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add jemalloc & pkg-config as build deps for Salmon 0.12.0#8264

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wpoely86 merged 4 commits intoeasybuilders:developfrom
boegel:Salmon_jemalloc
May 9, 2019
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add jemalloc & pkg-config as build deps for Salmon 0.12.0#8264
wpoely86 merged 4 commits intoeasybuilders:developfrom
boegel:Salmon_jemalloc

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@boegel boegel commented May 7, 2019

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@boegel boegel added the bug fix label May 7, 2019
@boegel boegel added this to the next release (3.9.1) milestone May 7, 2019
@boegel boegel requested a review from wpoely86 May 7, 2019 20:31
akesandgren
akesandgren previously approved these changes May 8, 2019
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LGTM

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boegel commented May 8, 2019

make test seems to be hanging with these changes, whereas it runs in just 1 second without including jemalloc as a dep, interesting...

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vanzod commented May 8, 2019

@boegel I confirm that the test hangs with jemalloc.

wpoely86
wpoely86 previously approved these changes May 9, 2019
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wpoely86 commented May 9, 2019

Which version of jemalloc does it ship with?

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boegel commented May 9, 2019

@wpoely86 Same version as the one I'm using here. Which makes it even weirder. Maybe they do something special that doesn't happen if an external jemalloc is used. Or maybe it's the $LD_PRELOAD we do in jemalloc?

@boegel boegel dismissed stale reviews from wpoely86 and akesandgren via 5e5e2de May 9, 2019 09:57
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boegel commented May 9, 2019

Unsetting $LD_PRELOAD before make test fixes the issue for me, but then I wonder what effect it's have on Salmon itself outside of the tests...

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wpoely86 commented May 9, 2019

but how does it use jemalloc then?

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boegel commented May 9, 2019

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2402.golett.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz, Python 2.7.5
See https://gist.github.com/78946bb19ac5946987267379c583f4d8 for a full test report.

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boegel commented May 9, 2019

@wpoely86 Salmon statically links in jemalloc, so just a build dep is sufficient (changed in b95f313).

I've retested the resulting salmon binary using the examples explained in https://combine-lab.github.io/salmon/getting_started/, works fine, so this is good to go imho...

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boegel commented May 9, 2019

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2727.swalot.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/7b8afabfde988cc5fab120e8b5335314 for a full test report.

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boegel commented May 9, 2019

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node3122.skitty.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 2.7.5
See https://gist.github.com/7462f47e66688b5091eda5914576dfd7 for a full test report.

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boegel commented May 9, 2019

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node2006.delcatty.os - Linux centos linux 7.6.1810, Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz, Python 2.7.5
See https://gist.github.com/7eff773ebe259a2ff36755826c785620 for a full test report.

Comment thread easybuild/easyconfigs/s/Salmon/Salmon-0.12.0-foss-2018b.eb
wpoely86
wpoely86 previously approved these changes May 9, 2019
@boegel boegel changed the title add jemalloc dep for Salmon 0.12.0 + pkg-config as build dep add jemalloc & pkg-config as build deps for Salmon 0.12.0 May 9, 2019
@wpoely86 wpoely86 merged commit 72668fa into easybuilders:develop May 9, 2019
@boegel boegel deleted the Salmon_jemalloc branch May 9, 2019 13:08
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