Running CentOS/RH 7.4? On 11/22/2017 11:36 AM, Paul Melis wrote: > Hi, > > This might be slightly off-topic with respects to EasyBuild, but I have > trouble running EB-built versions of Qt5 and am stuck in resolving the > issue. This is with both Qt5/5.7.0-intel-2016b and > Qt5/5.8.0-intel-2016b. Even the simplest Qt-application or the ones > included in the Qt5 package itself segfault on something related to what > seems text formatting (QTextEngine and/or Harfbuzz), see the details below. > > paulm@gcn12 11:31 ~$ DISPLAY=:0.0 xdpyinfo | head > name of display: :0.0 > version number: 11.0 > vendor string: The X.Org Foundation > vendor release number: 11702000 > X.Org version: 1.17.2 > maximum request size: 16777212 bytes > motion buffer size: 256 > bitmap unit, bit order, padding: 32, LSBFirst, 32 > image byte order: LSBFirst > number of supported pixmap formats: 7 > > paulm@gcn12 11:31 ~$ m av Qt5 > ------------------------------------------------------------------------------- > /home/paulm/.local/easybuild/RedHatEnterpriseServer7/modules/all > ------------------------------------------------------------------------------- > > Qt5/5.7.0-intel-2016b-nvidia Qt5/5.7.0-intel-2016b-nvidia-debug > Qt5/5.7.1-intel-2016b-nvidia > -------------------------------------------------------------------------------------- > /hpc/eb/RedHatEnterpriseServer7/modulefiles/devel > --------------------------------------------------------------------------------------- > > Qt5/5.7.0-intel-2016b(default) Qt5/5.7.0-intel-2016b-nvidia > Qt5/5.7.0-intel-2016b-nvidia-debug Qt5/5.8.0-intel-2016b > > # Load Qt5/5.8.0-intel-2016b, built using the .eb from the EB repo > paulm@gcn12 11:31 ~$ m load Qt5/5.8.0-intel-2016b > > paulm@gcn12 11:32 ~$ which assistant > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/assistant > > paulm@gcn12 11:32 ~$ DISPLAY=:0.0 assistant > Segmentation fault (core dumped) > > paulm@gcn12 11:32 ~$ gdb > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/assistant > core.40705 > GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-94.el7 > Copyright (C) 2013 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or later > <http://gnu.org/licenses/gpl.html> > This is free software: you are free to change and redistribute it. > There is NO WARRANTY, to the extent permitted by law. Type "show copying" > and "show warranty" for details. > This GDB was configured as "x86_64-redhat-linux-gnu". > For bug reporting instructions, please see: > <http://www.gnu.org/software/gdb/bugs/>... > Reading symbols from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/assistant...(no > debugging symbols found)...done. > [New LWP 40705] > [New LWP 40706] > [New LWP 40711] > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/usr/lib64/libthread_db.so.1". > Core was generated by `assistant'. > Program terminated with signal 11, Segmentation fault. > #0 0x00002b13f31715b3 in ?? () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > warning: File > "/nfs/admin/hpc/sw/RedHatEnterpriseServer7/GCCcore/5.4.0/lib64/libstdc++.so.6.0.21-gdb.py" > auto-loading has been declined by your `auto-load safe-path' set to > "$debugdir:$datadir/auto-load:/usr/bin/mono-gdb.py". > To enable execution of this file add > add-auto-load-safe-path > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/GCCcore/5.4.0/lib64/libstdc++.so.6.0.21-gdb.py > > line to your configuration file "/home/paulm/.gdbinit". > To completely disable this security protection add > set auto-load safe-path / > line to your configuration file "/home/paulm/.gdbinit". > For more information about this security protection see the > "Auto-loading safe path" section in the GDB manual. E.g., run from the > shell: > info "(gdb)Auto-loading safe path" > Missing separate debuginfos, use: debuginfo-install > dbus-libs-1.6.12-17.el7.x86_64 glibc-2.17-157.el7_3.4.x86_64 > graphite2-1.3.6-1.el7_2.x86_64 harfbuzz-0.9.36-1.el7.x86_64 > jasper-libs-1.900.1-30.el7_3.x86_64 libicu-50.1.2-15.el7.x86_64 > libjpeg-turbo-1.2.90-5.el7.x86_64 pcre-8.32-15.el7_2.1.x86_64 > (gdb) bt > #0 0x00002b13f31715b3 in ?? () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #1 0x00002b13f3170ce4 in ?? () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #2 0x00002b13f31700fb in ?? () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #3 0x00002b13f2e4f9c8 in > QTextEngine::shapeTextWithHarfbuzzNG(QScriptItem const&, unsigned short > const*, int, QFontEngine*, QVector<unsigned int> const&, bool, bool) > const () > from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #4 0x00002b13f2e4eba7 in QTextEngine::shapeText(int) const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #5 0x00002b13f2e43fa3 in QTextEngine::shape(int) const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #6 0x00002b13f2e6a3f3 in QTextLine::layout_helper(int) () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #7 0x00002b13f2e66531 in QTextLine::setLineWidth(double) () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #8 0x00002b13f3017597 in ?? () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #9 0x00002b13f30169b5 in ?? () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #10 0x00002b13f2e28f93 in QFontMetrics::boundingRect(QRect const&, int, > QString const&, int, int*) const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #11 0x00002b13f2e28ff8 in QFontMetrics::size(int, QString const&, int, > int*) const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > > #12 0x00002b13f2539453 in QToolButton::sizeHint() const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > > #13 0x00002b13f2302ec9 in QWidgetItemV2::updateCacheIfNecessary() const > () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > > #14 0x00002b13f2302daf in QWidgetItemV2::maximumSize() const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > > #15 0x00002b13f22e97b7 in ?? () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > > #16 0x00002b13f22e8019 in QBoxLayout::minimumSize() const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > > #17 0x00002b13f22fe798 in QLayout::totalMinimumSize() const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > > #18 0x00002b13f2315cf6 in QWidget::minimumSizeHint() const () from > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > > #19 0x0000000000447ccb in ?? () > #20 0x0000000000442628 in ?? () > #21 0x0000000000455ac3 in ?? () > #22 0x000000000045482f in ?? () > #23 0x00002b13f5422b35 in __libc_start_main () from /usr/lib64/libc.so.6 > #24 0x000000000042a8e9 in ?? () > (gdb) > > paulm@gcn12 11:34 ~$ ldd `which assistant` > linux-vdso.so.1 => (0x00007ffe87796000) > libQt5Help.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Help.so.5 > (0x00002b87f74aa000) > libQt5PrintSupport.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5PrintSupport.so.5 > (0x00002b87f7774000) > libQt5Widgets.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Widgets.so.5 > (0x00002b87f79ee000) > libQt5Gui.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Gui.so.5 > (0x00002b87f84b4000) > libQt5Network.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Network.so.5 > (0x00002b87f8dc2000) > libQt5Sql.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Sql.so.5 > (0x00002b87f9221000) > libQt5Core.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/libQt5Core.so.5 > (0x00002b87f947f000) > libGL.so.1 => > /hpc/eb/RedHatEnterpriseServer7/Mesa/12.0.2-intel-2016b/lib/libGL.so.1 > (0x00002b87f9cab000) > libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00002b87fa77b000) > libstdc++.so.6 => > /hpc/eb/RedHatEnterpriseServer7/GCCcore/5.4.0/lib64/libstdc++.so.6 > (0x00002b87f72d0000) > libm.so.6 => /usr/lib64/libm.so.6 (0x00002b87fa997000) > libgcc_s.so.1 => > /hpc/eb/RedHatEnterpriseServer7/GCCcore/5.4.0/lib64/libgcc_s.so.1 > (0x00002b87f7458000) > libc.so.6 => /usr/lib64/libc.so.6 (0x00002b87fac99000) > libdl.so.2 => /usr/lib64/libdl.so.2 (0x00002b87fb05a000) > libQt5CLucene.so.5 => > /hpc/eb/RedHatEnterpriseServer7/Qt5/5.8.0-intel-2016b/bin/../lib/../lib/libQt5CLucene.so.5 > (0x00002b87fb25e000) > libimf.so => > /hpc/eb/RedHatEnterpriseServer7/imkl/11.3.3.210-iimpi-2016b/lib/intel64/libimf.so > (0x00002b87fb5d2000) > libsvml.so => > /hpc/eb/RedHatEnterpriseServer7/imkl/11.3.3.210-iimpi-2016b/lib/intel64/libsvml.so > (0x00002b87fbad0000) > libirng.so => > /hpc/eb/RedHatEnterpriseServer7/imkl/11.3.3.210-iimpi-2016b/lib/intel64/libirng.so > (0x00002b87fc9dc000) > libintlc.so.5 => > /hpc/eb/RedHatEnterpriseServer7/imkl/11.3.3.210-iimpi-2016b/lib/intel64/libintlc.so.5 > (0x00002b87fcd4e000) > libpng16.so.16 => > /hpc/eb/RedHatEnterpriseServer7/libpng/1.6.24-intel-2016b/lib/libpng16.so.16 > (0x00002b87fcfb8000) > libz.so.1 => > /hpc/eb/RedHatEnterpriseServer7/zlib/1.2.8-intel-2016b/lib/libz.so.1 > (0x00002b87fd217000) > libicui18n.so.50 => /usr/lib64/libicui18n.so.50 (0x00002b87fd438000) > libicuuc.so.50 => /usr/lib64/libicuuc.so.50 (0x00002b87fd836000) > libicudata.so.50 => /usr/lib64/libicudata.so.50 (0x00002b87fdbaf000) > librt.so.1 => /usr/lib64/librt.so.1 (0x00002b87ff183000) > libpcre16.so.0 => /usr/lib64/libpcre16.so.0 (0x00002b87ff38b000) > libgthread-2.0.so.0 => > /hpc/eb/RedHatEnterpriseServer7/GLib/2.49.5-intel-2016b/lib/libgthread-2.0.so.0 > (0x00002b87ff5e3000) > libglib-2.0.so.0 => > /hpc/eb/RedHatEnterpriseServer7/GLib/2.49.5-intel-2016b/lib/libglib-2.0.so.0 > (0x00002b87ff7e5000) > /lib64/ld-linux-x86-64.so.2 (0x00002b87f7287000) > libnettle.so.6 => > /hpc/eb/RedHatEnterpriseServer7/nettle/3.2-intel-2016b/lib64/libnettle.so.6 > (0x00002b87ffb38000) > libglapi.so.0 => > /hpc/eb/RedHatEnterpriseServer7/Mesa/12.0.2-intel-2016b/lib/../lib/libglapi.so.0 > (0x00002b87ffd8c000) > libXext.so.6 => > /hpc/eb/RedHatEnterpriseServer7/X11/20160819-intel-2016b/lib/libXext.so.6 > (0x00002b87ffffd000) > > libX11.so.6 => > /hpc/eb/RedHatEnterpriseServer7/X11/20160819-intel-2016b/lib/libX11.so.6 > (0x00002b880021c000) > libxcb.so.1 => > /hpc/eb/RedHatEnterpriseServer7/X11/20160819-intel-2016b/lib/libxcb.so.1 > (0x00002b88005f3000) > libXau.so.6 => > /hpc/eb/RedHatEnterpriseServer7/X11/20160819-intel-2016b/lib/libXau.so.6 > (0x00002b8800816000) > libXdmcp.so.6 => > /hpc/eb/RedHatEnterpriseServer7/X11/20160819-intel-2016b/lib/libXdmcp.so.6 > (0x00002b8800a1a000) > libLLVMX86Disassembler.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMX86Disassembler.so > (0x00002b8800c23000) > libLLVMX86AsmParser.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMX86AsmParser.so > (0x00002b8800f8c000) > libLLVMX86CodeGen.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMX86CodeGen.so > (0x00002b880124b000) > libLLVMSelectionDAG.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMSelectionDAG.so > (0x00002b88017c5000) > libLLVMAsmPrinter.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMAsmPrinter.so > (0x00002b8801e0e000) > libLLVMCodeGen.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMCodeGen.so > (0x00002b8802111000) > libLLVMScalarOpts.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMScalarOpts.so > (0x00002b8802965000) > libLLVMInstCombine.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMInstCombine.so > (0x00002b8802ef1000) > libLLVMInstrumentation.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMInstrumentation.so > (0x00002b8803258000) > libLLVMProfileData.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMProfileData.so > (0x00002b880356c000) > libLLVMTransformUtils.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMTransformUtils.so > (0x00002b88037fb000) > libLLVMBitWriter.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMBitWriter.so > (0x00002b8803bd6000) > libLLVMX86Desc.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMX86Desc.so > (0x00002b8803e30000) > libLLVMMCDisassembler.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMMCDisassembler.so > (0x00002b8804247000) > libLLVMX86Info.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMX86Info.so > (0x00002b8804453000) > libLLVMX86AsmPrinter.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMX86AsmPrinter.so > (0x00002b8804655000) > libLLVMX86Utils.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMX86Utils.so > (0x00002b88048aa000) > libLLVMMCJIT.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMMCJIT.so > (0x00002b8804ab5000) > libLLVMExecutionEngine.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMExecutionEngine.so > (0x00002b8804cc9000) > libLLVMTarget.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMTarget.so > (0x00002b8804efb000) > libLLVMAnalysis.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMAnalysis.so > (0x00002b8805110000) > libLLVMRuntimeDyld.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMRuntimeDyld.so > (0x00002b8805728000) > libLLVMObject.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMObject.so > (0x00002b88059b0000) > libLLVMMCParser.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMMCParser.so > (0x00002b8805c6d000) > libLLVMBitReader.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMBitReader.so > (0x00002b8805ecc000) > libLLVMMC.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMMC.so > (0x00002b8806156000) > libLLVMCore.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMCore.so > (0x00002b880643d000) > libLLVMSupport.so => > /nfs/admin/hpc/sw/RedHatEnterpriseServer7/LLVM/3.8.1-intel-2016b/lib/libLLVMSupport.so > (0x00002b8806c81000) > libiomp5.so => > /hpc/eb/RedHatEnterpriseServer7/icc/2016.3.210-GCC-5.4.0-2.26/lib/intel64/libiomp5.so > (0x00002b8806ffd000) > libcilkrts.so.5 => > /hpc/eb/RedHatEnterpriseServer7/icc/2016.3.210-GCC-5.4.0-2.26/lib/intel64/libcilkrts.so.5 > (0x00002b8807341000) > libpcre.so.1 => > /hpc/eb/RedHatEnterpriseServer7/PCRE/8.39-intel-2016b/lib/libpcre.so.1 > (0x00002b880757c000) > libncurses.so.6 => > /hpc/eb/RedHatEnterpriseServer7/ncurses/6.0-intel-2016b/lib/libncurses.so.6 > (0x00002b88077d9000) > > I've been trying to figure out what is going on, but can't seem to get > anywhere. Google also doesn't offer any clues. Does this sound familiar > to anyone? Any tips on how to debug this? > > Regards, > Paul >
-- Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden Internet: a...@hpc2n.umu.se Phone: +46 90 7866134 Fax: +46 90-580 14 Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se
