Rebuilding = using “—force", which still ends up looking in the ebfiles_repo directory before looking in easybuild/easyconfigs/…, right?
From: <[email protected]<mailto:[email protected]>> on behalf of Kenneth Hoste <[email protected]<mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> List-Post: [email protected] Date: Wednesday, May 4, 2016 at 11:31 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: Re: [easybuild] binutils for foss/2016a On 04/05/16 16:34, Heywood, Todd wrote: For anyone else who hits this, you also need to remove the .eb file from your local repo (ebfiles_repo). EasyBuild should overwrite the zlib-1.2.8.eb in ebfiles_repo after reinstalling it? From: <[email protected]<mailto:[email protected]><mailto:[email protected]>> on behalf of Todd Heywood <[email protected]<mailto:[email protected]><mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]>> List-Post: [email protected] Date: Wednesday, May 4, 2016 at 10:14 AM To: "[email protected]<mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]>> Subject: Re: [easybuild] binutils for foss/2016a Thanks, that’s it. I should have guessed by noticing zlib in the satisfied dependencies list in the dry run. Todd From: <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> on behalf of Kenneth Hoste <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Reply-To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> List-Post: [email protected] Date: Wednesday, May 4, 2016 at 3:30 AM To: "[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>" <[email protected]<mailto:[email protected]><mailto:[email protected]><mailto:[email protected]>> Subject: Re: [easybuild] binutils for foss/2016a H i Todd, On 03/05/16 17:00, Heywood, Todd wrote: I started on foss/2016a with Easybuild 2.7.0, having successfully build all previous foss toolchain versions without problem with earlier EB versions. This time I don’t get far, with binutils-2.25-GCCcore-4.9.3.eb failing with: 'build failed (first 300 chars): cmd "LIBS="$EBROOTZLIB/lib/libz.a" make -j 32 "' I have cut/pasted the end of the log below. This seems rather basic, so Iam wondering what nobody else has hit this. The toolchain build is using the system GCC 4.4.7 (RHEL6). I think the problem is that your installation of zlib 1.2.8 with the dummy toolchain (the Core/zlib/1.2.8 module) was not installed with having -fPIC enabled. The zlib-1.2.8.eb easyconfig was changed to use -fPIC on Dec 14 2015 (so in EasyBuild v2.5.0 or newer). If you zlib 1.2.8 w/ dummy toolchain installation is older than that, you'll need to reinstall it. regards, Kenneth Thanks, T /bin/sh ./libtool --tag=CC --mode=link gcc -W -Wall -Wstrict-prototypes -Wmissing-prototypes -Wshadow -O2 -march=native -release `cat libtool-soversion` -static-libstdc++ -static-libgcc -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/GCCcore/4.9.3/lib64 -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/GCCcore/4.9.3/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/flex/2.5.39/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/Bison/3.0.4/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/lib -o libbfd.la -rpath /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Compiler/GCCcore/4.9.3/binutils/2.25/lib archive.lo archures.lo bfd.lo bfdio.lo bfdwin.lo cache.lo coffgen.lo corefile.lo format.lo init.lo libbfd.lo opncls.lo reloc.lo section.lo syms.lo targets.lo hash.lo linker.lo srec.lo binary.lo tekhex.lo ihex.lo stabs.lo stab-syms.lo merge.lo dwarf2.lo simple.lo compress.lo verilog.lo `cat ofiles` -L/sonas-hs/it/hpc/home/easybuild/build/binutils/2.25/GCCcore-4.9.3/binutils-2.25/bfd/../libiberty/pic -liberty -Wl,-lc,--as-needed,-lm,--no-as-needed -ldl -ldl /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a *** Warning: Linking the shared library libbfd.la against the *** static library /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a is not portable! libtool: link: gcc -shared .libs/archive.o .libs/archures.o .libs/bfd.o .libs/bfdio.o .libs/bfdwin.o .libs/cache.o .libs/coffgen.o .libs/corefile.o .libs/format.o .libs/init.o .libs/libbfd.o .libs/opncls.o .libs/reloc.o .libs/section.o .libs/syms.o .libs/targets.o .libs/hash.o .libs/linker.o .libs/srec.o .libs/binary.o .libs/tekhex.o .libs/ihex.o .libs/stabs.o .libs/stab-syms.o .libs/merge.o .libs/dwarf2.o .libs/simple.o .libs/compress.o .libs/verilog.o .libs/elf64-x86-64.o .libs/elf-ifunc.o .libs/elf-nacl.o .libs/elf64.o .libs/elf.o .libs/elflink.o .libs/elf-attrs.o .libs/elf-strtab.o .libs/elf-eh-frame.o .libs/dwarf1.o .libs/elf32-i386.o .libs/elf-vxworks.o .libs/elf32.o .libs/i386linux.o .libs/aout32.o .libs/pei-i386.o .libs/peigen.o .libs/cofflink.o .libs/pei-x86_64.o .libs/pex64igen.o .libs/elf64-gen.o .libs/elf32-gen.o .libs/plugin.o .libs/cpu-i386.o .libs/cpu-l1om.o .libs/cpu-k1om.o .libs/cpu-plugin.o .libs/archive64.o -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/GCCcore/4.9.3/lib64 -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/GCCcore/4.9.3/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/flex/2.5.39/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/Bison/3.0.4/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib -L/sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/lib -L/sonas-hs/it/hpc/home/easybuild/build/binutils/2.25/GCCcore-4.9.3/binutils-2.25/bfd/../libiberty/pic -liberty -ldl /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a -march=native -Wl,-lc -Wl,--as-needed -Wl,-lm -Wl,--no-as-needed -Wl,-soname -Wl,libbfd-2.25.so -o .libs/libbfd-2.25.so /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(inflate.o): requires dynamic R_X86_64_PC32 reloc against 'memcpy' which may overflow at runtime; recompile with -fPIC /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(inftrees.o): requires unsupported dynamic reloc 11; recompile with -fPIC /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(zutil.o): requires dynamic R_X86_64_32 reloc which may overflow at runtime; recompile with -fPIC /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(compress.o): requires dynamic R_X86_64_32 reloc which may overflow at runtime; recompile with -fPIC /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(crc32.o): requires dynamic R_X86_64_32 reloc which may overflow at runtime; recompile with -fPIC /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(deflate.o): requires dynamic R_X86_64_PC32 reloc against 'memcpy' which may overflow at runtime; recompile with -fPIC /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(inffast.o): requires unsupported dynamic reloc 11; recompile with -fPIC /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/binutils/2.25/bin/ld.gold: error: /sonas-hs/it/hpc/home/easybuild/install_sbox/software/Core/zlib/1.2.8/lib/libz.a(trees.o): requires unsupported dynamic reloc 11; recompile with -fPIC collect2: error: ld returned 1 exit status make[4]: *** [libbfd.la] Error 1 make[4]: Leaving directory `/sonas-hs/it/hpc/home/easybuild/build/binutils/2.25/GCCcore-4.9.3/binutils-2.25/bfd' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/sonas-hs/it/hpc/home/easybuild/build/binutils/2.25/GCCcore-4.9.3/binutils-2.25/bfd' make[2]: *** [all] Error 2 make[2]: Leaving directory `/sonas-hs/it/hpc/home/easybuild/build/binutils/2.25/GCCcore-4.9.3/binutils-2.25/bfd' make[1]: *** [all-bfd] Error 2 make[1]: Leaving directory `/sonas-hs/it/hpc/home/easybuild/build/binutils/2.25/GCCcore-4.9.3/binutils-2.25' make: *** [all] Error 2 (at easybuild/easybuild/lib/python2.7/site-packages/easybuild/tools/run.py:397 in parse_cmd_output) == 2016-05-03 10:31:53,742 easyblock.py:2296 WARNING build failed (first 300 chars): cmd "LIBS="$EBROOTZLIB/lib/libz.a" make -j 32 " exited with exitcode 2 and output: make[1]: Entering directory `/sonas-hs/it/hpc/home/easybuild/build/binutils/2.25/GCCcore-4.9.3/binutils-2.25' make[1]: Nothing to be done for `all-target'. Configuring in ./intl Configuring in ./libiberty Configuring == 2016-05-03 10:31:53,743 easyblock.py:267 INFO Closing log for application name binutils version 2.25
