Runtime error when running Savu

[aboulhaa]

Runtime error when running Savu

[dkazanc]

Hi, thanks for trying to use Savu. It seems that you're using python 3* when running Savu? We're in the process of upgrading to python 3 but for now you'll need to make sure that you're running Python 2. thanks

[aboulhaa]

Hello,
thanks for your reply.
The installation actually prompted me for using python 3 instead of 2 since the support for versions less than 3 stopped by January 2020. Would you advise with some solution?

[nicwade]

Hi @aboulhaa and good to see you having a go with Savu! At what point did the installation process prompt you to install python 3? I wrote the installation scripts and I'm not sure when that could happen. As @dkazanc states, it should install python 2 at the moment. So it would be great if I could get a bit more information. The Savu installation process outputs all information to a savu_error_log.txt file in your /tmp folder. If you could find it ("find . -name savu*" in the /tmp folder should do the trick) and upload it that would be useful.
Savu installs its own version of miniconda, so it could just be that there is another version in your path. If you change directory to the folder you installed Savu in and run "source savu_setup.sh", this will ensure that all paths are set correctly. Then you could try running Savu again. Let me know how it goes. Thanks.

[aboulhaa]

Hello Nicwade,
thanks you for your reply. I have made the following trials (on Ubuntu):

1- Run the following command:
bash savu_v2.4/savu_installer.sh

I got the following message:
"Pip subprocess error:
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support
ERROR: Package 'sphinxcontrib-websupport' requires a different Python: 2.7.16 not in '>=3.5'

CondaEnvException: Pip failed

***************************************************
          Package installation complete
  Check /tmp/tmp.LNeOKP6aVd/savu_error_log.txt for errors
***************************************************

"

2- Would you like to run the tests? (y/n):
I pressed y and got errors (sample):
ImportError: cannot import name _errors

---

Ran 81 tests in 0.006s

FAILED (errors=76)

************** Single-threaded local tests complete ******************

*************** SAVU TESTS COMPLETE! ******************

3- changed directory to the installation folder and Run
source savu_setup.sh
Then I run the following savu and got the following error:
File "MPI.pxd", line 28, in init h5py._errors
ValueError: mpi4py.MPI.Status size changed, may indicate binary incompatibility. Expected 48 from C header, got 40 from PyObject

[dkazanc]

Hi aboulhaa, could you please attach your log (/tmp/tmp.LNeOKP6aVd/savu_error_log.txt) somehow please?

[aboulhaa]

Hi dkazanc,

I checked the file /tmp/tmp.Em20K7KVG6/temp_output.txt, it is empty.

[aboulhaa]

Sorry wrong file!
Kindly find attached /tmp/tmp.LNeOKP6aVd/savu_error_log.txt
savu_error_log.txt

[nicwade]

Hi aboulhaa, thanks for the log file. We are currently working on improving the installation process so thank you for your patience. To fix this at the moment will require you to make an amendment to the environment.yml

Inside the savu folder (savu_v2.4) that you downloaded there is an environment.yml file. Can you replace sphinx-rtd-theme with sphinx-rtd-theme==0.4.3 and try the installation again. Please report back if you have any more difficulties.

[aboulhaa]

Hi Nicwade,

thank you for your help.
Kindly be noted that I tried this fix but unfortunately the same error still exists.

[aboulhaa]

savu_error_log.txt

[nicwade]

Ah sorry to hear that, it fixed the problem for me. Can you try removing the line then? It shouldn't cause any problems for running Savu. Thanks!

[aboulhaa]

Hello,
I made this new trial:
removed the line and run the installation again. Now I no longer get the installation error message.
But when
1- I cd the installed folder,
2- run source savu_setup.sh
3- run savu

I still get the same message!

Thank you.
savu_error_log.txt