Closed yoctocell closed 3 years ago
Thanks for spotting this. I guess we updated the environment without reflecting the notebooks. Note that the name of the resulting environment from the current "environment.yml" will be "ReinventCommunity". The problem you are encountering can be fixed by removing "ld_impl_linux-64=2.34=h53a641e_0" from the "environment.yml" file. Let me know if the problem still persists I will update the *.yml
Removing the line did fix the problem, but when I try to activate the environment with conda, it tells me that my shell hasn't been properly configured:
~/src/ReinventCommunity $ conda activate ReinventCommunity
CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run
$ conda init <SHELL_NAME>
Currently supported shells are:
- bash
- fish
- tcsh
- xonsh
- zsh
- powershell
See 'conda init --help' for more information and options.
IMPORTANT: You may need to close and restart your shell after running 'conda init'.
I follow their advice and run conda init bash
, but a big error comes
up.
~/src/ReinventCommunity $ conda init bash
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/yoctocell/.conda/lib/python3.7/site-packages/conda/exceptions.py", line 1003, in __call__
return func(*args, **kwargs)
File "/home/yoctocell/.conda/lib/python3.7/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/yoctocell/.conda/lib/python3.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/yoctocell/.conda/lib/python3.7/site-packages/conda/cli/main_init.py", line 51, in execute
anaconda_prompt, args.reverse)
File "/home/yoctocell/.conda/lib/python3.7/site-packages/conda/core/initialize.py", line 120, in initialize
run_plan_elevated(plan2)
File "/home/yoctocell/.conda/lib/python3.7/site-packages/conda/core/initialize.py", line 664, in run_plan_elevated
stdin=stdin
File "/home/yoctocell/.conda/lib/python3.7/site-packages/conda/gateways/subprocess.py", line 85, in subprocess_call
output=formatted_output)
subprocess.CalledProcessError: Command '['sudo', '/home/yoctocell/.conda/bin/python', '-m', 'conda.core.initialize']' died with <Signals.SIGABRT: 6>.
`$ /home/yoctocell/.conda/condabin/conda init bash`
environment variables:
ACLOCAL_PATH=/usr/share/aclocal
CIO_TEST=<not set>
CONDA_EXE=/home/yoctocell/.conda/bin/conda
CONDA_PYTHON_EXE=/home/yoctocell/.conda/bin/python
CONDA_ROOT=/home/yoctocell/.conda
CONDA_SHLVL=0
EMACSLOADPATH=/home/yoctocell/.guix-home-environment/profile/share/emacs/site-
lisp:/home/yoctocell/.guix-home-environment/profile/share/emacs/28.0.5
0/lisp:/gnu/store/qmm0a7lc6n937bjzj0mcyrw1bp1xip4q-emacs-native-
comp-28.0.50-162.7c901d9/share/emacs/28.0.50/lisp
GIT_EXEC_PATH=/home/yoctocell/.guix-home-environment/profile/libexec/git-core
GTK_PATH=/gnu/store/n1rnakk5limkpg59d3m3scj7h76il5y4-gtk+-3.24.24/lib/gtk-3.0:/
home/yoctocell/.nix-profile/lib/gtk-2.0:/home/yoctocell/.nix-
profile/lib/gtk-3.0:/etc/profiles/per-
user/yoctocell/lib/gtk-2.0:/etc/profiles/per-user/yoctocell/lib/gtk-3.
0:/nix/var/nix/profiles/default/lib/gtk-2.0:/nix/var/nix/profiles/defa
ult/lib/gtk-3.0:/run/current-system/sw/lib/gtk-2.0:/run/current-
system/sw/lib/gtk-3.0
GUILE_LOAD_COMPILED_PATH=/home/yoctocell/.config/guix/current/lib/guile/3.0/site-
ccache:/home/yoctocell/.config/guix/current/lib/guile/3.0/site-
ccache:/home/yoctocell/.guix-home-
environment/profile/lib/guile/3.0/site-ccache:/home/yoctocell/.guix-
home-environment/profile/share/guile/site/3.0
GUILE_LOAD_PATH=/home/yoctocell/src/guile-imanifest:/home/yoctocell/.guix-
profile/share/guile/site/3.0:/home/yoctocell/.guix-profile/share/guile
/3.0:/home/yoctocell/.config/guix/current/share/guile/site/3.0:/home/y
octocell/src/nonguix:/home/yoctocell/src/rde:/home/yoctocell/src/guix:
/home/yoctocell/src/guixpkgs:/home/yoctocell/.config/guix/current/shar
e/guile/site/3.0:/home/yoctocell/.guix-home-
environment/profile/share/guile/site/3.0
GUIX_LOCPATH=/home/yoctocell/.guix-profile/lib/locale
HOST_PATH=/nix/store/444qpkxxg4vb0y7wd813yiawiqv7ppl2-conda-
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e-4.7.1/bin:/nix/store/7pk3b5nibagszwq110vx7m7kbp3ak38l-python3.8-ipyt
hon-7.21.0/bin:/nix/store/6fykxraxpszsb5g52n37avjf0281s7ml-python3.8-P
ygments-2.8.1/bin:/nix/store/1zzcz9m7i9b16s5p1ajqafs0skisq463-python3.
8-docutils-0.16/bin:/nix/store/k3r7f87k6d762a9lyli9bfwg05lagqxs-python
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INFOPATH=/home/yoctocell/.guix-home-environment/profile/share/info:/home/yoctoc
ell/.config/guix/current/share/info:/home/yoctocell/.guix-home-
environment/profile/share/info:/home/yoctocell/.guix-
profile/share/info:/home/yoctocell/.guix-
profile/share/info:$INFOPATH:/home/yoctocell/.nix-
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user/yoctocell/info:/etc/profiles/per-user/yoctocell/share/info:/nix/v
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system/sw/share/info:/home/yoctocell/.nix-
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user/yoctocell/info:/etc/profiles/per-user/yoctocell/share/info:/nix/v
ar/nix/profiles/default/info:/nix/var/nix/profiles/default/share/info:
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LD_LIBRARY_PATH=/run/opengl-driver/lib:/run/opengl-driver-32/lib:/usr/lib:/usr/lib32
LIBEXEC_PATH=/home/yoctocell/.nix-profile/lib/libexec:/etc/profiles/per-user/yoctoc
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MANPATH=/home/yoctocell/.guix-home-environment/profile/share/man:
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source:nixos=/nix/store/p9spswwrjkvql21r2xmmf3wbiisxrcab-
source:stable=/nix/store/hnwnvbfh3jb4p4ar5hxyya027n0dcrgs-
source:small=/nix/store/2i157qvjbdwr8c58xlahri2yyb8cd0fm-source:master
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source:nur=/nix/store/c2p33y70g47dkwm04p9k26mbcjr1kq1j-source
PATH=/home/yoctocell/.conda/condabin:/home/yoctocell/.conda/bin:/run/wrappe
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nest_asyncio-1.5.1/lib/python3.8/site-packages:/nix/store/fbbcxnzpc89a
ndw9fzs2iqhxrxbrj9f5-python3.8-jupyterlab_pygments-0.1.2/lib/python3.8
/site-packages:/nix/store/kk81y8acgwphkcrd0q64hvh36wzzmyyh-
python3.8-terminado-0.9.3/lib/python3.8/site-packages:/nix/store/534d0
l78q3apma8naqgfkxf2vb1p7i0x-python3.8-requests-2.25.1/lib/python3.8/si
te-packages:/nix/store/xy13dlrqldl0c5p8lms1pdlri4gpmwip-
python3.8-certifi-2020.12.5/lib/python3.8/site-packages:/nix/store/8mk
ph96c97h87sdibvpms0x56pkzic3a-python3.8-chardet-4.0.0/lib/python3.8/si
te-packages:/nix/store/z8qgxgsdfan42zfricbikhlvnwyq9wb7-python3.8-idna
-3.1/lib/python3.8/site-packages:/nix/store/8c2hpw473d80yfw1nqyaxdkaz1
2rqj0w-python3.8-urllib3-1.26.4/lib/python3.8/site-packages:/nix/store
/j1ws3ipg9nwj22194xa7ql9d7637mjv8-python3.8-brotli-1.0.9/lib/python3.8
/site-packages:/nix/store/iwk66ibxs1k0hyyjlm388rckb4hd8f5x-python3.8-p
ysocks-1.7.1/lib/python3.8/site-
packages:/nix/store/zskq35q5jcralnkydvkwznv2hfj9aniq-
python3.8-prometheus_client-0.9.0/lib/python3.8/site-
packages:/nix/store/b0xwpjc8yji58ygazzkm1bxh99ndd2nb-
python3.8-argon2_cffi-20.1.0/lib/python3.8/site-packages:/nix/store/v4
ry8pvzz3kjp18g1l5zam67314s5gm8-python3.8-pycparser-2.20/lib/python3.8/
site-packages:/nix/store/cp9sgmd9zgjisyfjzl2rb4z88bx6iznj-
python3.8-cffi-1.14.5/lib/python3.8/site-packages
QTWEBKIT_PLUGIN_PATH=/home/yoctocell/.nix-profile/lib/mozilla/plugins/:/etc/profiles/per-us
er/yoctocell/lib/mozilla/plugins/:/nix/var/nix/profiles/default/lib/mo
zilla/plugins/:/run/current-system/sw/lib/mozilla/plugins/
QT_PLUGIN_PATH=/home/yoctocell/.nix-profile/lib/qt4/plugins:/home/yoctocell/.nix-
profile/lib/kde4/plugins:/etc/profiles/per-
user/yoctocell/lib/qt4/plugins:/etc/profiles/per-user/yoctocell/lib/kd
e4/plugins:/nix/var/nix/profiles/default/lib/qt4/plugins:/nix/var/nix/
profiles/default/lib/kde4/plugins:/run/current-
system/sw/lib/qt4/plugins:/run/current-system/sw/lib/kde4/plugins
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=/home/yoctocell/.guix-profile/etc/ssl/certs/ca-certificates.crt
WINDOWPATH=1
XCURSOR_PATH=/home/yoctocell/.guix-home-environment/profile/share/icons:/home/yocto
cell/.icons:/home/yoctocell/.local/share/icons:/home/yoctocell/.nix-
profile/share/icons:/home/yoctocell/.nix-
profile/share/pixmaps:/etc/profiles/per-
user/yoctocell/share/icons:/etc/profiles/per-user/yoctocell/share/pixm
aps:/nix/var/nix/profiles/default/share/icons:/nix/var/nix/profiles/de
fault/share/pixmaps:/run/current-system/sw/share/icons:/run/current-
system/sw/share/pixmaps
http_proxy=<set>
https_proxy=<set>
active environment : None
shell level : 0
user config file : /home/yoctocell/.condarc
populated config files :
conda version : 4.6.14
conda-build version : not installed
python version : 3.7.3.final.0
base environment : /home/yoctocell/.conda (writable)
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/free/linux-64
https://repo.anaconda.com/pkgs/free/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/yoctocell/.conda/pkgs
envs directories : /home/yoctocell/.conda/envs
platform : linux-64
user-agent : conda/4.6.14 requests/2.25.1 CPython/3.7.3 Linux/5.4.106 nixos/21.05.20210505.d3ba498 glibc/2.32
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers?
[y/N]:
Looking at the traceback, it looks like conda tried to call `python' with super user privileges, which I find weird as I thought it would only mess with things owned by the current user.
Do you have a .bashrc file? There was a bug once that made conda believe it requires sudo access to activate the environment if this file was missing (AFAIR).
Do you have a .bashrc file? There was a bug once that made conda believe it requires sudo access to activate the environment if this file was missing (AFAIR).
Yeah, below is the content of it (if you're curious).
# -*- mode: sh -*-
# Commands that should be applied only for interactive shells.
[[ $- == *i* ]] || return
HISTCONTROL=erasedups
HISTFILE="/home/yoctocell/.config/bash/history"
HISTFILESIZE=100000
HISTIGNORE=cd:pwd
HISTSIZE=10000
shopt -s histappend
shopt -s checkwinsize
shopt -s extglob
shopt -s globstar
shopt -s checkjobs
GPG_TTY="$(tty)"
export GPG_TTY
export PS1="\n\w $ "
# Only show 3 deepest directories
# <https://askubuntu.com/questions/145618/how-can-i-shorten-my-command-line-bash-prompt>
PROMPT_DIRTRIM=3
eval "$(/nix/store/h57n91xvgv3901v990zxiy96djwhl1zn-direnv-2.28.0/bin/direnv hook bash)"
Two more suggestions:
Try "conda init" (without the "bash", let it figure it out by itself). If that doesn't work, try "activate ReinventCommunity" (without the "conda").
Running conda init
results in the same error as above. Just running
activate ReinventCommunity
doesn't output anything (which is usually
a good thing on Unix). But trying to import a library from the REPL
doesn't seem to work.
~/src/ReinventCommunity $ python
Python 3.7.3 (default, Mar 27 2019, 22:11:17)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
Did you try closing and opening the console?
Is the python command executed under a given conda environment?
If you are under a conda environment the console should be showing something like:
(ReinventCommunity) [your_username]$
Another possibility is that there is some issue with the installation. Are you able to create/start other environments? Here is a useful link
Did you try closing and opening the console?
When exactly should I do that? I tried this multiple times and the result seems to be the same.
Is the python command executed under a given conda environment?
Presumably not; it's not able to import the Python libraries so I guess something is broken with conda.
If you are under a conda environment the console should be showing something like: (ReinventCommunity) [your_username]$
My PS1
didn't change so the environment was probably not active,
even though I ran activate ReinventCommunity
.
Another possibility is that there is some issue with the installation.
Yeah, that could be the case.
Are you able to create/start other environments?
I haven't tried it on other environments yet.
Here is a useful link
Thanks for the link, I will look into it.
The other day, @patronov wrote:
Another possibility is that there is some issue with the installation.
Yeah, that could be the case.
Trying to follow the official installation tutorial[1] didn't help
much, it drops a miniconda3/conda.exe
executable in my home
directory, but running it doesn't work.
~ $ ./miniconda3/conda.exe
./miniconda3/conda.exe: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
Are you able to create/start other environments?
I haven't tried it on other environments yet.
I tried to create a test environment, but it doesn't seem to be able to import the Python libraries
$ cd myenv
$ conda create -n test-env python numpy
$ activate myenv
$ python
Python 3.7.3 (default, Mar 27 2019, 22:11:17)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'
Running conda info --env
indicates that the environment wasn't
activated, but I already ran `activate test-env'.
~ $ conda info --env
# conda environments:
#
base * /home/yoctocell/.conda
ReinventCommunity /home/yoctocell/.conda/envs/ReinventCommunity
myenv /home/yoctocell/.conda/envs/myenv
test /home/yoctocell/.conda/envs/test
Installing numpy with conda install numpy
installs it into the base
environment and seems to work, I guess that's what I will have to do
then.
~ $ ./miniconda3/conda.exe
./miniconda3/conda.exe: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
OK, so this part is if you are running it under windows. Since you are under linux dont use the *.exe
To activate environment you can try something like:
source /path-to-miniconda-folder/miniconda3/bin/activate ReinventCommunity
The point is to use custom environments so dont work under base. Make sure you can create an environment and activate it and then operate from there. If there are issues with creating new environments maybe try starting clean and reinstall miniconda.
On Tue, May 11 2021, patronov wrote:
~ $ ./miniconda3/conda.exe ./miniconda3/conda.exe: error while loading shared libraries: libz.so.1: cannot open shared object file: No such file or directory
OK, so this part is if you are running it under windows.
I am running Linux, and this is what the Linux installer gives me after following the installation instructions.
To activate environment you can try something like:
source /path-to-miniconda-folder/miniconda3/bin/activate ReinventCommunity
Ah, this seems to do the trick, now I can import the Python libraries just fine. Thanks!
Something else I noted, it is unclear to me what the reinvent_dir
variable in the example notebooks refer to. Is it the path to my
local checkout of the Reinvent Git repository?
Yes, correct reinvent_dir
should be pointing where you have cloned the Reinvent code.
The
Complete_Use-Case-DRD2_Demo.ipynb
file, it tells me to runconda env create -f reinvent_shared.yml
, but there is noreinvent_shared.yml
file, only anenvironment.yml
file. However, when passingenvironment.yml
, conda fails to create the environment.