micromamba-docker
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warning libmamba linux version not found (virtual package skipped)
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:
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/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
warning libmamba linux version not found (virtual package skipped)
This warning appears whatever the package I try to install.
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.
Hello, thanks for your answer !
This warning appears when I am building the image with the given Dockerfile using the docker build . command.
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
-
uname -aLinux 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 --versionDocker version 20.10.20, build 9fdeb9c -
envSHELL=/bin/bash HISTCONTROL=ignoredups HISTSIZE=50000 MODULESHOME=/usr/share/Modules MANPATH=/usr/share/man: LANG=en_US.UTF-8
Thanks !
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?
After you build your image, could you run the image and get the output from micromamba info --log-level=1 ? thanks!
Sure,
micromamba info --log-level=1
__
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/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
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
If I run uname -r, I get 5.14.0-176.el9.x86_64 (same result inside as outside of the Docker image)
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!
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
__
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/ / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
/ /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
/ .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
/_/
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
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.
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 +++
`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`
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
@meridionaljet (or anyone else who is hitting this problem) - can you please:
- download
micromambadirectly to your computer (not in a container) - post the output of
micromamba info --log-level=1 - post what linux distribution you are running, including a version number
@meridionaljet (or anyone else who is hitting this problem) - can you please:
- download
micromambadirectly to your computer (not in a container)- post the output of
micromamba info --log-level=1- 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)
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!
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?
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:/#
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
Thanks for the intriguing report @pabloabur. It will be interesting to see if anyone else on this issue has success with the --ulimit flag.
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
@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.
I also tested the same solution on Ubuntu WSL under Windows 11, and it worked.
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.....