Hello,
I am using Kilosort software to do spike sorting. It is matlab written and it uses GPU. I tried several version (2.0, 2.5 and 3.0) on two datasets. I managed to run Kilosort on Yggdrasil, but it is not stable. Indeed, with some combination of dataset and software version, I get segmentation violation.
I found some similar issues (#85, #199 and #341) on the GitHub repo. The segmentation trouble seems to affect only Linux users. Apparently, Matlab 2019b for Linux is delivered with 2018 versions of mkl (in particular BLAS and LAPACK). I confirmed it by typing the following commands :
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module load matlab
[juventin@login1.yggdrasil ~]$ matlab
MATLAB is selecting SOFTWARE OPENGL rendering.
< M A T L A B (R) >
Copyright 1984-2019 The MathWorks, Inc.
R2019b Update 5 (9.7.0.1319299) 64-bit (glnxa64)
February 19, 2020
To get started, type doc.
For product information, visit www.mathworks.com.
>> version -lapack
ans =
'Intel(R) Math Kernel Library Version 2018.0.3 Product Build 20180406 for Intel(R) 64 architecture applications, CNR branch AVX512
Linear Algebra PACKage Version 3.7.0
'
>> version -blas
ans =
'Intel(R) Math Kernel Library Version 2018.0.3 Product Build 20180406 for Intel(R) 64 architecture applications, CNR branch AVX512
'
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On issue #341, the following fix is proposed :
The issue seems to happen only on Linux, and I solved this issue by installing the latest version of Intel MKL sudo apt install intel-mkl, and by adding these 2 lines to my .bashrc file:
export BLAS_VERSION=/usr/lib/x86_64-linux-gnu/mkl/libblas.so
export LAPACK_VERSION=/usr/lib/x86_64-linux-gnu/mkl/liblapack.so
So, now my question is, how could I apply this fix on Yggdrasil?
Thank you,
Maxime