Username: trigilia
Cluster: Baobab
Can you please assist me in installing SimNIBS ( SimNIBS 4.5 — SimNIBS 4.5.0 documentation ) in my hpc account? Or can you please show me if there are any steps that I can follow to install it myself?
Thank you
Dear @Myriam.Trigilia this is done but version 4.0.1 as newer version isn’t yet available in our software repository. Is this working for you?
Dear @Yann.Sagon,
Thank you for your help!
I tested SimNIBS/4.0.1 on my account. The main command (simnibs --version, simnibs --help) works and gmsh is available:
(baobab)-[trigilia@login1 ~]$ module load GCC/12.3.0
(baobab)-[trigilia@login1 ~]$ module load OpenMPI/4.1.5
(baobab)-[trigilia@login1 ~]$ module load SimNIBS/4.0.1
(baobab)-[trigilia@login1 ~]$ simnibs --version
4.0.1
(baobab)-[trigilia@login1 ~]$ gmsh --version
4.9.5
Is there something else that I need to check or is this fine?
Best regards,
Myriam
Hello,
the next step is that to try to use it I guess:)
Best regards
Yann
Hi Yann,
When testing the charm command in SimNIBS 4.0.1, the segmentation pipeline crashes at the post-processing step due to SimNIBS still using np.bool, which was removed in NumPy 1.24. Here’s the error:
Would it be possible for you to downgrade NumPy to ≤1.23 (e.g. 1.22.0) so that SimNIBS runs without crashing?
Thank you so much!
Myriam
Hi, thanks to Pavel’s commit, this should be fixed. Please give a try
Dear Yann,
Thank you so much. It is working successfully, except that in the end Simnibs tried to save a report in the WEBP format:
[ simnibs ]INFO: Creating report
[ simnibs ]CRITICAL: Uncaught exception
KeyError: ‘WEBP’
(baobab)-[trigilia@login1 jobs]$
For completeness, can you please let me know if you are able to also add the WEBP plugin?
Thank you very very much!
Myriam
Hi, can you try to simply load libwebp before running SimNIBS?
module load GCC/12.3.0 OpenMPI/4.1.5 SimNIBS/4.0.1 libwebp/1.3.1
Best
Hi Yann,
I loaded the module as request:
But, I still have the same error:
[ simnibs ]CRITICAL: Uncaught exception
KeyError: ‘WEBP’
(baobab)-[trigilia@login1 jobs]$
Can you please recommend me another option?
Thank you a lot!
Myriam
Hi, this should be ok now. The Pillow library was missing support for webp format. You can remove libwebp/1.3.1 from the module load line and try again.
Dear Yann,
Thank you so much! It worked!
Have a nice day!
Myriam
