GCC 10.3.0 fails to compile on Manjaro (GCC 12.2, binutils 2.39.0) #16235

baloe · 2022-09-11T13:50:39Z

I am unable to build GCC 10.3.0. Here is the output:

== Temporary log file in case of crash /tmp/eb-qe86ahz6/easybuild-ubithjku.log
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
Dry run: printing build status of easyconfigs and dependencies
CFGS=/tmp/bastian/eb_tmp/easybuild/easyconfigs
 * [x] $CFGS/m/M4/M4-1.4.19.eb (module: M4/1.4.19)
 * [x] $CFGS/b/Bison/Bison-3.8.2.eb (module: Bison/3.8.2)
 * [x] $CFGS/f/flex/flex-2.6.4.eb (module: flex/2.6.4)
 * [x] $CFGS/z/zlib/zlib-1.2.11.eb (module: zlib/1.2.11)
 * [x] $CFGS/b/binutils/binutils-2.36.1.eb (module: binutils/2.36.1)
 * [ ] $CFGS/g/GCCcore/GCCcore-10.3.0.eb (module: GCCcore/10.3.0)
 * [ ] $CFGS/z/zlib/zlib-1.2.11-GCCcore-10.3.0.eb (module: zlib/1.2.11-GCCcore-10.3.0)
 * [ ] $CFGS/h/help2man/help2man-1.48.3-GCCcore-10.3.0.eb (module: help2man/1.48.3-GCCcore-10.3.0)
 * [ ] $CFGS/m/M4/M4-1.4.18-GCCcore-10.3.0.eb (module: M4/1.4.18-GCCcore-10.3.0)
 * [ ] $CFGS/b/Bison/Bison-3.7.6-GCCcore-10.3.0.eb (module: Bison/3.7.6-GCCcore-10.3.0)
 * [ ] $CFGS/f/flex/flex-2.6.4-GCCcore-10.3.0.eb (module: flex/2.6.4-GCCcore-10.3.0)
 * [ ] $CFGS/b/binutils/binutils-2.36.1-GCCcore-10.3.0.eb (module: binutils/2.36.1-GCCcore-10.3.0)
 * [ ] $CFGS/g/GCC/GCC-10.3.0.eb (module: GCC/10.3.0)
== Temporary log file(s) /tmp/eb-qe86ahz6/easybuild-ubithjku.log* have been removed.
== Temporary directory /tmp/eb-qe86ahz6 has been removed.
== Temporary log file in case of crash /tmp/eb-u4d40mvn/easybuild-e7ypgify.log
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
== resolving dependencies ...
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
== processing EasyBuild easyconfig /tmp/bastian/eb_tmp/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb
== building and installing GCCcore/10.3.0...
== fetching files...
== creating build dir, resetting environment...
== starting iteration #0 ...
== ... (took 2 secs)
== unpacking...
== ... (took 10 secs)
== patching...
== preparing...
== configuring...
== FAILED: Installation ended unsuccessfully (build directory: /soft/modules/build/GCCcore/10.3.0/system-system): 
build failed (first 300 chars): cmd " ../configure   --enable-languages=c,c++,fortran --without-cuda-driver 
--enable-offload-targets=nvptx-none --enable-lto --enable-checking=release  --disable-multilib --enable-shared=yes 
--enable-static=yes  --enable-threads=posix  --enable-plugins  --enable-gold=default --enable-ld --with-plugi (took 
15 secs)
== Results of the build can be found in the log file(s) 
/tmp/eb-u4d40mvn/easybuild-GCCcore-10.3.0-20220911.094514.mAgTh.log
0:00:15  0 out of 8 easyconfigs done
ERROR: Build of /tmp/bastian/eb_tmp/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb failed (err: 'build failed (first 300 chars): cmd " ../configure   --enable-languages=c,c++,fortran --without-cuda-driver --enable-offload-targets=nvptx-none --enable-lto --enable-checking=release  --disable-multilib --enable-shared=yes --enable-static=yes  --enable-threads=posix  --enable-plugins  --enable-gold=default --enable-ld --with-plugi')

And here is the mentioned log file:
/tmp/eb-u4d40mvn/easybuild-GCCcore-10.3.0-20220911.094514.mAgTh.log

~~Is this issue possibly related to #16144 ?~~ I think not, because the error message is very different.

The log reads:

configure: error: in `/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj':
configure: error: C compiler cannot create executables
See `config.log' for more details

Here is the config.log file:
/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj/config.log

This one mentions a bunch of errors, but I have no idea how to fix them:

> grep -nir error /soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj/config.log
99:gcc: error: unrecognized command-line option '-V'
100:gcc: fatal error: no input files
104:gcc: error: unrecognized command-line option '-qversion'; did you mean '--version'?
105:gcc: fatal error: no input files
120:collect2: error: ld returned 1 exit status
140:configure:4535: error: in `/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj':
141:configure:4537: error: C compiler cannot create executables

The text was updated successfully, but these errors were encountered:

baloe · 2022-09-27T10:03:57Z

~~I guess my system GCC is too new for it to be able to compile the old GCC 10.3.0 module.~~

Here is the config.log file: /soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj/config.log

The first error appears in line 99, reading

gcc version 12.1.1 20220730 (GCC) 
configure:4446: $? = 0
configure:4435: gcc -V >&5
gcc: error: unrecognized command-line option '-V'
gcc: fatal error: no input files
compilation terminated.

I just tried a few versions of GCC on an HPC, ranging from 4 to 11. With none of them gcc -V is valid.
I don't get how this could ever have worked.

Is the intended command gcc -v?

Aha, this sheds light on the -V parameter:
https://superuser.com/a/847156

baloe · 2022-09-27T10:48:15Z

Once the issue regarding the unrecognized command line option -V is fixed, this fix may be needed as well: #16145

baloe · 2022-09-27T12:02:13Z

related:
#3405

jfgrimm · 2022-10-03T11:12:02Z

the unrecognized command line option error is not actually an issue, it's just configure determining what compiler is found. It iterates a bunch of options, and some will fail (and this is recorded in the logs).

To me, the following looks like the actual issue :

/soft/modules/software/binutils/2.36.1/bin/ld: /usr/lib/libc.so.6: unknown type [0x13] section `.relr.dyn'
/soft/modules/software/binutils/2.36.1/bin/ld: skipping incompatible /usr/lib/libc.so.6 when searching for /usr/lib/libc.so.6
/soft/modules/software/binutils/2.36.1/bin/ld: cannot find /usr/lib/libc.so.6
/soft/modules/software/binutils/2.36.1/bin/ld: /usr/lib/libc.so.6: unknown type [0x13] section `.relr.dyn'
/soft/modules/software/binutils/2.36.1/bin/ld: skipping incompatible /usr/lib/libc.so.6 when searching for /usr/lib/libc.so.6
/soft/modules/software/binutils/2.36.1/bin/ld: /usr/lib/ld-linux-x86-64.so.2: unknown type [0x13] section `.relr.dyn'
/soft/modules/software/binutils/2.36.1/bin/ld: skipping incompatible /usr/lib/ld-linux-x86-64.so.2 when searching for /usr/lib/ld-linux-x86-64.so.2
/soft/modules/software/binutils/2.36.1/bin/ld: cannot find /usr/lib/ld-linux-x86-64.so.2
/soft/modules/software/binutils/2.36.1/bin/ld: /usr/lib/ld-linux-x86-64.so.2: unknown type [0x13] section `.relr.dyn'
/soft/modules/software/binutils/2.36.1/bin/ld: skipping incompatible /usr/lib/ld-linux-x86-64.so.2 when searching for /usr/lib/ld-linux-x86-64.so.2

What operating system are you building on, and what are your system compiler and binutils versions?

baloe · 2022-10-03T11:35:18Z

I am on Manjaro, with

gcc version 12.2.0 (GCC)
GNU ld (GNU Binutils) 2.39.0

ocaisa · 2022-10-26T08:27:55Z

Looking at https://bbs.archlinux.org/viewtopic.php?id=278679, I believe the issue here is that the linker the build wants to use (binutils 2.36.1) is too old for your system. The way out of this is probably to just use the system linker (which is newer). You can do this with

eb --filter-deps=binutils GCCcore-10.3.0.eb

to set this for all your installations (probably a wise move) you can use the easybuild config file or

export EASYBUILD_FILTER_DEPS=binutils

baloe · 2022-10-27T21:59:44Z

The way out of this is probably to just use the system linker (which is newer). You can do this with
eb --filter-deps=binutils GCCcore-10.3.0.eb

Unfortunately, I was still not successful on my system:

== Temporary log file in case of crash /tmp/eb-wdd3b94y/easybuild-oe4qol7c.log
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
Dry run: printing build status of easyconfigs and dependencies
CFGS=/tmp/bastian/eb_tmp/easybuild/easyconfigs
 * [x] $CFGS/m/M4/M4-1.4.19.eb (module: M4/1.4.19)
 * [ ] $CFGS/g/GCCcore/GCCcore-10.3.0.eb (module: GCCcore/10.3.0)
 * [ ] $CFGS/g/GCC/GCC-10.3.0.eb (module: GCC/10.3.0)
== Temporary log file(s) /tmp/eb-wdd3b94y/easybuild-oe4qol7c.log* have been removed.
== Temporary directory /tmp/eb-wdd3b94y has been removed.
== Temporary log file in case of crash /tmp/eb-n9qdjdfy/easybuild-rqgo0e52.log
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
== resolving dependencies ...
== found valid index for /tmp/bastian/eb_tmp/easybuild/easyconfigs, so using it...
== processing EasyBuild easyconfig /tmp/bastian/eb_tmp/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb
== building and installing GCCcore/10.3.0...
== fetching files...
== ... (took 3 secs)
== creating build dir, resetting environment...
== starting iteration #0 ...
== ... (took 4 secs)
== unpacking...
== ... (took 10 secs)
== patching...
== preparing...
== configuring...
== ... (took 3 secs)
== building...
== ... (took 21 mins 53 secs)
== FAILED: Installation ended unsuccessfully (build directory: /soft/modules/build/GCCcore/10.3.0/system-system): build failed (first 300 chars): cmd " make -j 4 " exited with exit code 2 and output:
make[1]: Entering directory '/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj'
mkdir -p -- ./intl
mkdir -p -- ./libiberty
mkdir -p -- ./fixincludes
mkdir -p -- ./gmp
Configuring in ./intl
Configuring in ./libiberty
Configuri (took 22 mins 14 secs)
== Results of the build can be found in the log file(s) /tmp/eb-n9qdjdfy/easybuild-GCCcore-10.3.0-20221027.224031.hjDGl.log
0:22:14  0 out of 2 easyconfigs done
ERROR: Build of /tmp/bastian/eb_tmp/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb failed (err: 'build failed (first 300 chars): cmd " make -j 4 " exited with exit code 2 and output:\nmake[1]: Entering directory \'/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj\'\nmkdir -p -- ./intl\nmkdir -p -- ./libiberty\nmkdir -p -- ./fixincludes\nmkdir -p -- ./gmp\nConfiguring in ./intl\nConfiguring in ./libiberty\nConfiguri')

/tmp/eb-n9qdjdfy/easybuild-GCCcore-10.3.0-20221027.224031.hjDGl.log

baloe · 2022-10-27T22:04:52Z

The remaining error is probably

In file included from /usr/include/linux/fs.h:19,
                 from ../../../../libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp:75:
/usr/include/linux/mount.h:95:6: error: multiple definition of enum fsconfig_command
   95 | enum fsconfig_command {
      |      ^~~~~~~~~~~~~~~~
In file included from ../../../../libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp:62:
/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj/gcc/include-fixed/sys/mount.h:249:6: note: previous definition here
  249 | enum fsconfig_command
      |      ^~~~~~~~~~~~~~~~
In file included from /usr/include/linux/fs.h:19,
                 from ../../../../libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp:75:
/usr/include/linux/mount.h:129:8: error: redefinition of struct mount_attr
  129 | struct mount_attr {
      |        ^~~~~~~~~~
In file included from ../../../../libsanitizer/sanitizer_common/sanitizer_platform_limits_posix.cpp:62:
/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage1_obj/gcc/include-fixed/sys/mount.h:219:8: note: previous definition of struct mount_attr
  219 | struct mount_attr
      |        ^~~~~~~~~~
make[4]: *** [Makefile:611: sanitizer_platform_limits_posix.lo] Error 1

I had run into the exact same issue when trying to install GCC 11, and @branfosj and @boegel were able to fix it: #16144 (comment)

boegel · 2022-10-31T08:58:15Z

@baloe The problem should be fixed with the changes in #16502, can you verify with "eb --from-pr 16502 GCCcore-10.3.0.eb --robot?

baloe · 2022-11-05T00:31:17Z

Unfortunately

eb --prefix $PATH_MODULES --filter-deps=binutils --from-pr 16502 GCCcore-10.3.0.eb --robot -Dr
eb --prefix $PATH_MODULES --filter-deps=binutils --from-pr 16502 GCCcore-10.3.0.eb --robot

fails with

 * [x] /tmp/bastian/eb_tmp/easybuild/easyconfigs/m/M4/M4-1.4.19.eb (module: M4/1.4.19)
 * [ ] /tmp/eb-7b200ztj/files_pr16502/g/GCCcore/GCCcore-10.3.0.eb (module: GCCcore/10.3.0)

...

configure: error: could not find a working compiler, see config.log for details
 (at easybuild/tools/run.py:641 in parse_cmd_output)
== 2022-11-05 01:01:03,662 build_log.py:265 INFO ... (took 31 mins 11 secs)
== 2022-11-05 01:01:03,665 filetools.py:2014 INFO Removing lock /soft/modules/software/.locks/_soft_modules_software_GCCcore_10.3.0.lock...
== 2022-11-05 01:01:03,666 filetools.py:382 INFO Path /soft/modules/software/.locks/_soft_modules_software_GCCcore_10.3.0.lock successfully removed.
== 2022-11-05 01:01:03,666 filetools.py:2018 INFO Lock removed: /soft/modules/software/.locks/_soft_modules_software_GCCcore_10.3.0.lock
== 2022-11-05 01:01:03,666 easyblock.py:4097 WARNING build failed (first 300 chars): cmd " ./configure --prefix=/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage2_stuff --with-pic --disable-shared --enable-cxx  --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu" exited with exit code 1 and output:
checking build system type... x86_64-pc-linux-gnu
checking host sy

easybuild-GCCcore-10.3.0-20221105.002931.NKcuT.log

boegel · 2022-11-05T10:00:33Z

@baloe Can you also share the config.log from the build directory?

baloe · 2022-11-05T15:18:12Z

I think that this is the one that is relevant.
/soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage2_stuff/gmp/config.log
(The timestamps don't match the ones in my previous post, because I ran easybuild again, wrongly assuming that the build log would have been in my /tmp/ directory.)

It contains

/usr/bin/ld.gold: /soft/modules/build/GCCcore/10.3.0/system-system/GCC_stage1_eb/lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /usr/bin/ld.gold)
/usr/bin/ld.gold: /soft/modules/build/GCCcore/10.3.0/system-system/GCC_stage1_eb/lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/bin/ld.gold)

Mh, I am using --filter-deps=binutils, because @ocaisa observed:

Looking at https://bbs.archlinux.org/viewtopic.php?id=278679, I believe the issue here is that the linker the build wants to use (binutils 2.36.1) is too old for your system. The way out of this is probably to just use the system linker (which is newer).

but then my system binutils 2.39.0 appears to be too new for GCCcore/10.3.0. I have binutils/2.38 in my module system. Should I try to make eb use that one?

baloe · 2022-11-18T07:04:39Z

When using binutils/2.38 (instead of the 2.36.1, which eb would attempt to use, and instead of 2.39.0, which is my system binutils),

module load binutils/2.38
eb --prefix /soft/modules --allow-loaded-modules=binutils --filter-deps=binutils --from-pr 16502 GCCcore-10.3.0.eb --robot

I still get a failure:

msgfmt: /soft/modules/build/GCCcore/10.3.0/system-system/gcc-10.3.0/stage3_obj/x86_64-pc-linux-gnu/libstdc++-v3/src/.libs/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/lib/libicuuc.so.72)
make[5]: *** [Makefile:551: de.mo] Error 1

/tmp/eb-winj2kvt/easybuild-GCCcore-10.3.0-20221118.044301.kgzOS.log

I guess that's it, uninstallable on Manjaro.

ocaisa · 2022-11-18T16:13:24Z

Hmm, that's disappointing but in the EasyBuild slack today it was mentioned that this worked on Arch Linux a little while ago. Part of the problem is that the ground is shifting all the time on something like Manjaro, another is that EasyBuild is not isolated enough from the host OS (it is very hard to avoid some level of leakage though).

Are you aware of the EESSI project? That uses Gentoo Prefix to provide us with a compatibility OS on top of the system. Currently that includes GCC 10.3.0 and should work on any linux OS.

ocaisa · 2022-11-18T16:17:24Z

If you adopt some of the configuration used by EESSI, you can build on top of it, here's something that I use:

export EASYBUILD_PREFIX=/project/def-sponsor00/easybuild
export EASYBUILD_IGNORE_OSDEPS=1
export EASYBUILD_SYSROOT=${EPREFIX}
export EASYBUILD_RPATH=1
export EASYBUILD_FILTER_ENV_VARS=LD_LIBRARY_PATH
export EASYBUILD_FILTER_DEPS=Autoconf,Automake,Autotools,binutils,bzip2,cURL,DBus,flex,gettext,gperf,help2man,intltool,libreadline,libtool,Lua,M4,makeinfo,ncurses,util-linux,XZ,zlib
export EASYBUILD_MODULE_EXTENSIONS=1

Of course you'd have to customise EASYBUILD_PREFIX. With that you'd get additional modules under

module use $EASYBUILD_PREFIX/modules/all

baloe changed the title ~~GCC 10.3.0 fails~~ GCC 10.3.0 fails to compile Sep 27, 2022

jfgrimm added the problem report label Oct 3, 2022

baloe mentioned this issue Oct 26, 2022

Easybuild complains about rdma-core-dependencies even though they are present easybuilders/easybuild#818

Open

boegel added this to the 4.x milestone Oct 26, 2022

boegel changed the title ~~GCC 10.3.0 fails to compile~~ GCC 10.3.0 fails to compile on Manjaro (GCC 12.2, binutils 2.39.0) Oct 26, 2022

ocaisa mentioned this issue Oct 26, 2022

Refusing to build binutils when the system version is newer easybuilders/easybuild-easyblocks#2817

Open

branfosj mentioned this issue Oct 28, 2022

fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x #16502

Merged

boegel modified the milestones: 4.x, next release (4.6.3?) Oct 31, 2022

boegel added bug report and removed problem report labels Oct 31, 2022

boegel modified the milestones: next release (4.7.0), release after 4.7.0, 4.x Dec 20, 2022

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GCC 10.3.0 fails to compile on Manjaro (GCC 12.2, binutils 2.39.0) #16235

GCC 10.3.0 fails to compile on Manjaro (GCC 12.2, binutils 2.39.0) #16235

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GCC 10.3.0 fails to compile on Manjaro (GCC 12.2, binutils 2.39.0) #16235

GCC 10.3.0 fails to compile on Manjaro (GCC 12.2, binutils 2.39.0) #16235

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