Great, happy to hear you sorted this out by tweaking compilers.yaml
settings.
On Friday, October 4, 2019 at 12:38:20 PM UTC+2, Alberto Salvadori wrote:
>
> Hi Denis
>
> thanks for your note. I figured out that by adding the path in the
> compilers.yaml file, in this way
>
> - compiler:
>
> environment:
>
> append-path:
>
> LD_LIBRARY_PATH: /usr/local/lib64
>
> 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: gcc@9.2.0
>
> target: x86_64
>
> sorts out the issue.
>
>
> Il giorno mercoledì 2 ottobre 2019 19:26:06 UTC+2, Denis Davydov ha
> scritto:
>>
>> Hi Alberto,
>>
>> Looks like the issue is known to Spack community:
>> https://github.com/spack/spack/issues/11224 where there is also a
>> possible source of the problem you can try as a fix (un-do on-line PR).
>>
>> Regards,
>> Denis.
>>
>> On Wednesday, October 2, 2019 at 3:14:46 PM UTC+2, Bruno Turcksin wrote:
>>>
>>> Alberto,
>>>
>>> So what happens is that spack is using gcc 9.2 like you want but it
>>> usess the libstdc++ from gcc 4.8.5 I usually spack to install a new
>>> compiler and my compilers.yaml looks like your *but* I have the path
>>> to the correct libstdc++ in my LD_LIBRARY_PATH when I load the module.
>>> So I guess you need to add that path somewhere in your compilers.yaml
>>>
>>> Best,
>>>
>>> Bruno
>>>
>>> Le mer. 2 oct. 2019 à 08:51, Alberto Salvadori
>>> <alberto....@unibs.it> a écrit :
>>> >
>>> > 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:
>>> >
>>> > openmpi@3.1.4%gcc@9.2.0: /usr/local/
>>> >
>>> > buildable: False
>>> >
>>> > perl:
>>> >
>>> > paths:
>>> >
>>> > perl@5.16.3%gcc@9.2.0: /usr
>>> >
>>> > cmake:
>>> >
>>> > version: [3.15.3]
>>> >
>>> > paths:
>>> >
>>> > cmake@3.15.3%gcc@9.2.0: /usr/local/
>>> >
>>> > hdf5:
>>> >
>>> > version: [1.8.12]
>>> >
>>> > paths:
>>> >
>>> > hdf5@1.8.12%gcc@9.2.0: /usr
>>> >
>>> > variants: +hl+fortran
>>> >
>>> > netcdf:
>>> >
>>> > version: [7.2.0]
>>> >
>>> > paths:
>>> >
>>> > netcdf@7.2.0%gcc@9.2.0: /usr
>>> >
>>> > netcdf-cxx:
>>> >
>>> > version: [4.2.8]
>>> >
>>> > paths:
>>> >
>>> > netcdf-cxx@4.2.8%gcc@9.2.0: /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: gcc@4.8.5
>>> >
>>> > 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: gcc@9.2.0
>>> >
>>> > 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:
>>> > alberto....@unibs.it
>>> > web-page:
>>> > http://m4lab.unibs.it/faculty.html
>>> >
>>> >
>>> >
>>> > On Wed, Oct 2, 2019 at 2:41 PM Bruno Turcksin <bruno....@gmail.com>
>>> 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:
>>> >>> perl@5.26.2%gcc@9.2.0: /usr
>>> >>>
>>> >>> but I bumped into another issue:
>>> >>>
>>> >>> [deal.ii@localhost spack]$ spack install dealii^cmake@3.9.4
>>> >>>
>>> >>> ==> 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
>>>
>>>
>>> >>>
>>> >>> ==> perl@5.16.3 : externally installed in /usr
>>> >>>
>>> >>> ==> perl@5.16.3 : 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
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>>>
>>>
>>> >
>>> >
>>> >
>>> > Informativa sulla Privacy: 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
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>>>
>>>
>>>
>>
--
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