PyTorch not loading

[AndrewCSlater]

I have installed & run sjSDM on the cpu but can't get it to work on GPU. Followed the help with install vignette and am posting the output of r sjSDM::install_diagnostic() below. I'm not a techie so need really basic advice please.

      name                                                                       python

1 base C:\Users\acs_a\AppData\Local\r-miniconda/python.exe 2 r-reticulate C:\Users\acs_a\AppData\Local\r-miniconda\envs\r-reticulate/python.exe 3 r-sjsdm C:\Users\acs_a\AppData\Local\r-miniconda\envs\r-sjsdm/python.exe 4 anaconda3 C:\Users\acs_a\anaconda3/python.exe 5 r-sjsdm C:\Users\acs_a\anaconda3\envs\r-sjsdm/python.exe

ENV: base

torch:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1:

#

Name Version Build Channel

numpy:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1:

#

Name Version Build Channel

ENV: r-reticulate

torch:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1\envs\r-reticulate:

#

Name Version Build Channel

pytorch 1.9.1 py3.6_cpu_0 [cpuonly] pytorch pytorch-mutex 1.0 cuda pytorch pytorch-ranger 0.1.1 pypi_0 pypi torch-optimizer 0.3.0 pypi_0 pypi torchaudio 0.9.1 py36 pytorch torchvision 0.2.2 py_3 pytorch

numpy:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1\envs\r-reticulate:

#

Name Version Build Channel

numpy 1.19.5 py36h4b40d73_2 conda-forge

ENV: r-sjsdm

torch:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1\envs\r-sjsdm:

#

Name Version Build Channel

pytorch 1.12.1 py3.7_cpu_0 pytorch pytorch-mutex 1.0 cpu pytorch pytorch-ranger 0.1.1 pypi_0 pypi torch-optimizer 0.3.0 pypi_0 pypi torchaudio 0.12.1 py37_cpu pytorch torchvision 0.13.1 py37_cpu pytorch

numpy:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1\envs\r-sjsdm:

#

Name Version Build Channel

numpy 1.21.6 pypi_0 pypi numpy-base 1.21.5 py37hca35cd5_3

ENV: anaconda3

torch:

EnvironmentLocationNotFound: Not a conda environment: C:\Users\acs_a\AppData\Local\R-MINI~1\envs\anaconda3

numpy:

EnvironmentLocationNotFound: Not a conda environment: C:\Users\acs_a\AppData\Local\R-MINI~1\envs\anaconda3

ENV: r-sjsdm

torch:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1\envs\r-sjsdm:

#

Name Version Build Channel

pytorch 1.12.1 py3.7_cpu_0 pytorch pytorch-mutex 1.0 cpu pytorch pytorch-ranger 0.1.1 pypi_0 pypi torch-optimizer 0.3.0 pypi_0 pypi torchaudio 0.12.1 py37_cpu pytorch torchvision 0.13.1 py37_cpu pytorch

numpy:

packages in environment at C:\Users\acs_a\AppData\Local\R-MINI~1\envs\r-sjsdm:

#

Name Version Build Channel

numpy 1.21.6 pypi_0 pypi numpy-base 1.21.5 py37hca35cd5_3

python: C:/Users/acs_a/anaconda3/python.exe libpython: C:/Users/acs_a/anaconda3/python39.dll pythonhome: C:/Users/acs_a/anaconda3 version: 3.9.12 (main, Apr 4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)] Architecture: 64bit numpy: C:/Users/acs_a/anaconda3/Lib/site-packages/numpy numpy_version: 1.21.5 torch: [NOT FOUND]

NOTE: Python version was forced by RETICULATE_PYTHON

 active environment : C:/Users/acs_a/anaconda3
active env location : C:/Users/acs_a/anaconda3
   user config file : C:\Users\acs_a\.condarc

populated config files : C:\Users\acs_a.condarc conda version : 4.10.3 conda-build version : not installed python version : 3.9.5.final.0 virtual packages : cuda=11.8=0 win=0=0 __archspec=1=x86_64 base environment : C:\Users\acs_a\AppData\Local\R-MINI~1 (writable) conda av data dir : C:\Users\acs_a\AppData\Local\R-MINI~1\etc\conda conda av metadata url : None channel URLs : https://repo.anaconda.com/pkgs/main/win-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/r/win-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/msys2/win-64 https://repo.anaconda.com/pkgs/msys2/noarch package cache : C:\Users\acs_a\AppData\Local\R-MINI~1\pkgs C:\Users\acs_a.conda\pkgs C:\Users\acs_a\AppData\Local\conda\conda\pkgs envs directories : C:\Users\acs_a\AppData\Local\R-MINI~1\envs C:\Users\acs_a.conda\envs C:\Users\acs_a\AppData\Local\conda\conda\envs platform : win-64 user-agent : conda/4.10.3 requests/2.26.0 CPython/3.9.5 Windows/10 Windows/10.0.19044 administrator : False netrc file : None offline mode : False

[MaximilianPi]

Hi @AndrewCSlater, just to confirm, you have a NVIDIA GPU, right? Because other GPUs are not supported (Intel GPUs, Mac m1/m2 GPUs, AMD GPUs, etc.).

If you have a NVIDIA GPU, try the following steps (run from within R):

restart RStudio

reticulate::conda_remove('r-reticulate')
reticulate::conda_remove('r-sjsdm')
reticulate::conda_create('r-sjsdm', python_version='3.9')
reticulate::conda_install('r-sjsdm',packages = c("pytorch", "torchvision" ,"torchaudio", "cudatoolkit=11.3", "-c", "pytorch"))
reticulate::conda_install('r-sjsdm',packages = c("pyro-ppl", "torch_optimizer", "madgrad"), pip=TRUE)

restart RStudio

[AndrewCSlater]

Hi Max, I can't remember which one, but yes I definitely have an NVIDEA graphics card.I have zero experience with Python, or JSDM's etc, I'm far more a field ecologist and feel a bit out of my depth in this area, so any help aimed at non techies would really be greatly appreciated. Thanks a million for your time!CheersAndrew

On Thursday, 13 October 2022 at 07:52:48 BST, MaximilianPi ***@***.***> wrote:  

Hi @AndrewCSlater, just to confirm, you have a NVIDIA GPU, right? Because other GPUs are not supported (Intel GPUs, Mac m1/m2 GPUs, AMD GPUs, etc.)

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: @.***>

[MaximilianPi]

Don't worry, no technical knowledge is required. Try the steps above and let's see if it works.

[AndrewCSlater]

OK I ran the code as above, but when I reopened R Studio & ran sjSDM::install_sjSDM(), I went through the process and came back with the following message

installation of 'python=3.7.1' into environment 'r-sjsdm' failed [error code 1]

There is a huge amount of output in the R Studio console - do you need me to post it ? Additionally - Could I email you directly with another general query about the package...its also probably easier to send you the console output from above in an email rather than here as well?

[MaximilianPi]

Yes, sure (maximilian.pichler@ur.de), but please run the code above without running the 'sjSDM::install_sjSDM()' function (the code above is the manual install, sry I didn't mention this).

[MaximilianPi]

Okay, so it seems that the problems were caused by an old existing conda installation. It works now.