cuda-nvtx-12.1.105-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/cuda-libraries-12.1.0-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/cuda-runtime-12.1.0-0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/pytorch-mutex-1.0-cuda.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/blas-1.0-mkl.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/llvm-openmp-14.0.6-h9e868ea_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/lame-3.100-h7b6447c_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libpng-1.6.39-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libwebp-base-1.3.2-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/filelock-3.13.1-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/networkx-3.1-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/yaml-0.2.5-h7b6447c_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/typing_extensions-4.9.0-py310h06a4308_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/gmp-6.2.1-h295c915_3.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libunistring-0.9.10-h27cfd23_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libiconv-1.16-h7f8727e_2.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/openh264-2.1.1-h4ff587b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/mpmath-1.3.0-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/certifi-2024.2.2-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/idna-3.4-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/brotli-python-1.0.9-py310h6a678d5_7.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/pysocks-1.7.1-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/jpeg-9e-h5eee18b_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/lerc-3.0-h295c915_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/intel-openmp-2023.1.0-hdb19cb5_46306.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/tbb-2021.8.0-hdb19cb5_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libdeflate-1.17-h5eee18b_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/lz4-c-1.9.4-h6a678d5_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/markupsafe-2.1.3-py310h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libtasn1-4.19.0-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/freetype-2.12.1-h4a9f257_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/pyyaml-6.0.1-py310h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/nettle-3.7.3-hbbd107a_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/mpfr-4.0.2-hb69a4c5_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libidn2-2.3.4-h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/urllib3-2.1.0-py310h06a4308_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/mkl-2023.1.0-h213fc3f_46344.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/zstd-1.5.5-hc292b87_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/jinja2-3.1.3-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/mpc-1.1.0-h10f8cd9_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/gnutls-3.6.15-he1e5248_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/mkl-service-2.4.0-py310h5eee18b_1.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libtiff-4.5.1-h6a678d5_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/gmpy2-2.1.2-py310heeb90bb_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/numpy-base-1.26.4-py310hb5e798b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/openjpeg-2.4.0-h3ad879b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/lcms2-2.12-h3be6417_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/sympy-1.12-py310h06a4308_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/numpy-1.26.4-py310h5f9d8c6_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/mkl_fft-1.3.8-py310h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/pillow-10.2.0-py310h5eee18b_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/mkl_random-1.2.4-py310hdb19cb5_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/libjpeg-turbo-2.0.0-h9bf148f_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/pytorch-cuda-12.1-ha16c6d3_5.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/ffmpeg-4.3-hf484d3e_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/pytorch-2.2.0-py3.10_cuda12.1_cudnn8.9.2_0.json"
info     libmamba Loading single package record: "/cluster/home/kevidu/micromamba/envs/mlm/conda-meta/torchtriton-2.2.0-py310.json"
critical libmamba could not load prefix data

environment.yml

No response

~/.condarc

channels:
  - conda-forge
  - nodefaults
env_dirs:
  - /cluster/home/kevidu/micromamba/envs/
channel_priority: strict
kdu4108 commented 1 month ago

Update: I ended up deleting micromamba and restarting because some other messy errors were showing up which were immediately blocking me. After a fresh re-install, I no longer have an error when running micromamba env remove -n mlm. However the same error exists when running micromamba env remove -n /cluster/home/kevidu/micromamba/envs/mlm

Hind-M commented 1 month ago

With env remove and all micromamba commands requiring an environment as an argument , you can either use -n env_name or -p env_path. Have you tried micromamba env remove -p /cluster/home/kevidu/micromamba/envs/mlm instead?

kdu4108 commented 1 month ago

Thanks, yes I didn't realize I was using the wrong flag. Can confirm no more issues!