After much frustration with Windows updates I am looking at switching to Linux for my CPU crunchers. Are there optimised apps available, as in AVX or similar to take advantage of recent processor features?

I'm familiar with Debian so that will probably be my target OS. Initially I am looking at switching my i7-6700 machines.

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BOINC blog

I don't know for certain, but I don't think the Linux AVX CPU application is as good as the Lunatics one for Windows. But for Nvidia GPU hardware you'll want to check out thread below as there is an application that gives a huge boost to GPU output, with minimal CPU support required.
Linux CUDA 'Special' App finally available, featuring Low CPU use

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Grant
Darwin NT

http://lunatics.kwsn.info/index.php?action=downloads

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SETI apps news
We're not gonna fight them. We're gonna transcend them.

Currently I'm dual booting my i5 4460 between Win8 and Ubuntu and the CPU time is pretty darn close per task. with Window winning by a nose.

BUT, running 4 GPU tasks only leaves about 30% of a single core left on Win8. On Ubuntu's NVIDIA code it leaves about 3.8 cores left for CPU tasks to run, and the GPU tasks are 15-20% faster.

So do the math and Linux is doing laps around what Windows task can.

Can't wait for my new motherboard to be able to run them both!

@MarkJ
I have been using Debian Linux for a long time; for my modest GTX750Ti GPU I'm using the stock ..opencl_nvidia_SoG application. As for the optimized (Lunatics) CPU application I use the _avx_linux64 app. That means, of course, that I am an "anonymous platform" host with the implied extra duty of finding the stock applications (and opencl kernels) to download. The _avx_ app is 30% to 70% faster than the stock Linux CPU app so well worth the effort to use it. I have a "low end" (some would say "pitiful") AMD FX-4300 CPU with one core to feed the GPU and the remaining 3 cores keeping busy with the _avx_ application. The GPU produces the vast majority of the RAC but the CPUs do contribute some.
At @Raistmer's link you will find the Linux _avx_ application. I also suggest you fetch the Linux benchmark from the site as you may find it useful to test various command line options. Alas, the Lunatics "installer" is only available for Windows.
There is some effort needed to get a recent Linux boincmgr going. I think the stable (Debian) boinc versions are 7.4.23. I am using 7.6.22, which involved creating a non-standard folder and a short script to launch boinc with library references different than the current Debian library versions. (That may change early 2017 when I understand a major Debian upgrade will take place.) I also use the Nvidia driver (367.44) rather than any of the Linux-supplied GPU drivers.
Feel free to PM me if you have a Debian/Linux/BOINC question. At this Seti site my computer is "open" to inspect tasks and/or system specs. It looks like you have a "bunch" of computers so you can just pick one to use as your Linux testbed; then apply that experience to others if you are satisfied with the Linux system.
...Happy New Year...

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@MarkJ
I have been using Debian Linux for a long time; for my modest GTX750Ti GPU I'm using the stock ..opencl_nvidia_SoG application.

If you were to give the CUDA application compiled by TBar I linked to in the 2nd post in this thread a go, you'll find that you'll get even more work from your GTX 750Ti, as well as reduced CPU usage for the GPU application.

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Grant
Darwin NT

For sure the special CUDA60 app will get more work done by the 750 than the stock app.

Linux CUDA 6 Special App

Got debian installed. Managed to find intel GPU drivers and install them as well as beignet. BOINC installed and attached to the project to try with stock. It seems the linux64 app is corrupt (well specifically the AUTHORS file).

SETI@home 02-01-2017 03:08 PM Started download of setiathome-8.00_AUTHORS
SETI@home 02-01-2017 03:08 PM Incomplete read of 849.000000 < 5KB for setiathome-8.00_AUTHORS - truncating
SETI@home 02-01-2017 03:08 PM Finished download of setiathome-8.00_AUTHORS
SETI@home 02-01-2017 03:08 PM [error] File setiathome-8.00_AUTHORS has wrong size: expected 924, got 0
SETI@home 02-01-2017 03:08 PM [error] Checksum or signature error for setiathome-8.00_AUTHORS

Tried to use wget to pick it up and its 849 bytes but the project says its supposed to be 924 so it marked all CPU tasks as download failed.

The OpenCL tasks crapped out as well but they start and run for a few minutes and then fail, probably a driver issue.

I'll try Einstein next and maybe the Seti optimised ones after that.

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BOINC blog

Re: CUDA 6 Special App...
@Grant & Brent
I got the CUDA 6 file downloaded and ran it in a benchmark mode to see how it compares with the SoG app (and also to make sure it links up the right libraries and runs o.k.). Seems o.k., Q=99.7 on comparison to the nvidia_sah stock app and run times are ~30% shorter than the SoG app. And appears to use the same libcudart and libcufft as the earlier cuda x41zi application.
I see a post today (Jan 1) from TBar, in the Linux CUDA 'Special' App thread, to the effect that "Downloads have been suspended until the next revision is ready." So, I'll monitor messages for progress on the revision and, when available, proceed to switch from SoG to CUDA. Not exactly sure how to tell when the revised app is in place but I suppose a different file size is a sufficient indicator.

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Einstein tasks all failed with segfaults. I don't think their apps work with the Stretch release. I reinstalled the machine with Jessie and didn't bother with iGPU drivers. Its now crunching 8 gravity wave work units.

I still need to try optimised Seti apps but the Einstein gravity wave work usually takes from 8 to 16 hours to run.

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BOINC blog

Eric has fixed the AUTHORS file problem and the host is now running its first Seti work unit.

I installed beignet-opencl-icd from Jessie-backports. Its version 1.1.2. Unfortunately the version in there doesn't recognise the HD Graphics 530. The version in Stretch is more up to date (1.2.1) and does, but then all the Einstein apps will fail if I move up to the Stretch release, so I guess no iGPU any time soon.

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BOINC blog