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{bio}[foss/2021a] MAGeCK v0.5.9.4 w/ Python 3.9.5 #15082

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Merged
casparvl merged 3 commits into from
Mar 13, 2022
Merged

{bio}[foss/2021a] MAGeCK v0.5.9.4 w/ Python 3.9.5 #15082

casparvl merged 3 commits into from
Mar 13, 2022

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@branfosj branfosj commented Mar 4, 2022

(created using eb --new-pr)

@branfosj branfosj added the new label Mar 4, 2022
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branfosj commented Mar 4, 2022

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.5, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/006dacfce28e9b037b0b3c6fbe17e817 for a full test report.

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casparvl commented Mar 7, 2022

Test report by @casparvl
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
software1.lisa.surfsara.nl - Linux debian 10.11, x86_64, Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz, Python 2.7.16
See https://gist.github.com/85b66d2ad4a1b3bee86ca21df6e30ffd for a full test report.

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casparvl commented Mar 7, 2022

Hm, we run with RPATH. It seems that doesn't work:

== 2022-03-07 12:39:34,835 easyblock.py:2973 WARNING No '(RPATH)' found in 'readelf -d' output for /home/casparl/.local/easybuild/Debian10/2021/software/MAGeCK/0.5.9.4-foss-2021a/bin/RRA:
Dynamic section at offset 0xfdc0 contains 29 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]
....
== 2022-03-07 12:39:34,836 run.py:233 INFO running cmd: file /home/casparl/.local/easybuild/Debian10/2021/software/MAGeCK/0.5.9.4-foss-2021a/bin/mageckGSEA
== 2022-03-07 12:39:34,862 run.py:233 INFO running cmd: ldd /home/casparl/.local/easybuild/Debian10/2021/software/MAGeCK/0.5.9.4-foss-2021a/bin/mageckGSEA
== 2022-03-07 12:39:34,899 run.py:233 INFO running cmd: readelf -d /home/casparl/.local/easybuild/Debian10/2021/software/MAGeCK/0.5.9.4-foss-2021a/bin/mageckGSEA
== 2022-03-07 12:39:34,927 easyblock.py:2973 WARNING No '(RPATH)' found in 'readelf -d' output for /home/casparl/.local/easybuild/Debian10/2021/software/MAGeCK/0.5.9.4-foss-2021a/bin/mageckGSEA:
Dynamic section at offset 0x1fda0 contains 29 entries:
...

So, it's missing RPATH for the RRA and mageckGSEA binaries. @branfosj do you know of these binaries get compiled during the installation? Or is this essentially a binary installation? (some context to why RPATH doesn't work for binary installations with EasyBuild is here)

Anyway, I don't think this should block the PR itself, since most users seem to use EasyBuild without RPATH anyway... A fix can always be implemented in a future PR, for now we've logged here the fact that it fails with --rpath.

I'll rerun without rpath support and see if that passes correctly on my system.

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casparvl commented Mar 7, 2022

Test report by @casparvl
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
software1.lisa.surfsara.nl - Linux debian 10.11, x86_64, Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz, Python 2.7.16
See https://gist.github.com/135f1edf356c95374a08937433fa3523 for a full test report.

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branfosj commented Mar 7, 2022 •
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I can see the issue. The binaries should be compiled during install - it is in the setup.py to do so. However, they ship the binaries and so they are not getting compiled.

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branfosj commented Mar 7, 2022

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.5, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/50b6e164ec292344b7fb5c4984923348 for a full test report.

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branfosj commented Mar 7, 2022

@casparvl f9e95ca should fix the RPATH issue.

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casparvl commented Mar 7, 2022

Test report by @casparvl
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
software1.lisa.surfsara.nl - Linux debian 10.11, x86_64, Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz, Python 2.7.16
See https://gist.github.com/fdd3c9e434618ab8297192296f7d2c68 for a full test report.

@casparvl casparvl self-requested a review March 7, 2022 13:08
@casparvl casparvl added this to the next release (4.5.4?) milestone Mar 7, 2022
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casparvl commented Mar 7, 2022

Yes, all good now, also with --rpath. You found that issue quickly, kudo's! Since we're one of the few centers using --rpath, I know from experience it is sometimes not so easy to find out... (does a binary not get build but copied? Does it get build, but the EasyBuild RPATH wrappers somehow don't function properly? etc...)

casparvl
casparvl reviewed Mar 7, 2022
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easybuild/easyconfigs/m/MAGeCK/MAGeCK-0.5.9.4-foss-2021a.eb Outdated
sources = [SOURCELOWER_TAR_GZ]
checksums = ['42875b308f2d9ee38f083fb1020d7d48fca29e2100fdb09ced1969b738b8c939']

# remove the shipped mageckGSEA and RRA binaries so that the Python install will build them
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@casparvl casparvl Mar 7, 2022 •
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Maybe say in the comment that this is for RPATH to work correctly, and refer to this PR. Without such comments, it's a bit unclear why you'd want to do this (and it would be harder to tell in the future if the preinstallopts is still relevant)

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@branfosj branfosj Mar 10, 2022

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@casparvl casparvl self-assigned this Mar 7, 2022
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casparvl commented Mar 13, 2022

Test report by @casparvl
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
software1.lisa.surfsara.nl - Linux debian 10.11, x86_64, Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz, Python 2.7.16
See https://gist.github.com/621d3bfd222a9d55d824423b27534309 for a full test report.

casparvl
casparvl approved these changes Mar 13, 2022
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Thanks @branfosj , looks good to me now! :)

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casparvl commented Mar 13, 2022

Going in, thanks @branfosj!

@casparvl casparvl merged commit 5f58388 into easybuilders:develop Mar 13, 2022
@branfosj branfosj deleted the 20220304153542_new_pr_MAGeCK0594 branch March 13, 2022 20:58
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