On Wed, Jul 8, 2020 at 3:16 PM Tony Travis < [email protected]> wrote:
> Re: https://github.com/keylabivdc/VIP > > Hi, > Hey Tony, > Does anyone have experience of running VIP? > I don't, but I've taken a look. > I've been trying to get it working under Ubuntu 18.04/20.04 with > Debian-Med installed in a Bioconda environment, but I've only managed to > get it running in the author's Ubuntu 14.04 VIP Docker container... > 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. > 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. 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. Their script specifies 8 threads: https://github.com/keylabivdc/VIP/blob/d69b5e7615d8da76ef0dd66e51867c8ec42588d4/MSA.sh#L28 Though that is a different script than in the container, where it references `--thread $total_cores` where `total_cores` appears to be set to half of your available cores. Which matches your 12 of 24 cores report. You could replace that `--threads $total_cores` with `--threads -1` to see if that helps. > We're using the pipeline to check Tetse fly microbiota for viruses, but > it may also be useful for Covid-19 work because the host databases are > human by default. > > Thanks, > > Tony. > -- Michael R. Crusoe
