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warning libmamba linux version not found (virtual package skipped) #227

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thib12 opened this issue Oct 21, 2022 · 29 comments
Open

warning libmamba linux version not found (virtual package skipped) #227

thib12 opened this issue Oct 21, 2022 · 29 comments

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@thib12
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thib12 commented Oct 21, 2022

With the given dockerfile

FROM mambaorg/micromamba@sha256:efcb9c2334096f894c2ca748775f2619225515827e2b01db5ce5e90de100cb4e
RUN micromamba install -y -n base -c conda-forge pandas && \
    micromamba clean --all --yes

I get the following warning:

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

warning  libmamba linux version not found (virtual package skipped)

This warning appears whatever the package I try to install.

@wholtz
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wholtz commented Oct 21, 2022

Hello @thib12 - thank you for your interest in micromamba. Can you please supply me some more information to help me reproduce the issue.

You are seeing the warning when building an image with the given Dockerfile, or does the warning occur when you are running a command within a container? The complete set of commands used to produce the error would be helpful.

@thib12
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thib12 commented Oct 22, 2022

Hello, thanks for your answer !
This warning appears when I am building the image with the given Dockerfile using the docker build . command.

@wholtz
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wholtz commented Oct 24, 2022

I'm not seeing this message when I build on my mac. Can you please run the following 3 commands and post the output?

uname -a
docker --version
env

@thib12
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thib12 commented Oct 24, 2022

  • uname -a
    Linux d4ba25fcb683 5.14.0-163.el9.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Sep 8 13:52:29 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux

  • docker --version
    Docker version 20.10.20, build 9fdeb9c

  • env

    SHELL=/bin/bash
    HISTCONTROL=ignoredups
    HISTSIZE=50000
    MODULESHOME=/usr/share/Modules
    MANPATH=/usr/share/man:
    LANG=en_US.UTF-8
    

Thanks !

@wholtz
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wholtz commented Oct 25, 2022

It appears this is being caused by your kernel version not matching a regex. There was commit to fix this problem back in August, but it did not cover your corner case. What linux distribution are you running?

@thib12
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thib12 commented Oct 25, 2022

OK I see. I run CentOS Stream release 9.

@wholtz
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wholtz commented Oct 25, 2022

After you build your image, could you run the image and get the output from micromamba info --log-level=1 ? thanks!

@thib12
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thib12 commented Oct 25, 2022

Sure,

micromamba info --log-level=1
                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

debug    libmamba Loading configuration
debug    libmamba 105 configurables computed
debug    libmamba Loading virtual packages
debug    libmamba Loading distribution virtual packages
debug    libmamba Loading linux virtual package
debug    libmamba Could not find linux version by calling 'uname -r' (skipped)
warning  libmamba linux version not found (virtual package skipped)
debug    libmamba Loading CUDA virtual package
debug    libmamba Could not find CUDA version by calling 'nvidia-smi' (skipped)
    

            environment : base (active)
           env location : /opt/conda
      user config files : /home/mambauser/.mambarc
 populated config files : 
       libmamba version : 0.27.0
     micromamba version : 0.27.0
           curl version : libcurl/7.85.0 OpenSSL/1.1.1q zlib/1.2.12 libssh2/1.10.0 nghttp2/1.47.0
     libarchive version : libarchive 3.3.3 zlib/1.2.11 liblzma/5.2.5 bz2lib/1.0.8 liblz4/1.9.2 libzstd/1.4.5
       virtual packages : __unix=0=0
                          __glibc=2.27=0
                          __archspec=1=x86_64
               channels : 
       base environment : /opt/conda
               platform : linux-64

@wolfv
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wolfv commented Oct 25, 2022

Can you try uname -r just to be sure? Thanks!

@thib12
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thib12 commented Oct 25, 2022

If I run uname -r, I get 5.14.0-176.el9.x86_64 (same result inside as outside of the Docker image)

@wholtz
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wholtz commented Nov 3, 2022

I was wrong about the regex being the problem.

I still have not been able to reproduce this, which makes troubleshooting hard.

Inside your image, can you please run

uname -r
echo $?

and report back the output? Thanks!

@thib12
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thib12 commented Nov 8, 2022

Hello,

For the given Dockerfile:

FROM mambaorg/micromamba@sha256:efcb9c2334096f894c2ca748775f2619225515827e2b01db5ce5e90de100cb4e
RUN micromamba install -y -n base -c conda-forge pandas && \
    micromamba clean --all --yes
RUN uname -r && echo $?

This is what I get

Step 1/3 : FROM mambaorg/micromamba@sha256:efcb9c2334096f894c2ca748775f2619225515827e2b01db5ce5e90de100cb4e
 ---> 6810298e82d5
Step 2/3 : RUN micromamba install -y -n base -c conda-forge pandas &&     micromamba clean --all --yes
 ---> Running in 91f98e556c24

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

warning  libmamba linux version not found (virtual package skipped)

Transaction

  Prefix: /opt/conda

  Updating specs:

   - pandas


  Package               Version  Build                Channel                   Size
──────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex           0.1  conda_forge          conda-forge/linux-64       3kB
  + _openmp_mutex           4.5  2_gnu                conda-forge/linux-64      24kB
  + bzip2                 1.0.8  h7f98852_4           conda-forge/linux-64     496kB
  + ca-certificates   2022.9.24  ha878542_0           conda-forge/linux-64     154kB
  + ld_impl_linux-64       2.39  hc81fddc_0           conda-forge/linux-64     778kB
  + libblas               3.9.0  16_linux64_openblas  conda-forge/linux-64      13kB
  + libcblas              3.9.0  16_linux64_openblas  conda-forge/linux-64      13kB
  + libffi                3.4.2  h7f98852_5           conda-forge/linux-64      58kB
  + libgcc-ng            12.2.0  h65d4601_19          conda-forge/linux-64     954kB
  + libgfortran-ng       12.2.0  h69a702a_19          conda-forge/linux-64      23kB
  + libgfortran5         12.2.0  h337968e_19          conda-forge/linux-64       2MB
  + libgomp              12.2.0  h65d4601_19          conda-forge/linux-64     466kB
  + liblapack             3.9.0  16_linux64_openblas  conda-forge/linux-64      13kB
  + libnsl                2.0.0  h7f98852_0           conda-forge/linux-64      31kB
  + libopenblas          0.3.21  pthreads_h78a6416_3  conda-forge/linux-64      11MB
  + libsqlite            3.39.4  h753d276_0           conda-forge/linux-64     822kB
  + libstdcxx-ng         12.2.0  h46fd767_19          conda-forge/linux-64       4MB
  + libuuid              2.32.1  h7f98852_1000        conda-forge/linux-64      28kB
  + libzlib              1.2.13  h166bdaf_4           conda-forge/linux-64      66kB
  + ncurses                 6.3  h27087fc_1           conda-forge/linux-64       1MB
  + numpy                1.23.4  py311h7d28db0_1      conda-forge/linux-64       9MB
  + openssl               3.0.7  h166bdaf_0           conda-forge/linux-64       3MB
  + pandas                1.5.1  py311h8b32b4d_1      conda-forge/linux-64      16MB
  + pip                  22.3.1  pyhd8ed1ab_0         conda-forge/noarch         2MB
  + python               3.11.0  ha86cf86_0_cpython   conda-forge/linux-64      38MB
  + python-dateutil       2.8.2  pyhd8ed1ab_0         conda-forge/noarch       246kB
  + python_abi             3.11  2_cp311              conda-forge/linux-64       5kB
  + pytz                 2022.6  pyhd8ed1ab_0         conda-forge/noarch       240kB
  + readline              8.1.2  h0f457ee_0           conda-forge/linux-64     298kB
  + setuptools           65.5.1  pyhd8ed1ab_0         conda-forge/noarch       748kB
  + six                  1.16.0  pyh6c4a22f_0         conda-forge/noarch        14kB
  + tk                   8.6.12  h27826a3_0           conda-forge/linux-64       3MB
  + tzdata                2022f  h191b570_0           conda-forge/noarch       121kB
  + wheel                0.38.2  pyhd8ed1ab_0         conda-forge/noarch        32kB
  + xz                    5.2.6  h166bdaf_0           conda-forge/linux-64     418kB

  Summary:

  Install: 35 packages

  Total download: 94MB

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


Transaction starting
Linking _libgcc_mutex-0.1-conda_forge
Linking libstdcxx-ng-12.2.0-h46fd767_19
Linking libgfortran5-12.2.0-h337968e_19
Linking ld_impl_linux-64-2.39-hc81fddc_0
Linking ca-certificates-2022.9.24-ha878542_0
Linking libgomp-12.2.0-h65d4601_19
Linking libgfortran-ng-12.2.0-h69a702a_19
Linking _openmp_mutex-4.5-2_gnu
Linking libgcc-ng-12.2.0-h65d4601_19
Linking openssl-3.0.7-h166bdaf_0
Linking ncurses-6.3-h27087fc_1
Linking libuuid-2.32.1-h7f98852_1000
Linking libffi-3.4.2-h7f98852_5
Linking bzip2-1.0.8-h7f98852_4
Linking xz-5.2.6-h166bdaf_0
Linking libzlib-1.2.13-h166bdaf_4
Linking libnsl-2.0.0-h7f98852_0
Linking libopenblas-0.3.21-pthreads_h78a6416_3
Linking readline-8.1.2-h0f457ee_0
Linking tk-8.6.12-h27826a3_0
Linking libsqlite-3.39.4-h753d276_0
Linking libblas-3.9.0-16_linux64_openblas
Linking libcblas-3.9.0-16_linux64_openblas
Linking liblapack-3.9.0-16_linux64_openblas
Linking tzdata-2022f-h191b570_0
Linking python-3.11.0-ha86cf86_0_cpython
Linking wheel-0.38.2-pyhd8ed1ab_0
Linking setuptools-65.5.1-pyhd8ed1ab_0
Linking pip-22.3.1-pyhd8ed1ab_0
Linking six-1.16.0-pyh6c4a22f_0
Linking pytz-2022.6-pyhd8ed1ab_0
Linking python-dateutil-2.8.2-pyhd8ed1ab_0
Linking python_abi-3.11-2_cp311
Linking numpy-1.23.4-py311h7d28db0_1
Linking pandas-1.5.1-py311h8b32b4d_1
Transaction finished

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

Collect information..
Cleaning index cache..
Cleaning lock files..
  Package file                                       Size
───────────────────────────────────────────────────────────
  /opt/conda/pkgs
───────────────────────────────────────────────────────────

  _libgcc_mutex-0.1-conda_forge.tar.bz2               3kB
  _openmp_mutex-4.5-2_gnu.tar.bz2                    24kB
  bzip2-1.0.8-h7f98852_4.tar.bz2                    496kB
  ca-certificates-2022.9.24-ha878542_0.tar.bz2      154kB
  ld_impl_linux-64-2.39-hc81fddc_0.tar.bz2          778kB
  libblas-3.9.0-16_linux64_openblas.tar.bz2          13kB
  libcblas-3.9.0-16_linux64_openblas.tar.bz2         13kB
  libffi-3.4.2-h7f98852_5.tar.bz2                    58kB
  libgcc-ng-12.2.0-h65d4601_19.tar.bz2              954kB
  libgfortran-ng-12.2.0-h69a702a_19.tar.bz2          23kB
  libgfortran5-12.2.0-h337968e_19.tar.bz2             2MB
  libgomp-12.2.0-h65d4601_19.tar.bz2                466kB
  liblapack-3.9.0-16_linux64_openblas.tar.bz2        13kB
  libnsl-2.0.0-h7f98852_0.tar.bz2                    31kB
  libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2     11MB
  libsqlite-3.39.4-h753d276_0.tar.bz2               822kB
  libstdcxx-ng-12.2.0-h46fd767_19.tar.bz2             4MB
  libuuid-2.32.1-h7f98852_1000.tar.bz2               28kB
  libzlib-1.2.13-h166bdaf_4.tar.bz2                  66kB
  ncurses-6.3-h27087fc_1.tar.bz2                      1MB
  numpy-1.23.4-py311h7d28db0_1.tar.bz2                9MB
  openssl-3.0.7-h166bdaf_0.tar.bz2                    3MB
  pandas-1.5.1-py311h8b32b4d_1.tar.bz2               16MB
  pip-22.3.1-pyhd8ed1ab_0.tar.bz2                     2MB
  python-3.11.0-ha86cf86_0_cpython.tar.bz2           38MB
  python-dateutil-2.8.2-pyhd8ed1ab_0.tar.bz2        246kB
  python_abi-3.11-2_cp311.tar.bz2                     5kB
  pytz-2022.6-pyhd8ed1ab_0.tar.bz2                  240kB
  readline-8.1.2-h0f457ee_0.tar.bz2                 298kB
  setuptools-65.5.1-pyhd8ed1ab_0.tar.bz2            748kB
  six-1.16.0-pyh6c4a22f_0.tar.bz2                    14kB
  tk-8.6.12-h27826a3_0.tar.bz2                        3MB
  tzdata-2022f-h191b570_0.tar.bz2                   121kB
  wheel-0.38.2-pyhd8ed1ab_0.tar.bz2                  32kB
  xz-5.2.6-h166bdaf_0.tar.bz2                       418kB

  /home/mambauser/.mamba/pkgs
───────────────────────────────────────────────────────────


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

  Total size:                                        94MB
Cleaning tarballs..
Cleaning packages..
Removing intermediate container 91f98e556c24
 ---> 8e4d8b9eb090
Step 3/3 : RUN uname -r && echo $?
 ---> Running in cbe1f55e4819
5.14.0-176.el9.x86_64
0
Removing intermediate container cbe1f55e4819
 ---> c7b92e55620c
Successfully built c7b92e55620c

@rjpbonnal
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I have a very similar issue with RockyLinux 9

@sanderthierens
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Same issue on RockyLinux 9.1, any updates on the problem?

@wholtz
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wholtz commented Dec 16, 2022

I have not been able to reproduce this. I ran a Rocky 9.1 VM on my x86 mac using virtual box and did not see the reported error messages. I don't have any bare metal available to directly install Rocky Linux on.

On a system that is producing these error messages, I'd be interested in seeing the output from:

strace -f -e trace=%process  micromamba info --log-level=1 

Be warned, that command may take a couple of minutes to return.

@thib12
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thib12 commented Jan 4, 2023

Sure, @wholtz

For the given Dockerfile:

FROM mambaorg/micromamba@sha256:efcb9c2334096f894c2ca748775f2619225515827e2b01db5ce5e90de100cb4e
USER root
RUN apt-get update \
    && apt-get install -y strace \
    && apt-get clean \
    && rm -rf /var/lib/apt/lists/*
ARG MAMBA_USER=mambauser
USER $MAMBA_USER
RUN micromamba install -y -n base -c conda-forge pandas && \
    micromamba clean --all --yes
RUN uname -r
RUN echo $?
RUN strace -f -e trace=%process  micromamba info --log-level=1 

The output is

Step 9/9 : RUN strace -f -e trace=%process  micromamba info --log-level=1
 ---> Running in f40bb63cb016
execve("/bin/micromamba", ["micromamba", "info", "--log-level=1"], 0x7fffbd4638c8 /* 12 vars */) = 0
arch_prctl(ARCH_SET_FS, 0x7f5e4f375d00) = 0
clone(strace: Process 10 attached
child_stack=0x7f5e4e17e9f0, flags=CLONE_VM|CLONE_FS|CLONE_FILES|CLONE_SIGHAND|CLONE_THREAD|CLONE_SYSVSEM|CLONE_SETTLS|CLONE_PARENT_SETTID|CLONE_CHILD_CLEARTID, parent_tidptr=0x7f5e4e1809d0, tls=0x7f5e4e180700, child_tidptr=0x7f5e4e1809d0) = 10

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

debug    libmamba Loading configuration
debug    libmamba 105 configurables computed
debug    libmamba Loading virtual packages
debug    libmamba Loading distribution virtual packages
debug    libmamba Loading linux virtual package
[pid     9] clone(child_stack=NULL, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x7f5e4f375fd0) = 11
strace: Process 11 attached
[pid    11] exit_group(1)               = ?
[pid     9] wait4(11,  <unfinished ...>
[pid    11] +++ exited with 1 +++
[pid     9] <... wait4 resumed> NULL, 0, NULL) = 11
[pid     9] --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=11, si_uid=1000, si_status=1, si_utime=0, si_stime=0} ---
debug    libmamba Could not find linux version by calling 'uname -r' (skipped)
warning  libmamba linux version not found (virtual package skipped)
debug    libmamba Loading CUDA virtual package
[pid     9] clone(strace: Process 12 attached
child_stack=NULL, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x7f5e4f375fd0) = 12
[pid     9] wait4(12,  <unfinished ...>
[pid    12] exit_group(1)               = ?
[pid    12] +++ exited with 1 +++
[pid     9] <... wait4 resumed> NULL, 0, NULL) = 12
[pid     9] --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=12, si_uid=1000, si_status=1, si_utime=0, si_stime=0} ---
debug    libmamba Could not find CUDA version by calling 'nvidia-smi' (skipped)
    

            environment : None (not found)
           env location : -
      user config files : /home/mambauser/.mambarc
 populated config files : 
       libmamba version : 0.27.0
     micromamba version : 0.27.0
           curl version : libcurl/7.85.0 OpenSSL/1.1.1q zlib/1.2.12 libssh2/1.10.0 nghttp2/1.47.0
     libarchive version : libarchive 3.3.3 zlib/1.2.11 liblzma/5.2.5 bz2lib/1.0.8 liblz4/1.9.2 libzstd/1.4.5
       virtual packages : __unix=0=0
                          __glibc=2.27=0
                          __archspec=1=x86_64
               channels : 
       base environment : /opt/conda
               platform : linux-64
[pid     9] exit_group(0)               = ?
[pid    10] +++ exited with 0 +++
+++ exited with 0 +++

@sanderthierens
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`Step 6/8 : RUN strace -f -e trace=%process micromamba info --log-level=1
---> Running in 7034470ecfa8
execve("/bin/micromamba", ["micromamba", "info", "--log-level=1"], 0x7fff7e041498 /* 12 vars */) = 0
clone(child_stack=0x7fbc661de9f0, flags=CLONE_VM|CLONE_FS|CLONE_FILES|CLONE_SIGHAND|CLONE_THREAD|CLONE_SYSVSEM|CLONE_SETTLS|CLONE_PARENT_SETTID|CLONE_CHILD_CLEARTIDstrace: Process 10 attached
, parent_tid=[10], tls=0x7fbc661e0700, child_tidptr=0x7fbc661e09d0) = 10

                                       __
      __  ______ ___  ____ _____ ___  / /_  ____ _
     / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
    / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
   / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
  /_/

debug libmamba Loading configuration
debug libmamba 102 configurables computed
debug libmamba Loading virtual packages
debug libmamba Loading distribution virtual packages
debug libmamba Loading linux virtual package
[pid 9] clone(child_stack=NULL, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLDstrace: Process 11 attached
, child_tidptr=0x7fbc663b8fd0) = 11
[pid 9] wait4(11, <unfinished ...>
[pid 11] exit_group(1) = ?
[pid 11] +++ exited with 1 +++
[pid 9] <... wait4 resumed>NULL, 0, NULL) = 11
[pid 9] --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=11, si_uid=0, si_status=1, si_utime=0, si_stime=0} ---
debug libmamba Could not find linux version by calling 'uname -r' (skipped)
warning libmamba linux version not found (virtual package skipped)
debug libmamba Loading CUDA virtual package
[pid 9] clone(child_stack=NULL, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLDstrace: Process 12 attached
, child_tidptr=0x7fbc663b8fd0) = 12
[pid 9] wait4(12, <unfinished ...>
[pid 12] exit_group(1) = ?
[pid 12] +++ exited with 1 +++
[pid 9] <... wait4 resumed>NULL, 0, NULL) = 12
[pid 9] --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=12, si_uid=0, si_status=1, si_utime=0, si_stime=0} ---
debug libmamba Could not find CUDA version by calling 'nvidia-smi' (skipped)

        environment : None (not found)
       env location : -
  user config files : /root/.mambarc

populated config files :
libmamba version : 0.25.0
micromamba version : 0.25.1
curl version : libcurl/7.83.1 OpenSSL/1.1.1q zlib/1.2.12 libssh2/1.10.0 nghttp2/1.47.0
libarchive version : libarchive 3.3.3 zlib/1.2.11 liblzma/5.2.5 bz2lib/1.0.8 liblz4/1.9.2 libzstd/1.4.5
virtual packages : __unix=0=0
__glibc=2.31=0
__archspec=1=x86_64
channels :
base environment : /opt/conda
platform : linux-64
[pid 9] exit_group(0) = ?
[pid 10] +++ exited with 0 +++
+++ exited with 0 +++
Removing intermediate container 7034470ecfa8
---> 4c7c03b44bd2`

@meridionaljet
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Just popping in to say that I have this same issue with latest as of February 2023. Host's uname -r is 6.1.11-200.fc37.x86_64

(base) mambauser@cbbc0a16ca6c:/tmp$ micromamba info --log-level=1

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

debug    libmamba Loading configuration
debug    libmamba 109 configurables computed
debug    libmamba Loading virtual packages
debug    libmamba Loading distribution virtual packages
debug    libmamba Loading linux virtual package
debug    libmamba Could not find linux version by calling 'uname -r' (skipped)
warning  libmamba linux version not found (virtual package skipped)
debug    libmamba Loading CUDA virtual package
debug    libmamba Could not find CUDA version by calling 'nvidia-smi' (skipped)


            environment : base (active)
           env location : /opt/conda
      user config files : /home/mambauser/.mambarc
 populated config files :
       libmamba version : 1.3.1
     micromamba version : 1.3.1
           curl version : libcurl/7.87.0 OpenSSL/3.0.8 zlib/1.2.13 libssh2/1.10.0 nghttp2/1.47.0
     libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       virtual packages : __unix=0=0
                          __glibc=2.31=0
                          __archspec=1=x86_64
               channels :
       base environment : /opt/conda
               platform : linux-64

@wholtz
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wholtz commented Feb 21, 2023

@meridionaljet (or anyone else who is hitting this problem) - can you please:

  1. download micromamba directly to your computer (not in a container)
  2. post the output of micromamba info --log-level=1
  3. post what linux distribution you are running, including a version number

@meridionaljet
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@meridionaljet (or anyone else who is hitting this problem) - can you please:

  1. download micromamba directly to your computer (not in a container)
  2. post the output of micromamba info --log-level=1
  3. post what linux distribution you are running, including a version number
$ micromamba info --log-level=1

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

debug    libmamba Loading configuration
debug    libmamba 107 configurables computed
debug    libmamba Loading virtual packages
debug    libmamba Loading distribution virtual packages
debug    libmamba Loading linux virtual package
debug    libmamba linux version found: 6.1.11
debug    libmamba Loading CUDA virtual package
debug    libmamba CUDA driver version found: 11.7

            environment : env-name (active)
           env location : /home/user/micromamba/envs/env-name
      user config files : /home/user/.mambarc
 populated config files : /home/user/.condarc
       libmamba version : 1.1.0
     micromamba version : 1.1.0
           curl version : libcurl/7.87.0 OpenSSL/1.1.1s zlib/1.2.13 libssh2/1.10.0 nghttp2/1.47.0
     libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       virtual packages : __unix=0=0
                          __linux=6.1.11=0
                          __glibc=2.36=0
                          __archspec=1=x86_64
                          __cuda=11.7=0
               channels : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
       base environment : /home/user/micromamba
               platform : linux-64
$ cat /etc/fedora-release
Fedora release 37 (Thirty Seven)

@wholtz
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wholtz commented Feb 24, 2023

Thanks @meridionaljet!

I was hoping this was going to be a general micromamba issue, independent of being in docker, but that does not appear to be the case. I'll continue to try to find a way to reproduce this issue.... If anyone finds a way to reproduce on an arbitrary host, please post it!

@markgeejw
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Facing this problem as well. Using WSL with uname -r returning 5.15.90.1-microsoft-standard-WSL2.

I'm not sure if it's related but trying to install cudatoolkit with micromamba install -y -n base -c conda-forge cudatoolkit=11.6 is also returning an error:

error    libmamba response code: -1 error message: Invalid argument
critical libmamba failed to execute pre/post link script for cudatoolkit

Could anyone else facing this try installing cudatoolkit to see if it errors out for them too?

@void-spark
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Seeing this still:

Host os is ok:

# ./micromamba info --log-level=1

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

debug    libmamba Loading configuration
debug    libmamba 112 configurables computed
debug    libmamba Loading virtual packages
debug    libmamba Loading distribution virtual packages
debug    libmamba Loading linux virtual package
debug    libmamba linux version found: 6.3.0
debug    libmamba Loading CUDA virtual package
debug    libmamba Could not find CUDA version by calling 'nvidia-smi' (skipped)
    

            environment : None (not found)
           env location : -
      user config files : /home/me/.mambarc
 populated config files : 
       libmamba version : 1.4.3
     micromamba version : 1.4.3
           curl version : libcurl/7.88.1 OpenSSL/3.1.0 zlib/1.2.13 zstd/1.5.2 libssh2/1.10.0 nghttp2/1.52.0
     libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       virtual packages : __unix=0=0
                          __linux=6.3.0=0
                          __glibc=2.37=0
                          __archspec=1=x86_64
               channels : 
       base environment : /home/me/micromamba
               platform : linux-64
# uname -r
6.3.0-1-MANJARO

In docker not:

root@5dcac16608e4:/# micromamba info --log-level=1

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/

debug    libmamba Loading configuration
debug    libmamba 112 configurables computed
debug    libmamba Loading virtual packages
debug    libmamba Loading distribution virtual packages
debug    libmamba Loading linux virtual package
debug    libmamba Could not find linux version by calling 'uname -r' (skipped)
warning  libmamba linux version not found (virtual package skipped)
debug    libmamba Loading CUDA virtual package
debug    libmamba Could not find CUDA version by calling 'nvidia-smi' (skipped)
    

            environment : None (not found)
           env location : -
      user config files : /root/.mambarc
 populated config files : 
       libmamba version : 1.4.3
     micromamba version : 1.4.3
           curl version : libcurl/7.88.1 OpenSSL/3.1.0 zlib/1.2.13 zstd/1.5.2 libssh2/1.10.0 nghttp2/1.52.0
     libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       virtual packages : __unix=0=0
                          __glibc=2.31=0
                          __archspec=1=x86_64
               channels : 
       base environment : /root/micromamba
               platform : linux-64
root@5dcac16608e4:/# uname -r
6.3.0-1-MANJARO
root@5dcac16608e4:/# 

@pabloabur
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I also had this problem on a Manjaro machine, but then I followed the instructions in this comment in issue #267 and now things are working for me. The issue was specifically about pip, but maybe it will also help someone else.

$ uname -r -m
5.10.180-1-MANJARO x86_64

@wholtz
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wholtz commented May 29, 2023

Thanks for the intriguing report @pabloabur. It will be interesting to see if anyone else on this issue has success with the --ulimit flag.

@meridionaljet
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In my case, setting ulimit to a higher value in my docker compose file doesn't allow micromamba (version 1.4.4) to parse the correct linux version. This is frustrating because it forces noarch packages to be installed, which leads to downstream problems in some builds that cannot be solved currently.

In the current build I am working on, I have the following inside the container:

uname -r: 6.3.7-200.fc38.x86_64
uname -a: Linux buildkitsandbox 6.3.7-200.fc38.x86_64 #1 SMP PREEMPT_DYNAMIC Fri Jun 9 15:21:11 UTC 2023 x86_64 GNU/Linux

using the mambaorg/micromamba base image

@iamzoltan
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iamzoltan commented Jun 21, 2023

@wholtz I was running into the same issue. I had no issues installing my env with micromamba outside of a container, but was running into the same warning inside one. I am on arch linux, which seems to be to same systems having issues in @pabloabur comment link. With that flag, it seems to work fine inside of the container.

@pabloabur
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I also tested the same solution on Ubuntu WSL under Windows 11, and it worked.

@wholtz
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wholtz commented Jul 10, 2023

I was hoping that building an image with an artificially low ulimit nofiles would result in a reproducible method of generating this error, but I was I unsuccessful:

$ for lim in {1..100}; do \
>    docker build --progress=plain --no-cache --ulimit "nofile=${lim}:${lim}" -t "ulimit:${lim}" . 2> \
>    >(grep -A10 'libmamba Could not find linux version' && echo $lim); \
> done
$ 

I still want to find a reproducible way of causing this error.....

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