Re: [easybuild] Error while loading shared libraries occurs when building GCCcore-4.9.3

[Yoshihito Horigome]

Hello, Thank you for contacting me. Regarding the reason for using GCCcore-4.9.3, I was verifying the introduction of a single application. Now that I needed GCCcore-4.9.3 for introducing PETSc-3.7.3-foss-2016a-Python-2.7.11, I came up with this problem. It seems necessary for GCC core -4.9.3 build itself, and 2.25 seems to be the latest for the host itself's latest package. * [x] $CFGS/m/M4/M4-1.4.17.eb (module: M4/1.4.17) * [x] $CFGS/a/Autoconf/Autoconf-2.69.eb (module: Autoconf/2.69) * [x] $CFGS/a/Automake/Automake-1.15.eb (module: Automake/1.15) * [x] $CFGS/l/libtool/libtool-2.4.6.eb (module: libtool/2.4.6) * [x] $CFGS/f/flex/flex-2.5.39.eb (module: flex/2.5.39) * [x] $CFGS/a/Autotools/Autotools-20150215.eb (module: Autotools/20150215) * [x] $CFGS/b/Bison/Bison-3.0.4.eb (module: Bison/3.0.4) * [x] $CFGS/z/zlib/zlib-1.2.8.eb (module: zlib/1.2.8) * [x] $CFGS/b/binutils/binutils-2.25.eb (module: binutils/2.25) * [ ] $CFGS/g/GCCcore/GCCcore-4.9.3.eb (module: GCCcore/4.9.3) $ rpm -qa | grep binutils cross-binutils-common-2.27-9.el7.1.noarch binutils-2.25.1-22.base.el7.aarch64 binutils-aarch64-linux-gnu-2.27-9.el7.1.aarch64 binutils-devel-2.25.1-22.base.el7.aarch64 For GCCcore-4.9.3 and binutils-2.25 introduced with easybuild, it seems to be necessary for many other installable applications, so we would like to make the introduction successful if possible. In addition, when we changed the related to GCCcore-4.9.3 to binutils 2.26, we could introduce it without problems. Best regards. On 8月 24 2017, at 10:55 午後, Kenneth Hoste <kenneth.ho...@ugent.be> wrote: Dear Yoshihito, It seems like either this version of GCC or the version of binutils that is being used to build it (binutils 2.25) is too old for your recent operating system (or the binutils it includes...). Is there a reason why you specifically need that fairly old version of GCC? regards, Kenneth On 24/08/2017 14:31, Yoshihito Horigome wrote: Hi, all I could not judge whether it was an issue or not, so write it here. In Easybuild 3.3.1, when attempting to build GCCcore-4.9.3 which is the core of some applications,  the following error occurs at the stage of configure. $ cat /etc/redhat-release CentOS Linux release 7.3.1611 (AltArch) -- It was created by GNU OpenMP Runtime Library configure 1.0, which was generated by GNU Autoconf 2.64.  Invocation command line was <snip> ## ----------- ## ## Core tests. ## ## ----------- ## configure:2467: creating cache ./config.cache configure:2550: checking for --enable-version-specific-runtime-libs configure:2565: result: no configure:2573: checking for --enable-generated-files-in-srcdir configure:2588: result: no configure:2645: checking build system type configure:2659: result: aarch64-unknown-linux-gnu configure:2679: checking host system type configure:2692: result: aarch64-unknown-linux-gnu configure:2712: checking target system type configure:2725: result: aarch64-unknown-linux-gnu configure:2782: checking for a BSD-compatible install configure:2850: result: /usr/bin/install -c configure:2861: checking whether build environment is sane configure:2911: result: yes configure:3052: checking for a thread-safe mkdir -p configure:3091: result: /usr/bin/mkdir -p configure:3104: checking for gawk configure:3131: result: gawk configure:3142: checking whether make sets $(MAKE) configure:3164: result: yes configure:3328: checking for aarch64-unknown-linux-gnu-gcc configure:3355: result: /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc -B/home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/bin/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/lib/ -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/include -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/sys-include configure:3624: checking for C compiler version configure:3633: /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc -B/home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/bin/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/lib/ -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/include -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/sys-include    --version >&5 /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc: error while loading shared libraries: libgcc_s.so.1: ELF load command alignment not page-aligned configure:3644: $? = 127 configure:3633: /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc -B/home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/bin/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/lib/ -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/include -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/sys-include    -v >&5 /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc: error while loading shared libraries: libgcc_s.so.1: ELF load command alignment not page-aligned configure:3644: $? = 127 configure:3633: /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc -B/home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/bin/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/lib/ -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/include -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/sys-include    -V >&5 /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc: error while loading shared libraries: libgcc_s.so.1: ELF load command alignment not page-aligned configure:3644: $? = 127 configure:3633: /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc -B/home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/bin/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/lib/ -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/include -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/sys-include    -qversion >&5 /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc: error while loading shared libraries: libgcc_s.so.1: ELF load command alignment not page-aligned configure:3644: $? = 127 configure:3664: checking for C compiler default output file name configure:3686: /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc -B/home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/bin/ -B/home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/lib/ -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/include -isystem /home/horigome/easybuild/software/GCCcore/4.9.3/aarch64-unknown-linux-gnu/sys-include    -g -O2   conftest.c  >&5 /home/horigome/easybuild/build/GCCcore/4.9.3/dummy-/gcc-4.9.3/obj/./gcc/xgcc: error while loading shared libraries: libgcc_s.so.1: ELF load command alignment not page-aligned configure:3690: $? = 127 configure:3727: result: configure: failed program was: https://gist.github.com/kometchtech/d6a1617531248273fb2647b49db8c827 When building in some aarch64 environments there was never a problem. In addition, I set LD_LIBRARY_PATH to /usr/lib and /usr/lib64 in the problem environment,  but the situation did not change. However, when configure is executed in the current directory, this error did not occur. If there are problems other than LD_LIBRARY_PATH, which one should be checked? Please kindly advise. Best regards.