conda create --copy still creating symlinks

[alessandriniluca]

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What happened?

Hi to everyone,
I may be doing something wrong or I may be misunderstanding the guide, but by following the helper returned by conda create --help, --copy options should Install all packages using copies instead of hard- or soft-linking. If I try to create a test environment with the following command:

$ conda create --copy -n sot python=3.9 cudatoolkit-dev=11.7 -c conda-forge

I still have symlinks:
ls -la in the conda environment folder ($HOME/.conda/envs/sot) returns some lines as the following:

lrwxrwxrwx  1 landomix landomix    53 Feb 26 15:57 nvvm -> /home/landomix/.conda/envs/sot/pkgs/cuda-toolkit/nvvm

Conda Info

active environment : None
            shell level : 0
       user config file : /home/landomix/.condarc
 populated config files : /home/landomix/.condarc
          conda version : 23.10.0
    conda-build version : not installed
         python version : 3.11.5.final.0
       virtual packages : __archspec=1=skylake
                          __cuda=12.3=0
                          __glibc=2.39=0
                          __linux=6.7.6=0
                          __unix=0=0
       base environment : /opt/miniconda3  (read only)
      conda av data dir : /opt/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /opt/miniconda3/pkgs
                          /home/landomix/.conda/pkgs
       envs directories : /home/landomix/.conda/envs
                          /opt/miniconda3/envs
               platform : linux-64
             user-agent : conda/23.10.0 requests/2.31.0 CPython/3.11.5 Linux/6.7.6-arch1-1 arch/rolling glibc/2.39 solver/libmamba conda-libmamba-solver/23.11.1 libmambapy/1.5.3
                UID:GID : 1000:1000
             netrc file : None
           offline mode : False

Conda Config

==> /home/landomix/.condarc <==
allow_softlinks: False
always_softlink: False
always_copy: True

Conda list

# packages in environment at /opt/miniconda3:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main    defaults
_openmp_mutex             5.1                       1_gnu    defaults
archspec                  0.2.1              pyhd3eb1b0_0    defaults
boltons                   23.0.0          py311h06a4308_0    defaults
brotli-python             1.0.9           py311h6a678d5_7    defaults
bzip2                     1.0.8                h7b6447c_0    defaults
c-ares                    1.19.1               h5eee18b_0    defaults
ca-certificates           2023.08.22           h06a4308_0    defaults
certifi                   2023.7.22       py311h06a4308_0    defaults
cffi                      1.15.1          py311h5eee18b_3    defaults
charset-normalizer        2.0.4              pyhd3eb1b0_0    defaults
conda                     23.10.0         py311h06a4308_0    defaults
conda-content-trust       0.2.0           py311h06a4308_0    defaults
conda-libmamba-solver     23.11.1         py311h06a4308_0    defaults
conda-package-handling    2.2.0           py311h06a4308_0    defaults
conda-package-streaming   0.9.0           py311h06a4308_0    defaults
cryptography              41.0.3          py311hdda0065_0    defaults
fmt                       9.1.0                hdb19cb5_0    defaults
icu                       73.1                 h6a678d5_0    defaults
idna                      3.4             py311h06a4308_0    defaults
jsonpatch                 1.32               pyhd3eb1b0_0    defaults
jsonpointer               2.1                pyhd3eb1b0_0    defaults
krb5                      1.20.1               h143b758_1    defaults
ld_impl_linux-64          2.38                 h1181459_1    defaults
libarchive                3.6.2                h6ac8c49_2    defaults
libcurl                   8.4.0                h251f7ec_0    defaults
libedit                   3.1.20221030         h5eee18b_0    defaults
libev                     4.33                 h7f8727e_1    defaults
libffi                    3.4.4                h6a678d5_0    defaults
libgcc-ng                 11.2.0               h1234567_1    defaults
libgomp                   11.2.0               h1234567_1    defaults
libmamba                  1.5.3                haf1ee3a_0    defaults
libmambapy                1.5.3           py311h2dafd23_0    defaults
libnghttp2                1.57.0               h2d74bed_0    defaults
libsolv                   0.7.24               he621ea3_0    defaults
libssh2                   1.10.0               hdbd6064_2    defaults
libstdcxx-ng              11.2.0               h1234567_1    defaults
libuuid                   1.41.5               h5eee18b_0    defaults
libxml2                   2.10.4               hf1b16e4_1    defaults
lz4-c                     1.9.4                h6a678d5_0    defaults
ncurses                   6.4                  h6a678d5_0    defaults
openssl                   3.0.12               h7f8727e_0    defaults
packaging                 23.1            py311h06a4308_0    defaults
pcre2                     10.42                hebb0a14_0    defaults
pip                       23.3            py311h06a4308_0    defaults
pluggy                    1.0.0           py311h06a4308_1    defaults
pybind11-abi              4                    hd3eb1b0_1    defaults
pycosat                   0.6.6           py311h5eee18b_0    defaults
pycparser                 2.21               pyhd3eb1b0_0    defaults
pyopenssl                 23.2.0          py311h06a4308_0    defaults
pysocks                   1.7.1           py311h06a4308_0    defaults
python                    3.11.5               h955ad1f_0    defaults
readline                  8.2                  h5eee18b_0    defaults
reproc                    14.2.4               h295c915_1    defaults
reproc-cpp                14.2.4               h295c915_1    defaults
requests                  2.31.0          py311h06a4308_0    defaults
ruamel.yaml               0.17.21         py311h5eee18b_0    defaults
setuptools                68.0.0          py311h06a4308_0    defaults
sqlite                    3.41.2               h5eee18b_0    defaults
tk                        8.6.12               h1ccaba5_0    defaults
tqdm                      4.65.0          py311h92b7b1e_0    defaults
truststore                0.8.0           py311h06a4308_0    defaults
tzdata                    2023c                h04d1e81_0    defaults
urllib3                   1.26.18         py311h06a4308_0    defaults
wheel                     0.41.2          py311h06a4308_0    defaults
xz                        5.4.2                h5eee18b_0    defaults
yaml-cpp                  0.8.0                h6a678d5_0    defaults
zlib                      1.2.13               h5eee18b_0    defaults
zstandard                 0.19.0          py311h5eee18b_0    defaults
zstd                      1.5.5                hc292b87_0    defaults

Additional Context

O.s.: arch linux
Installed from: https://aur.archlinux.org/packages/miniconda3

[travishathaway]

Hi @alessandriniluca,

If I'm reading that correctly, the symlink you're seeing is simply referencing something within that environment, which is normal.

The --copy option only prevents hard linking from the <conda_installation_location>/pkgs directory and does nothing to prevent soft linking (i.e. symlinks) from within the the environment itself.

Let me know if that makes sense.

[alessandriniluca]

Thanks a lot, apparently I got tricked by the <...> hard- or soft-linking., now is more clear.

Knowing that, I'll leave here a command (just for reference) that could help who needs to generate an environment without any soft link at all. Yesterday I solved it by generating an environment on my laptop, and copied where needed with cp by adding -rL options, that (in few words) substitutes softlinks with pointed files (clearly this will waste some space).

[github-actions]

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