Hi,
>>> a small change to CMakeFile.txt over OpenMP
>>
>> Did you disable OpenMP altogether?
>> What happens if you use a compiler that supports OpenMP?
>> Can you provide more details of your use cases?
>
> I didn't disable OpenMP. Apple seems to have a different implementation (say it ain't so!) so it needs some special case handling - a block from my CMakeLists.txt is copied at the end of this email.
I see. I wonder if this is Mac OS X specific, LLVM specific,
ARM-specific or a general bug.
Can you open two issues in our GitHub
https://github.com/3dem/relion/issues reporting your problems in RELION 4.0?
> 3. Relion 4.0 also compiles (same CMakeFile.txt change) but fails in
Class2D:
> - with VDAM, it seems to be deadlocked in iteration 1 with
sampling of relion_refine showing MlOptimizer::storeWeightedSums() stuck
in a ptheread_mutex wait state, regardless of using 1 or more threads
(and only 1 MPI process is allowed anyway)
> - the older EM method crashes outright after "Estimating initial
noise spectra" and before "Estimating accuracies in the orientational
assignment ..." with what looks to be a memory allocation error.
Please include *all the details* needed to reproduce the issues,
such as: the compiler and library versions, source code
modifications and compilation options. If you install
compilers/libraries from HomeBrew or conda, please indicate how you did
it.
By the way, another possibility to run RELION on M1 Mac is to
use virtualization. Run ARM64 (not x86-64) Linux on Mac OS
and execute RELION inside it.
Best regards,
Takanori Nakane
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