I'm making slow progress on building the foss-2019a toolchain (for our
GPAW module GPAW-19.8.1-foss-2019a-Python-3.7.2.eb) on a Intel Xeon Gold
6230 CPU (Cascade Lake) running CentOS 7.6.
I fixed the isl issue described in
https://github.com/easybuilders/easybuild-easyconfigs/issues/9692 before
building GCCcore-8.2.0.eb.
After a very long time, the build process repeatedly aborts with an error:
* collect2: fatal error: ld terminated with signal 7 [Bus error]
with this output:
== processing EasyBuild easyconfig
/groups/others/ohni/skylake/software/EasyBuild/4.1.1/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb
== building and installing GCCcore/8.2.0...
== fetching files...
== creating build dir, resetting environment...
== unpacking...
== patching...
== preparing...
== configuring...
== building...
== FAILED: Installation ended unsuccessfully (build directory:
/groups/others/ohni/skylake/build/GCCcore/8.2.0/system-system): build
failed (first 300 chars): cmd " make -j 2 bootstrap " exited with exit
code 2 and output:
echo stage3 > stage_final
make[1]: Entering directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj'
make[2]: Entering directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-syst (took 1
hour 18 min 33 sec)
== Results of the build can be found in the log file(s)
/tmp/eb-CLzF4F/easybuild-GCCcore-8.2.0-20200124.145944.vrjZV.log
ERROR: Build of
/groups/others/ohni/skylake/software/EasyBuild/4.1.1/easybuild/easyconfigs/g/GCCcore/GCCcore-8.2.0.eb
failed (err: 'build failed (first 300 chars): cmd " make -j 2 bootstrap "
exited with exit code 2 and output:\necho stage3 > stage_final\nmake[1]:
Entering directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj\'\nmake[2]:
Entering directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-syst')
The last part of the build log file is:
g++ -std=gnu++98 -no-pie -g -DIN_GCC -fno-exceptions -fno-rtti
-fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings
-Wcast-qual -Wno-format -Wmissing-format-attribute -Woverloaded-virtual
-pedantic -Wno-
long-long -Wno-variadic-macros -Wno-overlength-strings -DHAVE_CONFIG_H
-static-libstdc++ -static-libgcc -o cc1 c/c-lang.o c-family/stub-objc.o
attribs.o c/c-errors.o c/c-decl.o c/c-typeck.o c/c-convert.o
c/c-aux-info.o c/c
-objc-common.o c/c-parser.o c/c-fold.o c/gimple-parser.o
c-family/c-common.o c-family/c-cppbuiltin.o c-family/c-dump.o
c-family/c-format.o c-family/c-gimplify.o c-family/c-indentation.o
c-family/c-lex.o c-family/c-omp.o c-fam
ily/c-opts.o c-family/c-pch.o c-family/c-ppoutput.o c-family/c-pragma.o
c-family/c-pretty-print.o c-family/c-semantics.o c-family/c-ada-spec.o
c-family/c-ubsan.o c-family/known-headers.o c-family/c-attribs.o
c-family/c-warn.o
c-family/c-spellcheck.o i386-c.o glibc-c.o \
cc1-checksum.o libbackend.a main.o libcommon-target.a libcommon.a
../libcpp/libcpp.a ../libdecnumber/libdecnumber.a libcommon.a
../libcpp/libcpp.a ../libbacktrace/.libs/libbacktrace.a
../libiberty/libiberty.a ../libdecnum
ber/libdecnumber.a
-L/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage2_stuff/lib
-lisl
-L/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj/./gmp/.libs
-L/
lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj/./mpfr/src/.libs
-L/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj/./mpc/src/.libs
-lmpc -lmpfr -lgm
p -rdynamic -ldl -L./../zlib -lz
collect2: fatal error: ld terminated with signal 7 [Bus error]
compilation terminated.
make[3]: *** [cc1] Error 1
make[3]: *** Waiting for unfinished jobs....
rm gcc.pod
make[3]: Leaving directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj/gcc'
make[2]: *** [all-stage1-gcc] Error 2
make[2]: Leaving directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj'
make[1]: *** [stage1-bubble] Error 2
make[1]: Leaving directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj'
make: *** [bootstrap] Error 2
(at easybuild/tools/run.py:529 in parse_cmd_output)
== 2020-01-24 16:18:18,131 easyblock.py:3109 WARNING build failed (first
300 chars): cmd " make -j 2 bootstrap " exited with exit code 2 and output:
echo stage3 > stage_final
make[1]: Entering directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-system/gcc-8.2.0/stage3_obj'
make[2]: Entering directory
`/lustre/hpc/others/ohni/skylake/build/GCCcore/8.2.0/system-syst
== 2020-01-24 16:18:18,131 easyblock.py:295 INFO Closing log for
application name GCCcore version 8.2.0
Can anyone help me debug this problem?
Thanks a lot,
Ole
--
Ole Holm Nielsen
PhD, Senior HPC Officer
Department of Physics, Technical University of Denmark
