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MolecularAI / ReinventCommunity

MIT License
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Outdated instructions? #5

Closed yoctocell closed 3 years ago

yoctocell commented 3 years ago

The Complete_Use-Case-DRD2_Demo.ipynb file, it tells me to run conda env create -f reinvent_shared.yml, but there is no reinvent_shared.yml file, only an environment.yml file. However, when passing environment.yml, conda fails to create the environment.

~/src/ReinventCommunity $ conda env create -f environment.yml
Collecting package metadata: done
Solving environment: failed

ResolvePackageNotFound:
  - ld_impl_linux-64==2.34=h53a641e_0
patronov commented 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

yoctocell commented 3 years ago

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-
                          shell/bin:/nix/store/a76bvbplz1wzbig24k099d5jzs6hx7ls-python3.8-notebo
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                          /bin:/nix/store/hyn2bg9zw5bbaghaqar2ss245wj40z1c-python3.8-jupyter_cor
                          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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                          environment/profile/share/info:/home/yoctocell/.guix-
                          profile/share/info:/home/yoctocell/.guix-
                          profile/share/info:$INFOPATH:/home/yoctocell/.nix-
                          profile/info:/home/yoctocell/.nix-
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                          ar/nix/profiles/default/info:/nix/var/nix/profiles/default/share/info:
                          /run/current-system/sw/info:/run/current-
                          system/sw/share/info:/home/yoctocell/.nix-
                          profile/info:/home/yoctocell/.nix-
                          profile/share/info:/etc/profiles/per-
                          user/yoctocell/info:/etc/profiles/per-user/yoctocell/share/info:/nix/v
                          ar/nix/profiles/default/info:/nix/var/nix/profiles/default/share/info:
                          /run/current-system/sw/info:/run/current-system/sw/share/info
          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
                          ell/lib/libexec:/nix/var/nix/profiles/default/lib/libexec:/run/current
                          -system/sw/lib/libexec
                  MANPATH=/home/yoctocell/.guix-home-environment/profile/share/man:
          MOZ_PLUGIN_PATH=/home/yoctocell/.nix-profile/lib/mozilla/plugins:/etc/profiles/per-use
                          r/yoctocell/lib/mozilla/plugins:/nix/var/nix/profiles/default/lib/mozi
                          lla/plugins:/run/current-system/sw/lib/mozilla/plugins
                 NIX_PATH=nixpkgs=/nix/store/p9spswwrjkvql21r2xmmf3wbiisxrcab-
                          source:nixos=/nix/store/p9spswwrjkvql21r2xmmf3wbiisxrcab-
                          source:stable=/nix/store/hnwnvbfh3jb4p4ar5hxyya027n0dcrgs-
                          source:small=/nix/store/2i157qvjbdwr8c58xlahri2yyb8cd0fm-source:master
                          =/nix/store/g47wh1q3sslml2cwfgpp1pbhz0kfr9g4-source:nixos-config=/nix/
                          store/vy0dl5c0kpk5j5waph2r2sf14zpkq88z-source/flake.nix:nixpkgs-overla
                          ys=/nix/store/vy0dl5c0kpk5j5waph2r2sf14zpkq88z-source/overlays:sops-
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                          manager=/nix/store/8fb7nbfs5w34nx5hh0xjdyi70gs3z1fg-
                          source:nur=/nix/store/c2p33y70g47dkwm04p9k26mbcjr1kq1j-source
                     PATH=/home/yoctocell/.conda/condabin:/home/yoctocell/.conda/bin:/run/wrappe
                          rs/bin:/usr/bin:/usr/sbin:/nix/store/jvkcxf8nl61albg0y0nh8wi4miyhsykp-
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                          packages:/nix/store/08qf1ig0n3h0yhgdiyl7fxpydqa5cyyj-
                          python3.8-packaging-20.9/lib/python3.8/site-packages:/nix/store/pngaip
                          659pn9bbhc5c2r9mxdisybqw2v-python3.8-pyparsing-2.4.7/lib/python3.8/sit
                          e-packages:/nix/store/8vfpi4jryhnkc2wj22hs2kx687ap18qh-
                          python3.8-html5lib-1.1/lib/python3.8/site-packages:/nix/store/zyv2dv5i
                          6vb35qxkckm0k65ni6h3np3v-python3.8-webencodings-0.5.1/lib/python3.8/si
                          te-packages:/nix/store/146nn9pkzkhijbs6qy6m1ngy67rri5p6-python3.8-mist
                          une-0.8.4/lib/python3.8/site-packages:/nix/store/3l9b7gk94f3sa24rgs33b
                          h3qs936943i-python3.8-ipykernel-5.5.0/lib/python3.8/site-
                          packages:/nix/store/wk9gnzlbc93vzpjyir5v26scssgf3dxa-
                          python3.8-pandocfilters-1.4.3/lib/python3.8/site-packages:/nix/store/w
                          bclqhqpb24lpvb47vxk150dracl15s0-python3.8-defusedxml-0.7.1/lib/python3
                          .8/site-packages:/nix/store/n1yzbdwfswp4mp2yr7b8wancgqaj04rd-
                          python3.8-nbclient-0.5.3/lib/python3.8/site-packages:/nix/store/2ilkq1
                          k958q8lb0dllqia6s32g022v4i-python3.8-async_generator-1.10/lib/python3.
                          8/site-packages:/nix/store/r1mjwgs21wq4p86j409d5krn85i4k65m-python3.8-
                          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.

CMargreitter commented 3 years ago

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).

yoctocell commented 3 years ago

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)"
CMargreitter commented 3 years ago

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").

yoctocell commented 3 years ago

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'
patronov commented 3 years ago

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

yoctocell commented 3 years ago

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.

yoctocell commented 3 years ago

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.

patronov commented 3 years ago 
~ $ ./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.

yoctocell commented 3 years ago

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!

yoctocell commented 3 years ago

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?

patronov commented 3 years ago

Yes, correct reinvent_dir should be pointing where you have cloned the Reinvent code.