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anuga-community / anuga_core

ANUGA for the simulation of the shallow water equation
https://anuga.anu.edu.au
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pybind11 not installed error #24

Closed PetarMilevski closed 1 year ago

PetarMilevski commented 1 year ago

Hi Steve, how are you going?

I cloned the latest anuga on my ubuntu 20.04lts box and did sudo bash anuga_core/tools/install_ubuntu_20_04.sh to install and this error occurred. Tried this python -m pip install pybind11, it says its installed but i keep getting the error.

Any ideas??

  Building wheel for meshpy (setup.py) ... error
  ERROR: Command errored out with exit status 1:
   command: /home/petar/anuga_env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"'; __file__='"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-gqp4dbqn
       cwd: /tmp/pip-install-wm9zkzsj/meshpy/
  Complete output (20 lines):
  ---------------------------------------------------------------------------
  Pybind11 is not installed.
  ---------------------------------------------------------------------------
  Very likely, the build process after this message will fail.

  Simply press Ctrl+C and type
  python -m pip install pybind11
  to fix this. If you don't, the build will continue
  in a few seconds.

  [1] https://pybind11.readthedocs.io/en/stable/
  ---------------------------------------------------------------------------
  Continuing in 1 seconds...    
  WARNING: The wheel package is not available.
  usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
     or: setup.py --help [cmd1 cmd2 ...]
     or: setup.py --help-commands
     or: setup.py cmd --help

  error: invalid command 'bdist_wheel'
  ----------------------------------------
  ERROR: Failed building wheel for meshpy
  Running setup.py clean for meshpy
^CERROR: Operation cancelled by user
petar@petar:~$ python -m pip install pybind11
Requirement already satisfied: pybind11 in ./.local/lib/python3.8/site-packages (2.10.0)
stoiver commented 1 year ago

Hi Peter,

Seems like there is a problem with installing meshpy.

Try installing meshpy via

python -m pip install meshpy

and see if that works.

Probably the installation script needs some work.

Cheers Steve

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From: Petar Milevski @.> Sent: Wednesday, August 24, 2022 8:19:44 AM To: anuga-community/anuga_core @.> Cc: Subscribed @.***> Subject: [anuga-community/anuga_core] pybind11 not installed error (Issue #24)

Hi Steve, how are you going?

I cloned the latest anuga on my ubuntu 20.04lts box and did sudo bash anuga_core/tools/install_ubuntu_20_04.sh to install and this error occurred. Tried this python -m pip install pybind11, it says its installed but i keep getting the error.

Any ideas??

Building wheel for meshpy (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/petar/anuga_env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"'; file='"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-gqp4dbqn cwd: /tmp/pip-install-wm9zkzsj/meshpy/ Complete output (20 lines): Pybind11 is not installed.

Very likely, the build process after this message will fail.

Simply press Ctrl+C and type python -m pip install pybind11 to fix this. If you don't, the build will continue in a few seconds.

[1] https://pybind11.readthedocs.io/en/stable/https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpybind11.readthedocs.io%2Fen%2Fstable%2F&data=05%7C01%7Cstephen.roberts%40anu.edu.au%7C7a24f2887ca149ff4f4508da8559c7b8%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637968917892263914%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0s82FMADRGmUqZUpbflAtnNrQVRYNch82VVP9fIkvZs%3D&reserved=0

Continuing in 1 seconds... WARNING: The wheel package is not available. usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

error: invalid command 'bdist_wheel'

ERROR: Failed building wheel for meshpy Running setup.py clean for meshpy ^CERROR: Operation cancelled by user @.***:~$ python -m pip install pybind11 Requirement already satisfied: pybind11 in ./.local/lib/python3.8/site-packages (2.10.0)

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stoiver commented 1 year ago

Hi Petar,

Another possible problem, the install script installs everything into a python env called anuga_env.

So you have to activate that environment via a command

source anuga_env/bin/activate

from your home directory. Your linux prompt should show that you are using the anuga_env environment. For instance my prompt looks like

(anuga_env) @.***:~/anuga_core$

Then you should be able to check if pybind11 is installed in this environment. And if not install pybind11 via

pip install pybind11

and then try to install meshpy via

pip install meshpy

Cheers Steve

============================== Emeritus Prof Stephen Roberts Mathematical Sciences Institute Hanna Neumann Building #145 The Australian National University Canberra, ACT 2600 AUSTRALIA T: +61 2 61254445 | E: @.***

CRICOS Provider: 00120C

From: Petar Milevski @.> Sent: Wednesday, 24 August 2022 8:19 AM To: anuga-community/anuga_core @.> Cc: Subscribed @.***> Subject: [anuga-community/anuga_core] pybind11 not installed error (Issue #24)

Hi Steve, how are you going?

I cloned the latest anuga on my ubuntu 20.04lts box and did sudo bash anuga_core/tools/install_ubuntu_20_04.sh to install and this error occurred. Tried this python -m pip install pybind11, it says its installed but i keep getting the error.

Any ideas??

Building wheel for meshpy (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/petar/anuga_env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"'; file='"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-gqp4dbqn cwd: /tmp/pip-install-wm9zkzsj/meshpy/ Complete output (20 lines): Pybind11 is not installed.

Very likely, the build process after this message will fail.

Simply press Ctrl+C and type python -m pip install pybind11 to fix this. If you don't, the build will continue in a few seconds.

[1] https://pybind11.readthedocs.io/en/stable/https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpybind11.readthedocs.io%2Fen%2Fstable%2F&data=05%7C01%7Cstephen.roberts%40anu.edu.au%7C7a24f2887ca149ff4f4508da8559c7b8%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637968917892263914%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0s82FMADRGmUqZUpbflAtnNrQVRYNch82VVP9fIkvZs%3D&reserved=0

Continuing in 1 seconds... WARNING: The wheel package is not available. usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

error: invalid command 'bdist_wheel'

ERROR: Failed building wheel for meshpy Running setup.py clean for meshpy ^CERROR: Operation cancelled by user @.***:~$ python -m pip install pybind11 Requirement already satisfied: pybind11 in ./.local/lib/python3.8/site-packages (2.10.0)

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PetarMilevski commented 1 year ago

Hi Steve, so did all that and still the same issue. its really odd because i did not have this issue when i installed on th ePC at the beginning of the year.

I'll just continue to use the previous install.

regard

On Wed, Aug 24, 2022 at 10:54 AM Stephen Roberts @.***> wrote:

Hi Petar,

Another possible problem, the install script installs everything into a python env called anuga_env.

So you have to activate that environment via a command

source anuga_env/bin/activate

from your home directory. Your linux prompt should show that you are using the anuga_env environment. For instance my prompt looks like

(anuga_env) @.***:~/anuga_core$

Then you should be able to check if pybind11 is installed in this environment. And if not install pybind11 via

pip install pybind11

and then try to install meshpy via

pip install meshpy

Cheers Steve

============================== Emeritus Prof Stephen Roberts Mathematical Sciences Institute Hanna Neumann Building #145 The Australian National University Canberra, ACT 2600 AUSTRALIA T: +61 2 61254445 | E: @.***

CRICOS Provider: 00120C

From: Petar Milevski @.> Sent: Wednesday, 24 August 2022 8:19 AM To: anuga-community/anuga_core @.> Cc: Subscribed @.***> Subject: [anuga-community/anuga_core] pybind11 not installed error (Issue

24)

Hi Steve, how are you going?

I cloned the latest anuga on my ubuntu 20.04lts box and did sudo bash anuga_core/tools/install_ubuntu_20_04.sh to install and this error occurred. Tried this python -m pip install pybind11, it says its installed but i keep getting the error.

Any ideas??

Building wheel for meshpy (setup.py) ... error ERROR: Command errored out with exit status 1: command: /home/petar/anuga_env/bin/python3 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"'; file='"'"'/tmp/pip-install-wm9zkzsj/meshpy/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-gqp4dbqn cwd: /tmp/pip-install-wm9zkzsj/meshpy/ Complete output (20 lines): Pybind11 is not installed.

Very likely, the build process after this message will fail.

Simply press Ctrl+C and type python -m pip install pybind11 to fix this. If you don't, the build will continue in a few seconds.

[1] https://pybind11.readthedocs.io/en/stable/< https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpybind11.readthedocs.io%2Fen%2Fstable%2F&data=05%7C01%7Cstephen.roberts%40anu.edu.au%7C7a24f2887ca149ff4f4508da8559c7b8%7Ce37d725cab5c46249ae5f0533e486437%7C0%7C0%7C637968917892263914%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0s82FMADRGmUqZUpbflAtnNrQVRYNch82VVP9fIkvZs%3D&reserved=0

Continuing in 1 seconds... WARNING: The wheel package is not available. usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...] or: setup.py --help [cmd1 cmd2 ...] or: setup.py --help-commands or: setup.py cmd --help

error: invalid command 'bdist_wheel'

ERROR: Failed building wheel for meshpy Running setup.py clean for meshpy ^CERROR: Operation cancelled by user @.***:~$ python -m pip install pybind11 Requirement already satisfied: pybind11 in ./.local/lib/python3.8/site-packages (2.10.0)

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stoiver commented 1 year ago

Hi @PetarMilevski ,

Just updated the install_ubuntu_20_04.sh script.

Could you try it again.

Thanks Steve

PetarMilevski commented 1 year ago

Hi Steve I'm working from home until Monday. It's my work PC that has the issue. Will try it then and gets back to you.

On Wed, 24 Aug 2022, 16:19 Stephen Roberts, @.***> wrote:

Hi Petar,

Just updated the install_ubuntu_20_04.sh script.

Could you try it again.

Thanks Steve

— Reply to this email directly, view it on GitHub https://github.com/anuga-community/anuga_core/issues/24#issuecomment-1225249592, or unsubscribe https://github.com/notifications/unsubscribe-auth/AETRNNRKBHQRBX6UOZNBXMLV2W5FVANCNFSM57NGSDZA . You are receiving this because you authored the thread.Message ID: @.***>

stoiver commented 1 year ago

Hi Petar,

I was able to install an ubuntu 22.04 via the wsl system on windows. So at least the installation worked for that system.

Cheers Steve

PetarMilevski commented 1 year ago

Hi Steve that's good to hear. My installs seen to be going ok. I have noticed the is lots of numbers being printed on the terminal when I first run the script. Looks like some debug must be set on when the mesh is created?

On Tue, 11 Oct 2022, 20:17 Stephen Roberts, @.***> wrote:

Hi Petar,

I was able to install an ubuntu 22.04 via the wsl system on windows. So at least the installation worked for that system.

Cheers Steve

============================== Emeritus Prof Stephen Roberts Mathematical Sciences Institute Hanna Neumann Building #145 The Australian National University Canberra, ACT 2600 AUSTRALIA T: +61 2 61254445 | E: @.***

CRICOS Provider: 00120C

From: Petar Milevski @.> Sent: Tuesday, 11 October 2022 7:29 PM To: anuga-community/anuga_core @.> Cc: Stephen Roberts @.>; Comment @.> Subject: Re: [anuga-community/anuga_core] pybind11 not installed error (Issue #24)

Hi Steve I'm working from home until Monday. It's my work PC that has the issue. Will try it then and gets back to you.

On Wed, 24 Aug 2022, 16:19 Stephen Roberts, @.***> wrote:

Hi Petar,

Just updated the install_ubuntu_20_04.sh script.

Could you try it again.

Thanks Steve

— Reply to this email directly, view it on GitHub < https://github.com/anuga-community/anuga_core/issues/24#issuecomment-1225249592 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AETRNNRKBHQRBX6UOZNBXMLV2W5FVANCNFSM57NGSDZA

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stoiver commented 1 year ago

@PetarMilevski is the lots of printout during the install procedure or when you run your own script?

PetarMilevski commented 1 year ago

When I'm running a model

On Tue, 11 Oct 2022, 21:49 Stephen Roberts, @.***> wrote:

@PetarMilevski https://github.com/PetarMilevski is the lots of printout during the install procedure or when you run your own script?

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stoiver commented 1 year ago

Seems the installation is now working for 22.04