Is Linux ARM64 a supported platform ?

[Mark Jens]

Hello community!

I'd like to ask whether Linux ARM64 is a recommended platform for running EMAN2 on ?

You know, ARM64/aarch64 is recommended because of its good performance with less power consumption.

I wasn't able to find anything related in the documentation and in the discussions here.

Thank you!

Mark

[Steve Ludtke]

ARM64 is not yet officially supported by Anaconda, which we use as a distribution platform. We have experimented with the conda-forge version for M1 Macs, but it isn't quite "there" yet either. Certainly it is possible to run on M1 Macs using the built in machine code translation, and performance is surprisingly good on that, which raises hopes that performance will be quite decent once ARM64 is properly supported. If you are talking about non-Mac ARM64 machines, you would need to be a bit more specific as to the machine you're considering. ARM chips span a massive range of computational capabilities, from Raspberry Pi's to Apple's M1 Ultra...

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Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Deputy Director, Advanced Technical Cores         (www.bcm.edu/research/atc-core-labs)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Mark Jens]

Thank you for the quick answer, Steve!

I am interested in Graviton [1] / Ampere [2] / TaiShan [3] type of machines. The ones used for server-side / cloud deployments.

1. https://aws.amazon.com/ec2/graviton/

2. https://amperecomputing.com/processors/ampere-altra/

3. https://e.huawei.com/en/products/servers/taishan-server

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/79B2B5DC-C5A5-4D3B-A372-13C78BCFAB85%40gmail.com.

[Steve Ludtke]

Yes, I've thought about trying graviton in the past, but never got around to any sort of testing, and at the moment, the Anaconda issue persists. If you want to see if there will be issues, you can try and install conda-forge miniconda for ARM64 on any one of those platforms and see how it goes. If that works, you can see if the eman2 dependencies are all available. If they are, we can probably put a package together for testing.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Deputy Director, Advanced Technical Cores         (www.bcm.edu/research/atc-core-labs)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/CAEVxhnbbnP5UwfX4c9HXRXhvSZTT3UiUMX4CJ48bQ%3DmNQZYj4g%40mail.gmail.com.

[Yikun Jiang]

@Mark Thanks for rasing this discussion. We are also interesting on eman2 on linux arm64

Here is some test from mine

> you can try and install conda-forge miniconda for ARM64

minicoda already supports aarch64: Miniconda3-py37_4.10.1-Linux-aarch64.sh    104.5M    2021-06-01 18:33:41 https://repo.anaconda.com/miniconda/

I can install successfully, and works well

> If that works, you can see if the eman2 dependencies are all available.

I also try to install dependencies mentioned in here:

https://github.com/cryoem/eman-deps-feedstock/blob/master/recipe/meta.yaml#L33

Looks like except bsddb3, pydusa, ftgl all deps can installed successfully.

PackagesNotFoundError: The following packages are not available from current channels:
  - bsddb3: I can install  python3-bsddb3 successfully, https://anaconda.org/conda-forge/bsddb3 support osx-arm64 now.
  - pydusa: https://anaconda.org/cryoem/pydusa looks like arm arch ddn't supported yet
  - ftgl: https://anaconda.org/conda-forge/ftgl/files, linux arm already supported in anaconda

Here is also a completed validation for eman2 on arm64 (sorry for only Chinese version): https://bbs.huaweicloud.com/forum/thread-180834-1-1.html

I'd like to work together with your guys to make eman2 available on linux arm64!

[Ludtke, Steven J.]

Thanks. Very useful. We'll take another look :^)

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/2f0aad27-e1df-465c-829c-deaf3cfc12a9n%40googlegroups.com.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                     

Deputy Director, Advanced Technical Cores        

Academic Director, CryoEM Core                                        
Co-Director CIBR Center                                   

[shadow walker]

Arch rebuild for bsddb3 has been submitted and should be available after the build PR is issued and completed. You can follow the arch migration status on conda-forge here, https://conda-forge.org/status/#aarch64andppc64leaddition. However, even after bsddb3 is available, as seen on the status page, qt and pyqt, which are eman2 dependencies, are not built yet.

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/36327667-A60A-4871-96DF-22E603C47EB8%40bcm.edu.

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shadow_walker