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.
