spack install and exodus.py #450

aperijake · 2024-04-08T16:31:24Z

aperijake
Apr 8, 2024

Hello. I have installed SEACAS via spack on an Ubuntu 20.04 system and have been using many of the tools successfully. I recently wanted to create an Exodus file using exodus.py, but I can't find the script. I have tried searching for exodus.py in my spack directory, and it doesn't appear to be there. I installed SEACAS with all the defaults (i.e., simply used spack add seacas). Do I need to specify something else to get exodus.py?

Answered by aperijake

Apr 12, 2024

Great! Thanks Greg.

So, in summary:

My issue was I just had python3 in my path and not python.
It required Python Development, but that is not really needed, and the requirement has been removed.

View full answer

gdsjaar · 2024-04-09T15:44:20Z

gdsjaar
Apr 9, 2024

It should build and install exodus.py and exomerge.py automatically ``` 08:43 $ spack load seacas ==> Error: seacas matches multiple packages. Matching packages: kg63w7i ***@***.******@***.******@***.******@***.***> arch=darwin-sonoma-m2 pl4xiwk ***@***.******@***.******@***.******@***.***> arch=darwin-sonoma-m2 Use a more specific spec (e.g., prepend '/' to the hash). 08:43 $ spack load /kg63w7i 08:43 $ which blot /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt/bin/blot 08:43 $ ls /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt/ bin include lib 08:43 $ find /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt/ -name \*.py … /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt//lib/exodus3.py /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt//lib/exomerge3.py /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt//lib/exodus.py /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt//lib/exomerge.py ``` My `PYTHONPATH` also seems to be set correctly by the `spack load seacas` command: ``` 08:55 $ echo $PYTHONPATH /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt/lib:/Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xcb-proto-1.16.0-d72dp4vfokxjmvyv3dzadrqb6waigtio/lib64/python3.12/site-packages:/Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/xcb-proto-1.16.0-d72dp4vfokxjmvyv3dzadrqb6waigtio/lib/python3.12/site-packages ``` This is just the result of a `spack install seacas~mpi` although it should be the same for a `spack install seacas` ..Greg From: Jake Koester ***@***.***> Date: Monday, April 8, 2024 at 10:32 AM To: sandialabs/seacas ***@***.***> Cc: Subscribed ***@***.***> Subject: [EXTERNAL] [sandialabs/seacas] spack install and exodus.py (Discussion #450) Hello. I have installed SEACAS via spack on an Ubuntu 20.04 system and have been using many of the tools successfully. I recently wanted to create an Exodus file using exodus.py, but I can't find the script. I have tried searching for exodus.py in my spack directory, and it doesn't appear to be there. I installed SEACAS with all the defaults (i.e., simply used spack add seacas). Do I need to specify something else to get exodus.py? — Reply to this email directly, view it on GitHub<#450>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AC626ROAEBX5Q2E6GCMDUW3Y4LA7DAVCNFSM6AAAAABF5BKHTGVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZWGQ3TSMRSG4>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

1 reply

aperijake Apr 9, 2024
Author

Thanks for the help, Greg. I tried a fresh install in a new spack environment using spack add --install seacas ~mpi, but still don't see exodus.py. I also have it installed on my Mac and it shows up there.

Ubuntu output:

azureuser@AperiAzureGPU1:~$ spack load seacas
==> Error: seacas matches multiple packages.
  Matching packages:
    ufsrfux seacas@2024-03-11%[email protected] arch=linux-ubuntu20.04-zen2
    qwvs6ck seacas@2024-03-11%[email protected] arch=linux-ubuntu20.04-zen2
  Use a more specific spec (e.g., prepend '/' to the hash).

azureuser@AperiAzureGPU1:~$ spack load /ufsrfux

azureuser@AperiAzureGPU1:~$ which blot
/home/azureuser/projects/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-10.5.0/seacas-2024-03-11-ufsrfux4lr2nhj4qmxi2scl2bi4weagd/bin/blot

azureuser@AperiAzureGPU1:~$ find /home/azureuser/projects/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-10.5.0/seacas-2024-03-11-ufsrfux4lr2nhj4qmxi2scl2bi4weagd/lib/ -name \*.py
azureuser@AperiAzureGPU1:~$

I tried searching the spack directory for exodus.py, exodus2.py, and exodus3.py and found nothing.

Mac output:

(base) [develop][~/projects/spack]$ spacktivate seacas                                                                 
(base) [develop][~/projects/spack]$ spack find seacas 
==> In environment seacas
==> Root specs
seacas 

==> Installed packages
-- darwin-sonoma-m1 / [email protected] ------------------------
seacas@2023-10-24
==> 1 installed package
(base) [develop][~/projects/spack]$ which blot                                                                         
/Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/bin/blot
(base) [develop][~/projects/spack]$ ll /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus*py
lrwxr-xr-x  1 jake  staff   137B Jan 16 16:15 /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus.py -> /Users/jake/projects/spack/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/seacas-2023-10-24-423wph62thxpet3q2hfhz6gl3r2cofzq/lib/exodus.py
lrwxr-xr-x  1 jake  staff   138B Jan 16 16:15 /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus2.py -> /Users/jake/projects/spack/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/seacas-2023-10-24-423wph62thxpet3q2hfhz6gl3r2cofzq/lib/exodus2.py
lrwxr-xr-x  1 jake  staff   138B Jan 16 16:15 /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus3.py -> /Users/jake/projects/spack/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/seacas-2023-10-24-423wph62thxpet3q2hfhz6gl3r2cofzq/lib/exodus3.py

gdsjaar · 2024-04-09T17:25:43Z

gdsjaar
Apr 9, 2024

There should be a file `spack-build-out.txt` that contains the configuration and build information. Mine is compressed and is at 520 ls /Users/gdsjaar/src/spack.fork/opt/spack/darwin-sonoma-m2/apple-clang-15.0.0/seacas-2024-04-03-kg63w7iuldibj2v435e2fxbabg3ofejt/.spack/spack-build-out.txt.gz. Do you have one of those and can you send it to me… Doesn’t have lots of information re python, but might be helpful… ..Greg From: Jake Koester ***@***.***> Date: Tuesday, April 9, 2024 at 10:54 AM To: sandialabs/seacas ***@***.***> Cc: Sjaardema, Greg ***@***.***>, Comment ***@***.***> Subject: [EXTERNAL] Re: [sandialabs/seacas] spack install and exodus.py (Discussion #450) Thanks for the help, Greg. I tried a fresh install in a new spack environment using spack add --install seacas ~mpi, but still don't see exodus.py. I also have it installed on my Mac and it shows up there. Ubuntu output: ***@***.***:~$ spack load seacas ==> Error: seacas matches multiple packages. Matching packages: ufsrfux ***@***.******@***.*** arch=linux-ubuntu20.04-zen2 qwvs6ck ***@***.******@***.*** arch=linux-ubuntu20.04-zen2 Use a more specific spec (e.g., prepend '/' to the hash). ***@***.***:~$ spack load /ufsrfux ***@***.***:~$ which blot /home/azureuser/projects/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-10.5.0/seacas-2024-03-11-ufsrfux4lr2nhj4qmxi2scl2bi4weagd/bin/blot ***@***.***:~$ find /home/azureuser/projects/spack/opt/spack/linux-ubuntu20.04-zen2/gcc-10.5.0/seacas-2024-03-11-ufsrfux4lr2nhj4qmxi2scl2bi4weagd/lib/ -name \*.py ***@***.***:~$ I tried searching the spack directory for exodus.py, exodus2.py, and exodus3.py and found nothing. Mac output: (base) [develop][~/projects/spack]$ spacktivate seacas (base) [develop][~/projects/spack]$ spack find seacas ==> In environment seacas ==> Root specs seacas ==> Installed packages

…

-- darwin-sonoma-m1 / ***@***.*** ------------------------ ***@***.*** ==> 1 installed package (base) [develop][~/projects/spack]$ which blot /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/bin/blot (base) [develop][~/projects/spack]$ ll /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus*py lrwxr-xr-x 1 jake staff 137B Jan 16 16:15 /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus.py -> /Users/jake/projects/spack/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/seacas-2023-10-24-423wph62thxpet3q2hfhz6gl3r2cofzq/lib/exodus.py lrwxr-xr-x 1 jake staff 138B Jan 16 16:15 /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus2.py -> /Users/jake/projects/spack/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/seacas-2023-10-24-423wph62thxpet3q2hfhz6gl3r2cofzq/lib/exodus2.py lrwxr-xr-x 1 jake staff 138B Jan 16 16:15 /Users/jake/projects/spack/var/spack/environments/seacas/.spack-env/view/lib/exodus3.py -> /Users/jake/projects/spack/opt/spack/darwin-sonoma-m1/apple-clang-15.0.0/seacas-2023-10-24-423wph62thxpet3q2hfhz6gl3r2cofzq/lib/exodus3.py — Reply to this email directly, view it on GitHub<#450 (reply in thread)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AC626ROU7CEMLRMNMNU6K7TY4QMNFAVCNFSM6AAAAABF5BKHTGVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TANRRHAZDS>. You are receiving this because you commented.Message ID: ***@***.***>

0 replies

aperijake · 2024-04-09T17:34:27Z

aperijake
Apr 9, 2024
Author

Here it is:
spack-build-out.txt.gz

0 replies

gdsjaar · 2024-04-09T17:41:25Z

gdsjaar
Apr 9, 2024

There is probably something missing in my seacas/package.py to put an explicit dependency on python. Currently, it just looks to see if it can find a python executable and if so, then it installs exodus.py an exomerge.py. In your case, it could not find a python, so it skips installing them:

…

-- Could NOT find Python (missing: Python_EXECUTABLE Python_INCLUDE_DIRS Python_LIBRARIES Interpreter Development Development.Module Development.Embed) -- Exodus.py and exomerge.py NOT installed since Python could not be found.

3 replies

aperijake Apr 9, 2024
Author

Yeah, I was just noticing the missing python. There was just python3 and no python. I added the symbolic link via:
sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10
and reinstalled seacas and it seems to find python now:
spack-build-out.txt
I still can't find exodus.py, though.

aperijake Apr 9, 2024
Author

Well, I guess it finds it in one spot, but later there is:

-- Could NOT find Python (missing: Python_EXECUTABLE Python_INCLUDE_DIRS Python_LIBRARIES Interpreter Development Development.Module Development.Embed) 
-- Exodus.py and exomerge.py NOT installed since Python could not be found.

aperijake Apr 9, 2024
Author

Okay did:
sudo apt install python3.8-dev
and reinstalled, and it is there now! Thanks for the help, Greg.

gsjaardema · 2024-04-09T19:30:32Z

gsjaardema
Apr 9, 2024
Maintainer

That shouldn't be needed, I'm not sure why it is looking for Python_LIBRARIES and a Development enviornment, so I will take a look at that, but glad to hear that it is now working for you.

0 replies

gsjaardema · 2024-04-09T19:32:21Z

gsjaardema
Apr 9, 2024
Maintainer

I guess it is explicitly asking for Python Development in the scripts subdirectory. I should be able to remove that and maybe it will then just look for the interpreter...

2 replies

gsjaardema Apr 12, 2024
Maintainer

This change has been done; python should now only need the interpreter and not require the development environment. This is available in seacas@master

aperijake Apr 12, 2024
Author

Great! Thanks Greg.

So, in summary:

My issue was I just had python3 in my path and not python.
It required Python Development, but that is not really needed, and the requirement has been removed.

Answer selected by aperijake

gsjaardema · 2024-04-12T15:37:21Z

gsjaardema
Apr 12, 2024
Maintainer

Great! Thanks Greg.

So, in summary:

My issue was I just had python3 in my path and not python.

It required Python Development, but that is not really needed, and the requirement has been removed.

Yes. I will take a look and see how to make it work with python3 as the executable name instead of python. I think CMake has that option, I just haven't had a chance to look (I had the same issue on my mac with python3 vs python awhile ago, but also did the symlink approach and then promptly forgot about it).

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spack install and exodus.py #450

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