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FastTreeDblMP doesn't work in docker #123

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fanninpm opened this issue Dec 22, 2022 · 3 comments · Fixed by #126
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FastTreeDblMP doesn't work in docker #123

fanninpm opened this issue Dec 22, 2022 · 3 comments · Fixed by #126
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@victorlin

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@fanninpm
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fanninpm commented Dec 22, 2022 •
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I tried running augur tree --alignment whatever.fasta --method fasttree and got the following error:

FastTreeDblMP: error while loading shared libraries: libgomp.so.1: cannot open shared object file: No such file or directory

Originally posted by @fanninpm in #97 (comment)

$ docker image ls --digests nextstrain/base
REPOSITORY          TAG                      DIGEST                                                                    IMAGE ID            CREATED             SIZE
nextstrain/base     build-20221214T204556Z   sha256:e341aadab5681050ddc751218b254b1172276d87516466103db84399fa808d54   84e33405645c        7 days ago          2.41GB
@victorlin
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@fanninpm thanks for submitting this issue! I can reproduce this with both your provided image digest as well as the latest image. Will look into it.

@victorlin victorlin self-assigned this Dec 22, 2022
This was referenced Dec 23, 2022
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Repository owner moved this from New to Done in Nextstrain planning (archived) Dec 23, 2022
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victorlin commented Dec 23, 2022 •
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@fanninpm this should be fixed by #126. The new image is building and should be available for nextstrain update in ~1 hour, but you can use the PR's test image if you want to use the fix immediately:

nextstrain build --image nextstrain/base:branch-victorlin-fix-fasttree …

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I updated to the latest image, and it works like a charm. Thanks!

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Add libgomp1 for running FastTree nextstrain/docker-base
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@victorlin @fanninpm