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Re: VIP

On 08/07/2020 14:56, Michael Crusoe wrote:

[...]
Perhaps try the author's vip2 container? https://hub.docker.com/r/yang4li/vip2 Though I can find no source for either container, so it is a bit risky.
The yang4li/vip-docker container uses a very old version of mafft, from 2013. 

Hi, Michael.

Thanks for your advice - I'm pulling it now...


    It's running, but very slowly, and "mafft" is only running on one core
    even though there are 24 cores available and the "mafft" command-line
    specifies 12 cores. I think it might be caused by running it on an AMD
    Opteron 6000 that does not support SSE2 instructions, but any advice
FYI: Mafft does not appear to use SSE2 in its codebase. I checked and the 32-bit mafft 7.467-1 binaries have no SSE2 operands. The 64-bit version (amd64) does use SSE2, probably due to optimizations by the compiler.
Anyhow, I thought the AMD Opterons are 64bit? Then the do support SSE2 for sure and https://en.wikipedia.org/wiki/List_of_AMD_Opteron_microprocessors#Opteron_6100-series_%22Magny-Cours%22_(45_nm) says they support SSE3 as well.
Sorry, my careless slip: I meant SSE4 - I had a problem with "salmon" recently running on AMD64 that turned out to be compiled with SSE4. As it happens, removing the SSE4 flag did not affect performance, so upstream changed it for me :-) 

  https://github.com/COMBINE-lab/salmon/issues/500


    about VIP would be welcome - It's been running for a week now :-(
Could be that mafft has reached a point in the computation that is still single threaded. 

Maybe, but it's taking a very l o n g time :-(

Thanks for your heads-up about the VIP2 container,

  Tony.

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