Bruno, I guess the point is that cmake invokes /lib64/libstdc++.so.6 rather than /usr/local/lib64/libstdc++.so.6 Is it correct?
*Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale (DIMI) Universita` di Brescia, via Branze 43, 25123 Brescia Italy tel 030 3711239 fax 030 3711312 e-mail: [email protected] web-page: http://m4lab.unibs.it/faculty.html On Wed, Oct 2, 2019 at 2:51 PM Alberto Salvadori <[email protected]> wrote: > Thank you, Bruno. In fact, my aim was to use my system compiler. > Here is my .spack/linux/packages.yaml: > > packages: > > all: > > compiler: [gcc] > > providers: > > mpi: [openmpi] > > openmpi: > > version: [3.1.4] > > paths: > > [email protected]%[email protected]: /usr/local/ > > buildable: False > > perl: > > paths: > > [email protected]%[email protected]: /usr > > cmake: > > version: [3.15.3] > > paths: > > [email protected]%[email protected]: /usr/local/ > > hdf5: > > version: [1.8.12] > > paths: > > [email protected]%[email protected]: /usr > > variants: +hl+fortran > > netcdf: > > version: [7.2.0] > > paths: > > [email protected]%[email protected]: /usr > > netcdf-cxx: > > version: [4.2.8] > > paths: > > [email protected]%[email protected]: /usr > > dealii: > > variants: +optflags~python > > Shall I perhaps add something to the compiler flag (paths or so)? > Here is also my .spack/linux/compilers.yaml > > compilers: > > - compiler: > > environment: {} > > extra_rpaths: [] > > flags: {} > > modules: [] > > operating_system: centos7 > > paths: > > cc: /usr/bin/gcc > > cxx: /usr/bin/g++ > > f77: /usr/bin/gfortran > > fc: /usr/bin/gfortran > > spec: [email protected] > > target: x86_64 > > - compiler: > > environment: {} > > extra_rpaths: [] > > flags: {} > > modules: [] > > operating_system: centos7 > > paths: > > cc: /usr/local/bin/gcc > > cxx: /usr/local/bin/g++ > > f77: /usr/local/bin/gfortran > > fc: /usr/local/bin/gfortran > > spec: [email protected] > > target: x86_64 > > > *Alberto* > > > > *Alberto Salvadori* Dipartimento di Ingegneria Meccanica e Industriale > (DIMI) > Universita` di Brescia, via Branze 43, 25123 Brescia > Italy > tel 030 3711239 > fax 030 3711312 > > e-mail: > [email protected] > web-page: > http://m4lab.unibs.it/faculty.html > > > > On Wed, Oct 2, 2019 at 2:41 PM Bruno Turcksin <[email protected]> > wrote: > >> Alberto, >> >> On Wednesday, October 2, 2019 at 7:24:32 AM UTC-4, Alberto Salvadori >> wrote: >>> >>> >>> Thank you so much W and D, >>> As you pointed out there seems to be a mistake in the most recent >>> version of perl during installation. >>> I will propagate this to the proper communities. >>> >>> As Denis proposed, I went on simply tell Spack to use Perl from system: >>> >>> perl: >>> paths: >>> [email protected]%[email protected]: /usr >>> >>> but I bumped into another issue: >>> >>> [deal.ii@localhost spack]$ spack install dealii^[email protected] >>> >>> *==>* libsigsegv is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libsigsegv-2.11-brkulrpubdu66nzym2zt2j6c3h6nw463 >>> >>> *==>* m4 is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/m4-1.4.18-23npyrcdfzqehgp4s2mhka4nknjjkbzt >>> >>> *==>* [email protected] : externally installed in /usr >>> >>> *==>* [email protected] : already registered in DB >>> >>> *==>* autoconf is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/autoconf-2.69-2vk2foufmuyjm2gh47u6nouxezza3p6p >>> >>> *==>* automake is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/automake-1.16.1-z52jybnv7ass3otkgegjazvdbbughw2q >>> >>> *==>* libtool is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/libtool-2.4.6-mr3m4npcnryydzctugoebk2zuoav7zte >>> >>> *==>* adol-c is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/adol-c-develop-xioth2pegguh6rb6mzfzk7zhvb2kgeue >>> >>> *==>* pkgconf is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/pkgconf-1.6.1-qtpkfoaa5ae54s4icmqie5hbtz6murqx >>> >>> *==>* ncurses is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/ncurses-6.1-awd5putjsuzsddipc35vxiupdjicseao >>> >>> *==>* zlib is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/zlib-1.2.11-fa7l75havytsbgz77sh6yyzvqgmmm5dj >>> >>> *==>* openssl is already installed in >>> /home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/openssl-1.1.1c-ou63dp5nv43t2vudcv44rc753i7yecl2 >>> >>> *==>* *Installing* *cmake* >>> >>> *==>* Searching for binary cache of cmake >>> >>> *==>* Warning: No Spack mirrors are currently configured >>> >>> *==>* No binary for cmake found: installing from source >>> >>> *==>* Using cached archive: >>> /home/deal.ii/spack/var/spack/cache/cmake/cmake-3.9.4.tar.gz >>> >>> *==>* Staging archive: >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/cmake-3.9.4.tar.gz >>> >>> *==>* Created stage in >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4 >>> >>> *==>* Applied patch >>> /home/deal.ii/spack/var/spack/repos/builtin/packages/cmake/nag-response-files.patch >>> >>> *==>* Building cmake [Package] >>> >>> *==>* Executing phase: 'bootstrap' >>> >>> *==>* Error: ProcessError: Command exited with status 11: >>> >>> './bootstrap' >>> '--prefix=/home/deal.ii/spack/opt/spack/linux-centos7-ivybridge/gcc-9.2.0/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4' >>> '--parallel=12' '--no-system-libs' '--no-qt-gui' '--' >>> '-DCMAKE_USE_OPENSSL=True' >>> >>> >>> 1 error found in build log: >>> >>> 196 /home/deal.ii/spack/lib/spack/env/gcc/g++ -std=gnu++14 >>> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk >>> >>> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-sr >>> >>> c/Source >>> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Source/LexerParser >>> >>> -I/tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Utilities >>> cmAddCustomCommandCommand.o cmAd >>> >>> dCustomTargetCommand.o cmAddDefinitionsCommand.o >>> cmAddDependenciesCommand.o cmAddExecutableCommand.o cmAddLibraryCommand.o >>> cmAddSubDirectoryCommand.o cmAddTestCommand.o cmBreakCommand.o >>> cmBuildCommand.o cmCMakeMinimumRequired.o cmCMakePoli >>> >>> cyCommand.o cmCPackPropertiesGenerator.o cmCacheManager.o >>> cmCommand.o cmCommandArgumentParserHelper.o cmCommandArgumentsHelper.o >>> cmCommands.o cmCommonTargetGenerator.o cmComputeComponentGraph.o >>> cmComputeLinkDepends.o cmComputeLinkInformati >>> >>> on.o cmComputeTargetDepends.o cmConditionEvaluator.o >>> cmConfigureFileCommand.o cmContinueCommand.o cmCoreTryCompile.o >>> cmCreateTestSourceList.o cmCustomCommand.o cmCustomCommandGenerator.o >>> cmDefinePropertyCommand.o cmDefinitions.o cmDepends. >>> >>> o cmDependsC.o cmDisallowedCommand.o >>> cmDocumentationFormatter.o cmEnableLanguageCommand.o >>> cmEnableTestingCommand.o cmExecProgramCommand.o cmExecuteProcessCommand.o >>> cmExpandedCommandArgument.o cmExportBuildFileGenerator.o cmExportFileGenera >>> >>> tor.o cmExportInstallFileGenerator.o cmExportSet.o >>> cmExportSetMap.o cmExportTryCompileFileGenerator.o cmExprParserHelper.o >>> cmExternalMakefileProjectGenerator.o cmFileCommand.o cmFileTimeComparison.o >>> cmFindBase.o cmFindCommon.o cmFindFileCo >>> >>> mmand.o cmFindLibraryCommand.o cmFindPackageCommand.o >>> cmFindPathCommand.o cmFindProgramCommand.o cmForEachCommand.o >>> cmFunctionCommand.o cmGeneratedFileStream.o cmGeneratorExpression.o >>> cmGeneratorExpressionContext.o cmGeneratorExpressionDAG >>> >>> Checker.o cmGeneratorExpressionEvaluationFile.o >>> cmGeneratorExpressionEvaluator.o cmGeneratorExpressionLexer.o >>> cmGeneratorExpressionNode.o cmGeneratorExpressionParser.o >>> cmGeneratorTarget.o cmGetCMakePropertyCommand.o cmGetDirectoryPropertyC >>> >>> ommand.o cmGetFilenameComponentCommand.o >>> cmGetPropertyCommand.o cmGetSourceFilePropertyCommand.o >>> cmGetTargetPropertyCommand.o cmGetTestPropertyCommand.o >>> cmGlobalCommonGenerator.o cmGlobalGenerator.o >>> cmGlobalUnixMakefileGenerator3.o cmHexFi >>> >>> leConverter.o cmIfCommand.o cmIncludeCommand.o >>> cmIncludeDirectoryCommand.o cmIncludeRegularExpressionCommand.o >>> cmInstallCommand.o cmInstallCommandArguments.o >>> cmInstallDirectoryGenerator.o cmInstallExportGenerator.o >>> cmInstallFilesCommand.o >>> >>> cmInstallFilesGenerator.o cmInstallGenerator.o >>> cmInstallScriptGenerator.o cmInstallTargetGenerator.o >>> cmInstallTargetsCommand.o cmInstalledFile.o cmLinkDirectoriesCommand.o >>> cmLinkLineComputer.o cmListCommand.o cmListFileCache.o cmLocalCommo >>> >>> nGenerator.o cmLocalGenerator.o >>> cmLocalUnixMakefileGenerator3.o cmMSVC60LinkLineComputer.o cmMacroCommand.o >>> cmMakeDirectoryCommand.o cmMakefile.o cmMakefileExecutableTargetGenerator.o >>> cmMakefileLibraryTargetGenerator.o cmMakefileTargetGene >>> >>> rator.o cmMakefileUtilityTargetGenerator.o >>> cmMarkAsAdvancedCommand.o cmMathCommand.o cmMessageCommand.o cmMessenger.o >>> cmNewLineStyle.o cmOSXBundleGenerator.o cmOptionCommand.o >>> cmOrderDirectories.o cmOutputConverter.o cmParseArgumentsComman >>> >>> d.o cmPathLabel.o cmPolicies.o cmProcessOutput.o >>> cmProjectCommand.o cmProperty.o cmPropertyDefinition.o >>> cmPropertyDefinitionMap.o cmPropertyMap.o cmReturnCommand.o >>> cmRulePlaceholderExpander.o cmScriptGenerator.o cmSearchPath.o cmSeparateAr >>> >>> gumentsCommand.o cmSetCommand.o >>> cmSetDirectoryPropertiesCommand.o cmSetPropertyCommand.o >>> cmSetSourceFilesPropertiesCommand.o cmSetTargetPropertiesCommand.o >>> cmSetTestsPropertiesCommand.o cmSiteNameCommand.o cmSourceFile.o >>> cmSourceFileLocati >>> >>> on.o cmState.o cmStateDirectory.o cmStateSnapshot.o >>> cmStringCommand.o cmSubdirCommand.o cmSystemTools.o cmTarget.o >>> cmTargetLinkLibrariesCommand.o cmTargetPropertyComputer.o cmTest.o >>> cmTestGenerator.o cmTimestamp.o cmTryCompileCommand.o cmT >>> >>> ryRunCommand.o cmUnexpectedCommand.o cmUnsetCommand.o >>> cmVersion.o cmWhileCommand.o cmWorkingDirectory.o cmake.o cmakemain.o >>> cmcmd.o cmCommandArgumentLexer.o cmCommandArgumentParser.o cmExprLexer.o >>> cmExprParser.o cmListFileLexer.o Directory >>> >>> .o EncodingCXX.o FStream.o Glob.o RegularExpression.o >>> SystemTools.o EncodingC.o ProcessUNIX.o String.o System.o Terminal.o -o >>> cmake >>> >>> 197 >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: >>> /lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfb >>> >>> q4/spack-src/Bootstrap.cmk/cmake) >>> >>> 198 >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: >>> /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4 >>> >>> /spack-src/Bootstrap.cmk/cmake) >>> >>> 199 >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: >>> /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfb >>> >>> q4/spack-src/Bootstrap.cmk/cmake) >>> >>> 200 >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-src/Bootstrap.cmk/cmake: >>> /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfb >>> >>> q4/spack-src/Bootstrap.cmk/cmake) >>> >>> 201 --------------------------------------------- >>> >>> >> 202 Error when bootstrapping CMake: >>> >>> 203 Problem while running initial CMake >>> >>> 204 --------------------------------------------- >>> >>> >>> See build log for details: >>> >>> >>> /tmp/deal.ii/spack-stage/cmake-3.9.4-jy2ih5ctlebz57xqk7kvgzv22tabfbq4/spack-build-out.txt >>> >>> >>> >>> >>> Is it perhaps due to a conflict between cmake and the gcc compiler >>> versions? Can you perhaps address me how to sort this out? >>> >> It looks to me that spack is trying to compile cmake with gcc 9.2 but >> somehow it is using the libstdc++ library from your system. You can try to >> load gcc 9.2 or you could just tell spack to use your system compiler. >> >> Best, >> >> Bruno >> >> >> -- >> The deal.II project is located at http://www.dealii.org/ >> For mailing list/forum options, see >> https://groups.google.com/d/forum/dealii?hl=en >> --- >> You received this message because you are subscribed to the Google Groups >> "deal.II User Group" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/dealii/81fc18b4-00b7-4d91-9b4d-166fd2a013dd%40googlegroups.com >> <https://groups.google.com/d/msgid/dealii/81fc18b4-00b7-4d91-9b4d-166fd2a013dd%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- Informativa sulla Privacy: http://www.unibs.it/node/8155 <http://www.unibs.it/node/8155> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/CABcATpcP69tAE35mYpPL%3DM3a-aYupM%3DMKdHe-2dmCnvtmBD3DA%40mail.gmail.com.
