cannot find sundials when using google colab

[userrand]

Thank you for this package.

I am trying to install this package on google colab but none of the methods I tried so far worked.

I am having trouble getting nix installed on google colab as it seems to install but the nix commands that I tried do not work.

Using pip install, the package seems to have trouble finding sundials. This might be linked to https://scikits-odes.readthedocs.io/en/stable/installation.html?highlight=%24SUNDIALS_INST#linking-errors but I do not understand that paragraph. What does pass the correct one via the $SUNDIALS_INST environment variable. mean in code ?

[aragilar]

How did you install SUNDIALS? If you have not installed it, you'll need to install it first.

Once you've installed SUNDIALS, in a bash shell, run
export SUNDIALS_INST=<path_you_installed_sundials_at>, and then run pip.

[userrand]

How did you install SUNDIALS? If you have not installed it, you'll need to install it first.

Once you've installed SUNDIALS, in a bash shell, run export SUNDIALS_INST=<path_you_installed_sundials_at>, and then run pip.

Thank you for your very quick reply

I did the following in a google colab notebook (the ! are used to execute shell commands in one line, ----\ is a personal notation to indicate different jupyter cells (might be irrelevant), %%shell is used to consider the entire cell as a shell command

! wget https://github.com/LLNL/sundials/releases/download/v6.5.1/sundials-6.5.1.tar.gz

 \----\

! mkdir sundial

\----\

! tar -xzvf sundials-6.5.1.tar.gz -C sundials

\----\

%%shell

cd sundials
mkdir build-sundials-6.5.1
cd build-sundials-6.5.1
cmake -DLAPACK_ENABLE=ON -DSUNDIALS_INDEX_SIZE=64 ../sundials-6.5.1/
make 
make install

\-----\

%%shell

export SUNDIALS_INST=/usr/local

export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH

pip install scikits.odes

\----\

import pkg_resources
pkg_resources.get_distribution("scikits.odes").version


\----\

pip install nose

\-----\

import collections
collections.Callable = collections.abc.Callable
import scikits.odes as od; od.test()

[userrand]

@aragilar

just mentioning that the code above did not work as my answer did not mention that

[userrand]

I tried with nix

 ! bash <(curl -L https://nixos.org/nix/install) --daemon --yes

\----\

%%shell

source /etc/bashrc

nix-shell -p python37Packages.scikits-odes -p python37Packages.numpy --run "python3"

and got the following error

error:
       … while calling the 'derivationStrict' builtin

         at /builtin/derivation.nix:9:12: (source not available)

       … while evaluating derivation 'shell'
         whose name attribute is located at /nix/store/l6fcz7knk5y1p8zz3fn9l7ifg8jvjhpc-nixpkgs/nixpkgs/pkgs/stdenv/generic/make-derivation.nix:303:7

       … while evaluating attribute 'buildInputs' of derivation 'shell'

         at /nix/store/l6fcz7knk5y1p8zz3fn9l7ifg8jvjhpc-nixpkgs/nixpkgs/pkgs/stdenv/generic/make-derivation.nix:350:7:

          349|       depsHostHost                = lib.elemAt (lib.elemAt dependencies 1) 0;
          350|       buildInputs                 = lib.elemAt (lib.elemAt dependencies 1) 1;
             |       ^
          351|       depsTargetTarget            = lib.elemAt (lib.elemAt dependencies 2) 0;

       error: undefined variable 'python37Packages'

       at «string»:1:107:

            1| {...}@args: with import <nixpkgs> args; (pkgs.runCommandCC or pkgs.runCommand) "shell" { buildInputs = [ (python37Packages.scikits-odes) (python37Packages.numpy) ]; } ""
             |                                                                                                           ^
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
[<ipython-input-6-6d90f54bf14f>](https://localhost:8080/#) in <cell line: 1>()
----> 1 get_ipython().run_cell_magic('shell', '', '\nsource /etc/bashrc\n\nnix-shell -p python37Packages.scikits-odes -p python37Packages.numpy --run "python3"\n')

3 frames
[/usr/local/lib/python3.10/dist-packages/google/colab/_system_commands.py](https://localhost:8080/#) in check_returncode(self)
    135   def check_returncode(self):
    136     if self.returncode:
--> 137       raise subprocess.CalledProcessError(
    138           returncode=self.returncode, cmd=self.args, output=self.output
    139       )

CalledProcessError: Command '
source /etc/bashrc

nix-shell -p python37Packages.scikits-odes -p python37Packages.numpy --run "python3"
' returned non-zero exit status 1.