Install VTK in Savio using Spack

#1

Currently I got most of the package for LEM installed in Savio, except VTK.

But I can’t install VTK using spack, with this error message.

I’m not sure whether this is because there are something else should be installed before VTK? So I tried to install mesa with spack as well, but got error at icu4c part and cannot finish the installation, with following error message.

Could you tell me what’s the problem here and how to get VTK installed? Thanks

#2

Try the following:

  • vim $HOME/.spack/linux/packages.yaml

Then add the following, please use the path where the system opengl is installed.

packages:
 opengl:
   paths:
     opengl@4.5.0: /opt/opengl
   buildable: False
  • Once done run spack install opengl this should say using system Opengl, registering in db.

  • Now run spack install vtk

#3

If you don’t have opengl, you might have to install mesa manually

# Get and extract mesa
wget https://mesa.freedesktop.org/archive/mesa-17.0.0.tar.gz
tar xf ./mesa-17.0.0.tar.gz

# configure and install mesa
mkdir $HOME/mesa
cd mesa-17.0.0
./configure --prefix=$HOME/mesa
make -j4
make install
#4

I tried to install mesa using the command as you said, and an error occur when configuring.

Perhaps this means llvm should be installed? So I try to install llvm with spack, and error happen in installing cmake part.

==> Installing cmake
==> Fetching https://cmake.org/files/v3.12/cmake-3.12.1.tar.gz
################################################################################################ 100.0%
==> Staging archive: /global/home/users/zhenxiang_su/spack/var/spack/stage/cmake-3.12.1-mrgfhmti4pwdsfy           jaozzuc5gjrizrjj7/cmake-3.12.1.tar.gz
==> Created stage in /global/home/users/zhenxiang_su/spack/var/spack/stage/cmake-3.12.1-mrgfhmti4pwdsfy           jaozzuc5gjrizrjj7
==> Applied patch nag-response-files.patch
==> Building cmake [Package]
==> Executing phase: 'bootstrap'
==> Error: ProcessError: Command exited with status 11:
    './bootstrap' '--prefix=/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.           0/cmake-3.12.1-mrgfhmti4pwdsfyjaozzuc5gjrizrjj7' '--parallel=20' '--no-system-libs' '--no-qt-gui' '--'            '-DCMAKE_USE_OPENSSL=ON'

1 error found in build log:
     219    /global/home/users/zhenxiang_su/spack/lib/spack/env/gcc/gcc           -I/tmp/zhenxiang_su/
            spack-stage/spack-stage-81lwytdj/cmake-3.12.1/Bootstrap.cmk   -I/tmp/zhenxiang_su/spack-st
            age/spack-stage-81lwytdj/cmake-3.12.1/Source   -I/tmp/zhenxiang_su/spack-stage/spack-stage
            -81lwytdj/cmake-3.12.1/Source/LexerParser   -I/tmp/zhenxiang_su/spack-stage/spack-stage-81
            lwytdj/cmake-3.12.1/Utilities  -DCMAKE_BOOTSTRAP -D_GNU_SOURCE -I/tmp/zhenxiang_su/spack-s
            tage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/include -I/tmp/zhenxiang_su/spack
            -stage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/src/unix -I/tmp/zhenxiang_su/sp
            ack-stage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/src -c /tmp/zhenxiang_su/spa
            ck-stage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/src/unix/stream.c -o uv-src-u
            nix-stream.c.o
     220    /global/home/users/zhenxiang_su/spack/lib/spack/env/gcc/gcc           -I/tmp/zhenxiang_su/
            spack-stage/spack-stage-81lwytdj/cmake-3.12.1/Bootstrap.cmk   -I/tmp/zhenxiang_su/spack-st
            age/spack-stage-81lwytdj/cmake-3.12.1/Source   -I/tmp/zhenxiang_su/spack-stage/spack-stage
            -81lwytdj/cmake-3.12.1/Source/LexerParser   -I/tmp/zhenxiang_su/spack-stage/spack-stage-81
            lwytdj/cmake-3.12.1/Utilities  -DCMAKE_BOOTSTRAP -D_GNU_SOURCE -I/tmp/zhenxiang_su/spack-s
            tage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/include -I/tmp/zhenxiang_su/spack
            -stage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/src/unix -I/tmp/zhenxiang_su/sp
            ack-stage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/src -c /tmp/zhenxiang_su/spa
            ck-stage/spack-stage-81lwytdj/cmake-3.12.1/Utilities/cmlibuv/src/unix/timer.c -o uv-src-un
            ix-timer.c.o
     221    /global/home/users/zhenxiang_su/spack/lib/spack/env/gcc/g++   -std=gnu++11      -I/tmp/zhe
            nxiang_su/spack-stage/spack-stage-81lwytdj/cmake-3.12.1/Bootstrap.cmk   -I/tmp/zhenxiang_s
            u/spack-stage/spack-stage-81lwytdj/cmake-3.12.1/Source   -I/tmp/zhenxiang_su/spack-stage/s
            pack-stage-81lwytdj/cmake-3.12.1/Source/LexerParser   -I/tmp/zhenxiang_su/spack-stage/spac
            k-stage-81lwytdj/cmake-3.12.1/Utilities  cmAddCustomCommandCommand.o cmAddCustomTargetComm
            and.o cmAddDefinitionsCommand.o cmAddDependenciesCommand.o cmAddExecutableCommand.o cmAddL
            ibraryCommand.o cmAddSubDirectoryCommand.o cmAddTestCommand.o cmBreakCommand.o cmBuildComm
            and.o cmCMakeMinimumRequired.o cmCMakePolicyCommand.o cmCPackPropertiesGenerator.o cmCache
            Manager.o cmCommand.o cmCommandArgumentParserHelper.o cmCommandArgumentsHelper.o cmCommand
            s.o cmCommonTargetGenerator.o cmComputeComponentGraph.o cmComputeLinkDepends.o cmComputeLi
            nkInformation.o cmComputeTargetDepends.o cmConditionEvaluator.o cmConfigureFileCommand.o c
            mContinueCommand.o cmCoreTryCompile.o cmCreateTestSourceList.o cmCustomCommand.o cmCustomC
            ommandGenerator.o cmDefinePropertyCommand.o cmDefinitions.o cmDepends.o cmDependsC.o cmDis
            allowedCommand.o cmDocumentationFormatter.o cmEnableLanguageCommand.o cmEnableTestingComma
            nd.o cmExecProgramCommand.o cmExecuteProcessCommand.o cmExpandedCommandArgument.o cmExport
            BuildFileGenerator.o cmExportFileGenerator.o cmExportInstallFileGenerator.o cmExportSet.o
            cmExportSetMap.o cmExportTryCompileFileGenerator.o cmExprParserHelper.o cmExternalMakefile
            ProjectGenerator.o cmFileCommand.o cmFileTimeComparison.o cmFindBase.o cmFindCommon.o cmFi
            ndFileCommand.o cmFindLibraryCommand.o cmFindPackageCommand.o cmFindPathCommand.o cmFindPr
            ogramCommand.o cmForEachCommand.o cmFunctionCommand.o cmFSPermissions.o cmGeneratedFileStr
            eam.o cmGeneratorExpression.o cmGeneratorExpressionContext.o cmGeneratorExpressionDAGCheck
            er.o cmGeneratorExpressionEvaluationFile.o cmGeneratorExpressionEvaluator.o cmGeneratorExp
            ressionLexer.o cmGeneratorExpressionNode.o cmGeneratorExpressionParser.o cmGeneratorTarget
            .o cmGetCMakePropertyCommand.o cmGetDirectoryPropertyCommand.o cmGetFilenameComponentComma
            nd.o cmGetPropertyCommand.o cmGetSourceFilePropertyCommand.o cmGetTargetPropertyCommand.o
            cmGetTestPropertyCommand.o cmGlobalCommonGenerator.o cmGlobalGenerator.o cmGlobalUnixMakef
            ileGenerator3.o cmGlobVerificationManager.o cmHexFileConverter.o cmIfCommand.o cmIncludeCo
            mmand.o cmIncludeGuardCommand.o cmIncludeDirectoryCommand.o cmIncludeRegularExpressionComm
            and.o cmInstallCommand.o cmInstallCommandArguments.o cmInstallDirectoryGenerator.o cmInsta
            llExportGenerator.o cmInstallFilesCommand.o cmInstallFilesGenerator.o cmInstallGenerator.o
             cmInstallScriptGenerator.o cmInstallTargetGenerator.o cmInstallTargetsCommand.o cmInstall
            edFile.o cmLinkDirectoriesCommand.o cmLinkLineComputer.o cmListCommand.o cmListFileCache.o
             cmLocalCommonGenerator.o cmLocalGenerator.o cmLocalUnixMakefileGenerator3.o cmMSVC60LinkL
            ineComputer.o cmMacroCommand.o cmMakeDirectoryCommand.o cmMakefile.o cmMakefileExecutableT
            argetGenerator.o cmMakefileLibraryTargetGenerator.o cmMakefileTargetGenerator.o cmMakefile
            UtilityTargetGenerator.o cmMarkAsAdvancedCommand.o cmMathCommand.o cmMessageCommand.o cmMe
            ssenger.o cmNewLineStyle.o cmOSXBundleGenerator.o cmOptionCommand.o cmOrderDirectories.o c
            mOutputConverter.o cmParseArgumentsCommand.o cmPathLabel.o cmPolicies.o cmProcessOutput.o
            cmProjectCommand.o cmProperty.o cmPropertyDefinition.o cmPropertyDefinitionMap.o cmPropert
            yMap.o cmReturnCommand.o cmRulePlaceholderExpander.o cmScriptGenerator.o cmSearchPath.o cm
            SeparateArgumentsCommand.o cmSetCommand.o cmSetDirectoryPropertiesCommand.o cmSetPropertyC
            ommand.o cmSetSourceFilesPropertiesCommand.o cmSetTargetPropertiesCommand.o cmSetTestsProp
            ertiesCommand.o cmSiteNameCommand.o cmSourceFile.o cmSourceFileLocation.o cmState.o cmStat
            eDirectory.o cmStateSnapshot.o cmStringReplaceHelper.o cmStringCommand.o cmSubdirCommand.o
             cmSystemTools.o cmTarget.o cmTargetCompileDefinitionsCommand.o cmTargetCompileFeaturesCom
            mand.o cmTargetCompileOptionsCommand.o cmTargetIncludeDirectoriesCommand.o cmTargetLinkLib
            rariesCommand.o cmTargetPropCommandBase.o cmTargetPropertyComputer.o cmTargetSourcesComman
            d.o cmTest.o cmTestGenerator.o cmTimestamp.o cmTryCompileCommand.o cmTryRunCommand.o cmUne
            xpectedCommand.o cmUnsetCommand.o cmUVHandlePtr.o cmVersion.o cmWhileCommand.o cmWorkingDi
            rectory.o cmake.o cmakemain.o cmcmd.o cmCommandArgumentLexer.o cmCommandArgumentParser.o c
            mExprLexer.o cmExprParser.o cmListFileLexer.o Directory.o EncodingCXX.o FStream.o Glob.o R
            egularExpression.o SystemTools.o EncodingC.o ProcessUNIX.o String.o System.o Terminal.o uv
            -src-uv-common.c.o uv-src-unix-cmake-bootstrap.c.o uv-src-unix-core.c.o uv-src-unix-fs.c.o
             uv-src-unix-loop.c.o uv-src-unix-loop-watcher.c.o uv-src-unix-no-fsevents.c.o uv-src-unix
            -pipe.c.o uv-src-unix-poll.c.o uv-src-unix-posix-hrtime.c.o uv-src-unix-posix-poll.c.o uv-
            src-unix-process.c.o uv-src-unix-signal.c.o uv-src-unix-stream.c.o uv-src-unix-timer.c.o
            -ldl -lrt -o cmake
     222    /tmp/zhenxiang_su/spack-stage/spack-stage-81lwytdj/cmake-3.12.1/Bootstrap.cmk/cmake: /lib6
            4/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /tmp/zhenxiang_su/spack-
            stage/spack-stage-81lwytdj/cmake-3.12.1/Bootstrap.cmk/cmake)
     223    /tmp/zhenxiang_su/spack-stage/spack-stage-81lwytdj/cmake-3.12.1/Bootstrap.cmk/cmake: /lib6
            4/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /tmp/zhenxiang_su/spack-
            stage/spack-stage-81lwytdj/cmake-3.12.1/Bootstrap.cmk/cmake)
     224    ---------------------------------------------
  >> 225    Error when bootstrapping CMake:
     226    Problem while running initial CMake
     227    ---------------------------------------------

See build log for details:
  /global/home/users/zhenxiang_su/spack/var/spack/stage/cmake-3.12.1-mrgfhmti4pwdsfyjaozzuc5gjrizrjj7/c           make-3.12.1/spack-build.out

Then I try to install llvm manually, but it seems that it cannot be configured and made.

#5

I don’t know, I didn’t need llvm, I just had gcc and cmake loaded in the Cambridge HPC cluster.

#6

I solved above problem by using

./configure --prefix=$HOME/mesa --with-gallium-drivers=""

to disable Gallium, and so got mesa and opengl installed. But then had another problem when installing vtk.

If I used gcc 6.3.0 as compiler, do spack install vtk%gcc@6.3.0, error happens when installing cmake, as below,

[zhenxiang_su@ln003 ~]$ spack install vtk%gcc@6.3.0
==> pkgconf is already installed in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/pkgconf-1.4.2-ltcxdnqhvbuuw2w3gbivw5nwgkkwmmkd
==> ncurses is already installed in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/ncurses-6.1-s7q7pbjzysccmhxvgjcjhxubrto722ky
==> zlib is already installed in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/zlib-1.2.11-xlu5yhwc73h5zfhknod7iopr7veg6cmv
==> openssl is already installed in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/openssl-1.0.2o-dqnf56z6xmoptixbukmcc23bbq7i22bs
==> Installing cmake
==> Using cached archive: /global/home/users/zhenxiang_su/spack/var/spack/cache/cmake/cmake-3.12.1.tar.gz
==> Staging archive: /global/home/users/zhenxiang_su/spack/var/spack/stage/cmake-3.12.1-mrgfhmti4pwdsfyjaozzuc5gjrizrjj7/cmake-3.12.1.tar.gz
==> Created stage in /global/home/users/zhenxiang_su/spack/var/spack/stage/cmake-3.12.1-mrgfhmti4pwdsfyjaozzuc5gjrizrjj7
==> Applied patch nag-response-files.patch
==> Building cmake [Package]
==> Executing phase: 'bootstrap'
==> Error: ProcessError: Command exited with status 11:
    './bootstrap' '--prefix=/global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-6.3.0/cmake-3.12.1-mrgfhmti4pwdsfyjaozzuc5gjrizrjj7' '--parallel=20' '--no-system-libs' '--no-qt-gui' '--' '-DCMAKE_USE_OPENSSL=ON'

1 error found in build log:
     219    /global/home/users/zhenxiang_su/spack/lib/spack/env/gcc/gcc           -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3
            .12.1/Bootstrap.cmk   -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Source   -I/tmp/zhenxiang_su/spack-stage/s
            pack-stage-lhh5xcjg/cmake-3.12.1/Source/LexerParser   -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities
             -DCMAKE_BOOTSTRAP -D_GNU_SOURCE -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv/include -I/tm
            p/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv/src/unix -I/tmp/zhenxiang_su/spack-stage/spack-stag
            e-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv/src -c /tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv
            /src/unix/stream.c -o uv-src-unix-stream.c.o
     220    /global/home/users/zhenxiang_su/spack/lib/spack/env/gcc/gcc           -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3
            .12.1/Bootstrap.cmk   -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Source   -I/tmp/zhenxiang_su/spack-stage/s
            pack-stage-lhh5xcjg/cmake-3.12.1/Source/LexerParser   -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities
             -DCMAKE_BOOTSTRAP -D_GNU_SOURCE -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv/include -I/tm
            p/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv/src/unix -I/tmp/zhenxiang_su/spack-stage/spack-stag
            e-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv/src -c /tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Utilities/cmlibuv
            /src/unix/timer.c -o uv-src-unix-timer.c.o
     221    /global/home/users/zhenxiang_su/spack/lib/spack/env/gcc/g++   -std=gnu++11      -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xc
            jg/cmake-3.12.1/Bootstrap.cmk   -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Source   -I/tmp/zhenxiang_su/spa
            ck-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Source/LexerParser   -I/tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/
            Utilities  cmAddCustomCommandCommand.o cmAddCustomTargetCommand.o cmAddDefinitionsCommand.o cmAddDependenciesCommand.o cmAddExecut
            ableCommand.o cmAddLibraryCommand.o cmAddSubDirectoryCommand.o cmAddTestCommand.o cmBreakCommand.o cmBuildCommand.o cmCMakeMinimum
            Required.o cmCMakePolicyCommand.o cmCPackPropertiesGenerator.o cmCacheManager.o cmCommand.o cmCommandArgumentParserHelper.o cmComm
            andArgumentsHelper.o cmCommands.o cmCommonTargetGenerator.o cmComputeComponentGraph.o cmComputeLinkDepends.o cmComputeLinkInformat
            ion.o cmComputeTargetDepends.o cmConditionEvaluator.o cmConfigureFileCommand.o cmContinueCommand.o cmCoreTryCompile.o cmCreateTest
            SourceList.o cmCustomCommand.o cmCustomCommandGenerator.o cmDefinePropertyCommand.o cmDefinitions.o cmDepends.o cmDependsC.o cmDis
            allowedCommand.o cmDocumentationFormatter.o cmEnableLanguageCommand.o cmEnableTestingCommand.o cmExecProgramCommand.o cmExecutePro
            cessCommand.o cmExpandedCommandArgument.o cmExportBuildFileGenerator.o cmExportFileGenerator.o cmExportInstallFileGenerator.o cmEx
            portSet.o cmExportSetMap.o cmExportTryCompileFileGenerator.o cmExprParserHelper.o cmExternalMakefileProjectGenerator.o cmFileComma
            nd.o cmFileTimeComparison.o cmFindBase.o cmFindCommon.o cmFindFileCommand.o cmFindLibraryCommand.o cmFindPackageCommand.o cmFindPa
            thCommand.o cmFindProgramCommand.o cmForEachCommand.o cmFunctionCommand.o cmFSPermissions.o cmGeneratedFileStream.o cmGeneratorExp
            ression.o cmGeneratorExpressionContext.o cmGeneratorExpressionDAGChecker.o cmGeneratorExpressionEvaluationFile.o cmGeneratorExpres
            sionEvaluator.o cmGeneratorExpressionLexer.o cmGeneratorExpressionNode.o cmGeneratorExpressionParser.o cmGeneratorTarget.o cmGetCM
            akePropertyCommand.o cmGetDirectoryPropertyCommand.o cmGetFilenameComponentCommand.o cmGetPropertyCommand.o cmGetSourceFilePropert
            yCommand.o cmGetTargetPropertyCommand.o cmGetTestPropertyCommand.o cmGlobalCommonGenerator.o cmGlobalGenerator.o cmGlobalUnixMakef
            ileGenerator3.o cmGlobVerificationManager.o cmHexFileConverter.o cmIfCommand.o cmIncludeCommand.o cmIncludeGuardCommand.o cmInclud
            eDirectoryCommand.o cmIncludeRegularExpressionCommand.o cmInstallCommand.o cmInstallCommandArguments.o cmInstallDirectoryGenerator
            .o cmInstallExportGenerator.o cmInstallFilesCommand.o cmInstallFilesGenerator.o cmInstallGenerator.o cmInstallScriptGenerator.o cm
            InstallTargetGenerator.o cmInstallTargetsCommand.o cmInstalledFile.o cmLinkDirectoriesCommand.o cmLinkLineComputer.o cmListCommand
            .o cmListFileCache.o cmLocalCommonGenerator.o cmLocalGenerator.o cmLocalUnixMakefileGenerator3.o cmMSVC60LinkLineComputer.o cmMacr
            oCommand.o cmMakeDirectoryCommand.o cmMakefile.o cmMakefileExecutableTargetGenerator.o cmMakefileLibraryTargetGenerator.o cmMakefi
            leTargetGenerator.o cmMakefileUtilityTargetGenerator.o cmMarkAsAdvancedCommand.o cmMathCommand.o cmMessageCommand.o cmMessenger.o
            cmNewLineStyle.o cmOSXBundleGenerator.o cmOptionCommand.o cmOrderDirectories.o cmOutputConverter.o cmParseArgumentsCommand.o cmPat
            hLabel.o cmPolicies.o cmProcessOutput.o cmProjectCommand.o cmProperty.o cmPropertyDefinition.o cmPropertyDefinitionMap.o cmPropert
            yMap.o cmReturnCommand.o cmRulePlaceholderExpander.o cmScriptGenerator.o cmSearchPath.o cmSeparateArgumentsCommand.o cmSetCommand.
            o cmSetDirectoryPropertiesCommand.o cmSetPropertyCommand.o cmSetSourceFilesPropertiesCommand.o cmSetTargetPropertiesCommand.o cmSe
            tTestsPropertiesCommand.o cmSiteNameCommand.o cmSourceFile.o cmSourceFileLocation.o cmState.o cmStateDirectory.o cmStateSnapshot.o
             cmStringReplaceHelper.o cmStringCommand.o cmSubdirCommand.o cmSystemTools.o cmTarget.o cmTargetCompileDefinitionsCommand.o cmTarg
            etCompileFeaturesCommand.o cmTargetCompileOptionsCommand.o cmTargetIncludeDirectoriesCommand.o cmTargetLinkLibrariesCommand.o cmTa
            rgetPropCommandBase.o cmTargetPropertyComputer.o cmTargetSourcesCommand.o cmTest.o cmTestGenerator.o cmTimestamp.o cmTryCompileCom
            mand.o cmTryRunCommand.o cmUnexpectedCommand.o cmUnsetCommand.o cmUVHandlePtr.o cmVersion.o cmWhileCommand.o cmWorkingDirectory.o
            cmake.o cmakemain.o cmcmd.o cmCommandArgumentLexer.o cmCommandArgumentParser.o cmExprLexer.o cmExprParser.o cmListFileLexer.o Dire
            ctory.o EncodingCXX.o FStream.o Glob.o RegularExpression.o SystemTools.o EncodingC.o ProcessUNIX.o String.o System.o Terminal.o uv
            -src-uv-common.c.o uv-src-unix-cmake-bootstrap.c.o uv-src-unix-core.c.o uv-src-unix-fs.c.o uv-src-unix-loop.c.o uv-src-unix-loop-w
            atcher.c.o uv-src-unix-no-fsevents.c.o uv-src-unix-pipe.c.o uv-src-unix-poll.c.o uv-src-unix-posix-hrtime.c.o uv-src-unix-posix-po
            ll.c.o uv-src-unix-process.c.o uv-src-unix-signal.c.o uv-src-unix-stream.c.o uv-src-unix-timer.c.o  -ldl -lrt -o cmake
     222    /tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.2
            0' not found (required by /tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Bootstrap.cmk/cmake)
     223    /tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Bootstrap.cmk/cmake: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.2
            1' not found (required by /tmp/zhenxiang_su/spack-stage/spack-stage-lhh5xcjg/cmake-3.12.1/Bootstrap.cmk/cmake)
     224    ---------------------------------------------
  >> 225    Error when bootstrapping CMake:
     226    Problem while running initial CMake
     227    ---------------------------------------------

See build log for details:
  /global/home/users/zhenxiang_su/spack/var/spack/stage/cmake-3.12.1-mrgfhmti4pwdsfyjaozzuc5gjrizrjj7/cmake-3.12.1/spack-build.out

Then I used gcc 4.8.5 as compiler, spack install vtk%gcc@4.8.5, and error happens when installing perl,

==> Installing perl
==> Using cached archive: /global/home/users/zhenxiang_su/spack/var/spack/cache/perl/perl-5.26.2.tar.gz
==> Using cached archive: /global/home/users/zhenxiang_su/spack/var/spack/cache/perl/cpanm-5.26.2.tar.gz
==> Staging archive: /global/home/users/zhenxiang_su/spack/var/spack/stage/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/perl-5.26.2.tar.gz
==> Created stage in /global/home/users/zhenxiang_su/spack/var/spack/stage/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij
==> Staging archive: /global/home/users/zhenxiang_su/spack/var/spack/stage/resource-cpanm-ka6syh2hjjqi345yvu6fq5johc7i57ij/App-cpanminus-1.7042.tar.gz
==> Created stage in /global/home/users/zhenxiang_su/spack/var/spack/stage/resource-cpanm-ka6syh2hjjqi345yvu6fq5johc7i57ij
==> Moving resource stage
        source : /global/home/users/zhenxiang_su/spack/var/spack/stage/resource-cpanm-ka6syh2hjjqi345yvu6fq5johc7i57ij/App-cpanminus-1.7042/
        destination : /global/home/users/zhenxiang_su/spack/var/spack/stage/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/perl-5.26.2/cpanm/cpanm
==> Using cached archive: /global/home/users/zhenxiang_su/spack/var/spack/cache/perl/perl-5.26.1-guard_old_libcrypt_fix.patch
==> Applied patch https://src.fedoraproject.org/rpms/perl/raw/004cea3a67df42e92ffdf4e9ac36d47a3c6a05a4/f/perl-5.26.1-guard_old_libcrypt_fix.patch
==> Building perl [Package]
==> Executing phase: 'configure'
==> Executing phase: 'build'
==> Executing phase: 'install'
==> Warning: Patch file did not exist: /global/home/users/zhenxiang_su/spack/var/spack/stage/spack-stage-it66j8ss/perl-5.26.1-guard_old_libcrypt_fix.patch
==> Warning: Module file already exists : skipping creation
file : /global/home/users/zhenxiang_su/spack/share/spack/modules/linux-rhel7-x86_64/perl-5.26.2-gcc-4.8.5-ka6syh2
spec : perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-rhel7-x86_64  ^gdbm@1.14.1%gcc@4.8.5 arch=linux-rhel7-x86_64  ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-rhel7-x86_64  ^pkgconf@1.4.2%gcc@4.8.5 arch=linux-rhel7-x86_64  ^readline@7.0%gcc@4.8.5 arch=linux-rhel7-x86_64
==> Warning: Module file already exists : skipping creation
file : /global/home/users/zhenxiang_su/spack/share/spack/dotkit/linux-rhel7-x86_64/perl-5.26.2-gcc-4.8.5-ka6syh2.dk
spec : perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-rhel7-x86_64  ^gdbm@1.14.1%gcc@4.8.5 arch=linux-rhel7-x86_64  ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-rhel7-x86_64  ^pkgconf@1.4.2%gcc@4.8.5 arch=linux-rhel7-x86_64  ^readline@7.0%gcc@4.8.5 arch=linux-rhel7-x86_64
==> Warning: Patched overlong shebang in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/bin/encguess
==> Warning: Patched overlong shebang in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/bin/pod2text
==> Warning: Patched overlong shebang in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/bin/perlthanks
==> Warning: Patched overlong shebang in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/bin/h2ph
==> Warning: Patched overlong shebang in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/bin/prove
==> Warning: Patched overlong shebang in /global/home/users/zhenxiang_su/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/bin/podchecker
==> Error: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe3 in position 2982: ordinal not in range(128)

/global/home/users/zhenxiang_su/spack/lib/spack/spack/package.py:1505, in build_process:
       1502                    echo = logger.echo
       1503                    self.log()
       1504
  >>   1505                # Run post install hooks before build stage is removed.
       1506                spack.hooks.post_install(self.spec)
       1507
       1508            # Stop timer.

See build log for details:
  /global/home/users/zhenxiang_su/spack/var/spack/stage/perl-5.26.2-ka6syh2hjjqi345yvu6fq5johc7i57ij/perl-5.26.2/spack-build.out

Then I tried to load perl directly from savio,

But when I ran spack install vtk%gcc@4.8.5, it still install perl and I got the same error as above. How can I solve this? Any way that I can skip installing perl? Can I do this? since it was already loaded from Savio.

#7

Can we try installing a different GCC? Maybe GCC 7 or 8?

#8

It seems that the latest version of GCC available in Savio is 6.3.0. If I tried to install it with spack, it will still install perl and the same error happens as above. (Error: UnicodeDecodeError: 'ascii' codec can't decode byte 0xe3 in position 2982: ordinal not in range(128))

#9

How can I check where opengl was installed?

#10

If I load perl from Savio, can I use it as external package of spack? so that I can skip the step that installing it with spack, where error occers. And how can I check the path where perl is installed?

#11

Yes for using the system perl do the following:

  • vim $HOME/.spack/linux/packages.yaml

Then add the following, please use the path where the system perl is installed.

packages:
 perl:
   paths:
     perl@version: /path/to/perl
   buildable: False
#12

Try which perl or locate perl

#13

I use which perl and it shows like this,

Untitled

I think I didn’t install it properly from Savio. But when I tried to load it, this error shows.

But as the website shows, perl is available from Savio. It there any depandency I show load first? How should I load perl from the Savio system?

#14

perl already exists in /bin/perl so just fill the packages.yaml file and in path use /bin/perl

#15

I tried and it doesn’t work.

I modified the packages.yaml like this

Untitled

And when I tried to install vtk using spack, the error shows,

I think it’s because perl was not installed properly. So I want to load the one from Savio, but had above error

#16

Other option is to contact Savio support to get help installing VTK

#17

I contacted Savio support and figured it out. Use following works and VTK was installed.

packages:
 perl:
   paths:
     perl@5.16.3: /
   buildable: False

But then I had several errors when compiling the LEM code. I’ll open another post.