Fix for building GCC with --sysroot on ppc64le #2315

bedroge · 2021-01-25T14:35:21Z

When using --sysroot (and --rpath) on ppc64le (and possibly more PowerPC systems), the dynamic linker does not get injected into executables correctly: it will pick up the one from the host, instead of the one from the sysroot location.

I ran into the same issue when building Gentoo Prefix on a ppc64le system, see:
https://bugs.gentoo.org/755551

The proposed fix there solved that issue, see here for an extensive description of the cause and solution:
https://755551.bugs.gentoo.org/attachment.cgi?id=684058

So I'm now including a similar fix here.

bedroge · 2021-01-25T14:35:57Z

Still marked as draft, as I still need to verify that this indeed works on my POWER9 system.

bedroge · 2021-01-25T18:47:59Z

Tested it on a POWER9 system. and it solved the issue.

== temporary log file in case of crash /tmp/eb-5dzgmoek/easybuild-jp6bd5_v.log
  >> running command:
	[started at: 2021-01-25 16:07:20]
	[working dir: /tmp/eb-5dzgmoek/tmpd7di3qop/easybuilders]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-mnnstpp_.log]
	tar xzf /tmp/eb-5dzgmoek/tmpd7di3qop/easybuilders/develop.tar.gz
  >> command completed: exit 0, ran in < 1s
== easyblock gcc.py included from PR #2315
== found valid index for /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/EasyBuild/4.3.2/easybuild/easyconfigs, so using it...
== resolving dependencies ...
== found valid index for /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/EasyBuild/4.3.2/easybuild/easyconfigs, so using it...
== processing EasyBuild easyconfig /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/EasyBuild/4.3.2/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0.eb
== building and installing GCCcore/9.3.0...
  >> installation prefix: /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/GCCcore/9.3.0
== fetching files...
  >> sources:
  >> /tmp/centos/easybuild/sources/g/GCCcore/gcc-9.3.0.tar.gz [SHA256: 5258a9b6afe9463c2e56b9e8355b1a4bee125ca828b8078f910303bc2ef91fa6]
  >> /tmp/centos/easybuild/sources/g/GCCcore/gmp-6.2.0.tar.bz2 [SHA256: f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea]
  >> /tmp/centos/easybuild/sources/g/GCCcore/mpfr-4.0.2.tar.bz2 [SHA256: c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc]
  >> /tmp/centos/easybuild/sources/g/GCCcore/mpc-1.1.0.tar.gz [SHA256: 6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e]
  >> /tmp/centos/easybuild/sources/g/GCCcore/isl-0.22.1.tar.bz2 [SHA256: 1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd]
  >> patches:
  >> /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/EasyBuild/4.3.2/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch [SHA256: 5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68]
  >> /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/EasyBuild/4.3.2/easybuild/easyconfigs/g/GCCcore/GCCcore-9.3.0_gmp-c99.patch [SHA256: 0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e]
== creating build dir, resetting environment...
  >> build dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system
== unpacking...
  >> running command:
	[started at: 2021-01-25 16:07:31]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-revodbt6.log]
	tar xzf /tmp/centos/easybuild/sources/g/GCCcore/gcc-9.3.0.tar.gz
  >> command completed: exit 0, ran in 00h00m19s
  >> running command:
	[started at: 2021-01-25 16:07:50]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-kjzhicow.log]
	tar xjf /tmp/centos/easybuild/sources/g/GCCcore/gmp-6.2.0.tar.bz2
  >> command completed: exit 0, ran in 00h00m01s
  >> running command:
	[started at: 2021-01-25 16:07:51]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-yt_1salv.log]
	tar xjf /tmp/centos/easybuild/sources/g/GCCcore/mpfr-4.0.2.tar.bz2
  >> command completed: exit 0, ran in 00h00m01s
  >> running command:
	[started at: 2021-01-25 16:07:53]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-wjnyqz26.log]
	tar xzf /tmp/centos/easybuild/sources/g/GCCcore/mpc-1.1.0.tar.gz
  >> command completed: exit 0, ran in < 1s
  >> running command:
	[started at: 2021-01-25 16:07:53]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-bd4962vp.log]
	tar xjf /tmp/centos/easybuild/sources/g/GCCcore/isl-0.22.1.tar.bz2
  >> command completed: exit 0, ran in < 1s
== patching...
  >> applying patch GCCcore-6.2.0-fix-find-isl.patch
  >> applying patch GCCcore-9.3.0_gmp-c99.patch
== preparing...
== configuring...
  >> running command:
	[started at: 2021-01-25 16:07:55]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage1_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-z7gbzvn2.log]
	/tmp/centos/easybuild/sources/generic/eb_v4.3.2/ConfigureMake/config.guess
  >> command completed: exit 0, ran in < 1s
  >> running command:
	[started at: 2021-01-25 16:07:55]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage1_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-iubtuxqf.log]
	../configure   --with-sysroot=/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/ppc64le  --enable-languages=c,c++,fortran --enable-lto --enable-checking=release  --disable-multilib --enable-shared=yes --enable-static=yes  --enable-threads=posix  --enable-plugins  --enable-gold=default --enable-ld --with-plugin-ld=ld.gold  --disable-bootstrap --prefix=/tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/GCC_stage1_eb --with-local-prefix=/tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/GCC_stage1_eb --build=powerpc64le-unknown-linux-gnu --host=powerpc64le-unknown-linux-gnu
  >> command completed: exit 0, ran in 00h00m12s
== building...
  >> running command:
	[started at: 2021-01-25 16:08:07]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage1_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-29jxs5tg.log]
	make -j 8
  >> command completed: exit 0, ran in 00h32m55s
  >> running command:
	[started at: 2021-01-25 16:41:05]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage1_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-y87p55tm.log]
	make install
  >> command completed: exit 0, ran in 00h01m41s
  >> running command:
	[started at: 2021-01-25 16:42:48]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/gmp]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-1jah5kkb.log]
	/tmp/centos/easybuild/sources/generic/eb_v4.3.2/ConfigureMake/config.guess
  >> command completed: exit 0, ran in < 1s
  >> running command:
	[started at: 2021-01-25 16:42:48]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/gmp]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-d9m509k3.log]
	./configure --prefix=/tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff --with-pic --disable-shared --enable-cxx  --build=powerpc64le-unknown-linux-gnu --host=powerpc64le-unknown-linux-gnu
  >> command completed: exit 0, ran in 00h01m18s
  >> running command:
	[started at: 2021-01-25 16:44:07]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/gmp]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-ht9_xtm9.log]
	make -j 8
  >> command completed: exit 0, ran in 00h00m51s
  >> running command:
	[started at: 2021-01-25 16:44:58]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/gmp]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-klxdgam7.log]
	make install
  >> command completed: exit 0, ran in 00h00m01s
  >> running command:
	[started at: 2021-01-25 16:45:00]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/isl]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-e682f15w.log]
	/tmp/centos/easybuild/sources/generic/eb_v4.3.2/ConfigureMake/config.guess
  >> command completed: exit 0, ran in < 1s
  >> running command:
	[started at: 2021-01-25 16:45:00]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/isl]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-m_2oqs4r.log]
	./configure --prefix=/tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff --with-pic --disable-shared --with-gmp=system --with-gmp-prefix=/tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff  --build=powerpc64le-unknown-linux-gnu --host=powerpc64le-unknown-linux-gnu
  >> command completed: exit 0, ran in 00h00m19s
  >> running command:
	[started at: 2021-01-25 16:45:20]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/isl]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-ay087kzy.log]
	make -j 8
  >> command completed: exit 0, ran in 00h00m26s
  >> running command:
	[started at: 2021-01-25 16:45:47]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff/isl]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-lkz6prtu.log]
	make install
  >> command completed: exit 0, ran in 00h00m01s
  >> running command:
	[started at: 2021-01-25 16:45:48]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage3_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-otzzuemc.log]
	/tmp/centos/easybuild/sources/generic/eb_v4.3.2/ConfigureMake/config.guess
  >> command completed: exit 0, ran in < 1s
  >> running command:
	[started at: 2021-01-25 16:45:48]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage3_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-zphv2uh1.log]
	../configure  --with-sysroot=/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/ppc64le  --enable-languages=c,c++,fortran --enable-lto --enable-checking=release  --disable-multilib --enable-shared=yes --enable-static=yes  --enable-threads=posix  --enable-plugins  --enable-gold=default --enable-ld --with-plugin-ld=ld.gold  --prefix=/cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/GCCcore/9.3.0 --with-local-prefix=/cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/GCCcore/9.3.0 --enable-bootstrap --with-isl=/tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage2_stuff  --build=powerpc64le-unknown-linux-gnu --host=powerpc64le-unknown-linux-gnu
  >> command completed: exit 0, ran in 00h00m08s
  >> running command:
	[started at: 2021-01-25 16:45:56]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage3_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-ku22cwyg.log]
	make -j 8  bootstrap
  >> command completed: exit 0, ran in 01h28m24s
== testing...
== installing...
  >> running command:
	[started at: 2021-01-25 18:14:27]
	[working dir: /tmp/centos/easybuild/build/GCCcore/9.3.0/system-system/gcc-9.3.0/stage3_obj]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-l4e84eq1.log]
	make install
  >> command completed: exit 0, ran in 00h01m18s
== taking care of extensions...
== restore after iterating...
== postprocessing...
== sanity checking...
  >> file 'bin/gcov' found: OK
  >> file 'bin/cpp' found: OK
  >> file 'bin/gcc' found: OK
  >> file 'bin/c++' found: OK
  >> file 'bin/g++' found: OK
  >> file 'bin/gfortran' found: OK
  >> file 'lib64/libgcc_s.so' or 'lib/libgcc_s.so' or 'lib32/libgcc_s.so' found: OK
  >> file 'lib64/libasan.so' or 'lib/libasan.so' or 'lib32/libasan.so' found: OK
  >> file 'lib64/libasan.a' or 'lib/libasan.a' or 'lib32/libasan.a' found: OK
  >> file 'lib64/libstdc++.so' or 'lib/libstdc++.so' or 'lib32/libstdc++.so' found: OK
  >> file 'lib64/libstdc++.a' or 'lib/libstdc++.a' or 'lib32/libstdc++.a' found: OK
  >> file 'lib64/libgfortran.so' or 'lib/libgfortran.so' or 'lib32/libgfortran.so' found: OK
  >> file 'lib64/libgfortran.a' or 'lib/libgfortran.a' or 'lib32/libgfortran.a' found: OK
  >> file 'libexec/gcc/powerpc64le-unknown-linux-gnu/9.3.0/lto1' or 'lib/gcc/powerpc64le-unknown-linux-gnu/9.3.0/lto1' found: OK
  >> file 'libexec/gcc/powerpc64le-unknown-linux-gnu/9.3.0/lto-wrapper' or 'lib/gcc/powerpc64le-unknown-linux-gnu/9.3.0/lto-wrapper' found: OK
  >> file 'libexec/gcc/powerpc64le-unknown-linux-gnu/9.3.0/liblto_plugin.so' or 'lib/gcc/powerpc64le-unknown-linux-gnu/9.3.0/liblto_plugin.so' found: OK
  >> file 'bin/cc' found: OK
  >> file 'bin/c++' found: OK
  >> file 'bin/f77' found: OK
  >> file 'bin/f95' found: OK
  >> (non-empty) directory 'lib/gcc/powerpc64le-unknown-linux-gnu/9.3.0' found: OK
  >> (non-empty) directory 'include/c++/9.3.0' found: OK
== cleaning up...
== creating module...
  >> generating module file @ /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/modules/all/GCCcore/9.3.0.lua
== permissions...
== packaging...
  >> running command:
	[started at: 2021-01-25 18:16:27]
	[working dir: /swlayer]
	[output logged in /tmp/eb-5dzgmoek/easybuild-run_cmd-ik0nioin.log]
	bzip2 /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/GCCcore/9.3.0/easybuild/easybuild-GCCcore-9.3.0-20210125.181627.log
  >> command completed: exit 0, ran in 00h00m13s
== COMPLETED: Installation ended successfully (took 2 hours 9 min 18 sec)
== Results of the build can be found in the log file(s) /cvmfs/pilot.eessi-hpc.org/2020.12/software/ppc64le/power9le/software/GCCcore/9.3.0/easybuild/easybuild-GCCcore-9.3.0-20210125.181627.log.bz2

This shows that the regex replaced the right thing:

== 2021-01-25 16:07:54,336 filetools.py:1387 INFO Replacing line 252 in gcc/config/rs6000/linux64.h: 'DYNAMIC_LINKER_PREFIX	""' -> '\1"/cvmfs/pilot.eessi-hpc.org/2020.12/compat/linux/ppc64le"'

boegel · 2021-02-17T09:52:37Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS GCCcore-4.9.3.eb
SUCCESS GCCcore-6.3.0.eb
SUCCESS GCCcore-7.3.0.eb

Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3108.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/85195323d0f89929d4c82565f98a2615 for a full test report.

boegel · 2021-02-17T10:36:00Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS GCCcore-10.2.0.eb
SUCCESS GCCcore-8.3.0.eb
SUCCESS GCCcore-9.3.0.eb

Build succeeded for 3 out of 3 (3 easyconfigs in total)
node2614.swalot.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/afd61f13a3fd31cd0b1514044db27d03 for a full test report.

boegel · 2021-02-17T12:46:38Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS GCCcore-9.3.0.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3401.kirlia.os - Linux UNKNOWN UNKNOWN, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 3.8.7
See https://gist.github.com/6072c34cb5ba1b23e13ab4964a049bcd for a full test report.

edit: this was tested in a --sysroot configuration

boegel · 2021-02-17T13:18:31Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS GCCcore-8.3.0.eb
SUCCESS GCCcore-9.3.0.eb
SUCCESS GCCcore-10.2.0.eb

Build succeeded for 3 out of 3 (3 easyconfigs in total)
easybuild2.novalocal - Linux centos linux 8.3.2011, POWER, IBM pSeries (emulated by qemu) (power9le), Python 3.6.8
See https://gist.github.com/53661bfc45a54906e9b5974686900002 for a full test report.

boegel · 2021-02-17T18:57:59Z

Test report by @boegel

Overview of tested easyconfigs (in order)

SUCCESS GCCcore-9.3.0.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild2.novalocal - Linux UNKNOWN UNKNOWN, POWER, IBM pSeries (emulated by qemu) (power9le), Python 3.8.7
See https://gist.github.com/45bc0e7165250cc02fd110f1ed1eccd0 for a full test report.

edit: this was tested in a --sysroot configuration

boegel

lgtm

set DYNAMIC_LINKER_PREFIX for rs6000 config file

99a6e3f

bedroge added 2 commits January 25, 2021 15:39

Espace special sequence

c36c7a8

remove redundant space in regex

f806105

bedroge marked this pull request as ready for review January 25, 2021 18:48

boegel added the bug fix label Feb 3, 2021

boegel added this to the next release (4.3.3?) milestone Feb 3, 2021

boegel changed the title ~~Fix for using GCC with --sysroot on ppc64le~~ Fix for building GCC with --sysroot on ppc64le Feb 3, 2021

boegel approved these changes Feb 17, 2021

View reviewed changes

boegel merged commit ffc9105 into easybuilders:develop Feb 17, 2021

bedroge deleted the fix_gcc_rs6000_sysroot branch February 17, 2021 19:04

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Fix for building GCC with --sysroot on ppc64le #2315

Fix for building GCC with --sysroot on ppc64le #2315

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Fix for building GCC with --sysroot on ppc64le #2315

Fix for building GCC with --sysroot on ppc64le #2315

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bedroge commented Jan 25, 2021

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boegel commented Feb 17, 2021

Overview of tested easyconfigs (in order)

boegel commented Feb 17, 2021

Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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Overview of tested easyconfigs (in order)

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