[micromamba] cannot delete environment

Question

[micromamba] cannot delete environment

kdu4108 opened this issue 3 months ago · comments

Kevin Du commented 3 months ago

Troubleshooting docs

My problem is not solved in the Troubleshooting docs

Anaconda default channels

I do NOT use the Anaconda default channels (pkgs/* etc.)

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

My problem is not solved with the latest version

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

Kevin Du · Answer 1 · Mon May 20 2024 07:07:58 GMT+0800 (China Standard Time)

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 · Answer 2 · Mon May 20 2024 17:36:20 GMT+0800 (China Standard Time)

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?

Kevin Du · Answer 3 · Fri May 24 2024 04:51:06 GMT+0800 (China Standard Time)

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