How to properly diagnose a cmake GLIBC version error?

Question

Some background: I'm trying to use easybuild to build different versions of a rather complicated scientific software stack on the same HPC system. I am new to building software like this and could use some guidance on debugging. My current error when running command:

cmake  -DCMAKE_INSTALL_PREFIX=/home/user/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF  -G"Unix Makefiles" -DWITH_JPEG8=1 /home/user/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0/libjpeg-turbo-2.1.3/

is

cmake: /home/user/.local/easybuild/software/GCCcore/11.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/lib/libicuuc.so.72)

I actually saw a similar error before when easybuild was running just cmake --version. This was because (I think), in the easybuild environment, cmake was linked to the c++ library (libstdc++) located in /home/user/.local/easybuild/software/GCCcore/11.3.0/lib64/libstdc++.so.6, but it was running my newer system cmake, which required a more recent version of GBLIC. I solved this by having it use an older version of cmake in the easybuild environment.

EDIT: full build log output:

== 2022-12-01 12:19:27,264 easyblock.py:304 INFO This is EasyBuild 4.6.2 (framework: 4.6.2, easyblocks: 4.6.2) on host luke-30bgs2s000.
== 2022-12-01 12:19:27,264 easyblock.py:310 INFO This is easyblock CMakeMake from module easybuild.easyblocks.generic.cmakemake (/home/luke/git/easybuild-easyblocks/easybuild/easyblocks/generic/cmakemake.py)
== 2022-12-01 12:19:27,264 easyblock.py:990 INFO Build dir set to /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0
== 2022-12-01 12:19:27,264 easyblock.py:1047 INFO Software install dir set to /home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0
== 2022-12-01 12:19:27,264 easyblock.py:1052 INFO Module install dir set to /home/luke/.local/easybuild/modules/all
== 2022-12-01 12:19:27,264 easyblock.py:279 INFO Init completed for application name libjpeg-turbo version 2.1.3
== 2022-12-01 12:19:27,264 easyblock.py:4040 INFO Obtained application instance of for libjpeg-turbo (easyblock: CMakeMake)
== 2022-12-01 12:19:27,265 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,265 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', github_account='libjpeg-turbo', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,265 one.py:178 INFO Skipping reformatting value for parameter 'toolchain'
== 2022-12-01 12:19:27,266 one.py:178 INFO Skipping reformatting value for parameter 'toolchainopts'
== 2022-12-01 12:19:27,266 filetools.py:1913 INFO Creating directory /tmp/eb-e_8gs5x5/reprod_20221201121927_27457 (parents: True, set_gid: False, sticky: False)
== 2022-12-01 12:19:27,266 easyblock.py:4294 INFO Dumped easyconfig instance to /tmp/eb-e_8gs5x5/reprod_20221201121927_27457/libjpeg-turbo-2.1.3-GCCcore-11.3.0.eb
== 2022-12-01 12:19:27,266 filetools.py:1913 INFO Creating directory /tmp/eb-e_8gs5x5/reprod_20221201121927_27457/easyblocks (parents: True, set_gid: False, sticky: False)
== 2022-12-01 12:19:27,267 filetools.py:2426 INFO /home/luke/git/easybuild-easyblocks/easybuild/easyblocks/generic/cmakemake.py copied to /tmp/eb-e_8gs5x5/reprod_20221201121927_27457/easyblocks/cmakemake.py
== 2022-12-01 12:19:27,267 easyblock.py:4274 INFO Dumped easyblock cmakemake.py required for reproduction to /tmp/eb-e_8gs5x5/reprod_20221201121927_27457/easyblocks
== 2022-12-01 12:19:27,267 filetools.py:2426 INFO /home/luke/git/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /tmp/eb-e_8gs5x5/reprod_20221201121927_27457/easyblocks/configuremake.py
== 2022-12-01 12:19:27,267 easyblock.py:4274 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-e_8gs5x5/reprod_20221201121927_27457/easyblocks
== 2022-12-01 12:19:27,267 easyblock.py:2125 INFO Number of iterations to perform for central part of installation procedure: 1
== 2022-12-01 12:19:27,267 build_log.py:265 INFO building and installing libjpeg-turbo/2.1.3-GCCcore-11.3.0...
== 2022-12-01 12:19:27,270 filetools.py:2006 INFO Lock /home/luke/.local/easybuild/software/.locks/_home_luke_.local_easybuild_software_libjpeg-turbo_2.1.3-GCCcore-11.3.0.lock does not exist
== 2022-12-01 12:19:27,270 filetools.py:1947 INFO Creating lock at /home/luke/.local/easybuild/software/.locks/_home_luke_.local_easybuild_software_libjpeg-turbo_2.1.3-GCCcore-11.3.0.lock...
== 2022-12-01 12:19:27,270 filetools.py:1913 INFO Creating directory /home/luke/.local/easybuild/software/.locks/_home_luke_.local_easybuild_software_libjpeg-turbo_2.1.3-GCCcore-11.3.0.lock (parents: True, set_gid: False, sticky: False)
== 2022-12-01 12:19:27,270 filetools.py:1956 INFO Lock created: /home/luke/.local/easybuild/software/.locks/_home_luke_.local_easybuild_software_libjpeg-turbo_2.1.3-GCCcore-11.3.0.lock
== 2022-12-01 12:19:27,270 build_log.py:265 INFO fetching files...
== 2022-12-01 12:19:27,273 easyblock.py:3766 INFO Starting fetch step
== 2022-12-01 12:19:27,273 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,273 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', builddir='/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0', github_account='libjpeg-turbo', installdir='/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,274 easyblock.py:3774 INFO Running method fetch_step part of step fetch
== 2022-12-01 12:19:27,274 easyblock.py:2247 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2022-12-01 12:19:27,274 easyblock.py:759 INFO Considering directory in which easyconfig file is located when searching for libjpeg-turbo-2.1.3.tar.gz: /home/luke/.local/easybuild/easyconfigs/l/libjpeg-turbo
== 2022-12-01 12:19:27,274 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /home/luke/.local/bin/eb
== 2022-12-01 12:19:27,274 tools.py:288 INFO Also considering installation prefix /home/luke/.local (determined via path to 'eb' script)...
== 2022-12-01 12:19:27,274 easyblock.py:801 INFO Found file libjpeg-turbo-2.1.3.tar.gz at /home/luke/.local/easybuild/sources/l/libjpeg-turbo/libjpeg-turbo-2.1.3.tar.gz
== 2022-12-01 12:19:27,275 easyblock.py:454 INFO Added sources: [{'name': 'libjpeg-turbo-2.1.3.tar.gz', 'path': '/home/luke/.local/easybuild/sources/l/libjpeg-turbo/libjpeg-turbo-2.1.3.tar.gz', 'cmd': None, 'checksum': '467b310903832b033fe56cd37720d1b73a6a3bd0171dbf6ff0b620385f4f76d0', 'finalpath': '/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0'}]
== 2022-12-01 12:19:27,275 easyblock.py:2290 INFO no patches provided
== 2022-12-01 12:19:27,279 easyblock.py:2300 INFO md5 checksum for /home/luke/.local/easybuild/sources/l/libjpeg-turbo/libjpeg-turbo-2.1.3.tar.gz: 85244dedeaf06f636a9e7ddea6d236d8
== 2022-12-01 12:19:27,286 easyblock.py:2300 INFO sha256 checksum for /home/luke/.local/easybuild/sources/l/libjpeg-turbo/libjpeg-turbo-2.1.3.tar.gz: 467b310903832b033fe56cd37720d1b73a6a3bd0171dbf6ff0b620385f4f76d0
== 2022-12-01 12:19:27,287 easyblock.py:2335 INFO Checking dirs that need to be created: ['/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', '/home/luke/.local/easybuild/modules/all/libjpeg-turbo', '/home/luke/.local/easybuild/modules/lib/libjpeg-turbo']
== 2022-12-01 12:19:27,287 configuremake.py:94 INFO config.guess version: 2018-08-29 (last updated: 2022-10-25T19:08:19.943320, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c)
== 2022-12-01 12:19:27,288 configuremake.py:150 INFO Found config.guess at /home/luke/.local/easybuild/sources/generic/eb_v4.6.2/ConfigureMake/config.guess
== 2022-12-01 12:19:27,288 build_log.py:265 INFO creating build dir, resetting environment...
== 2022-12-01 12:19:27,291 easyblock.py:3766 INFO Starting ready step
== 2022-12-01 12:19:27,291 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,291 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', builddir='/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0', github_account='libjpeg-turbo', installdir='/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,291 easyblock.py:3774 INFO Running method check_readiness_step part of step ready
== 2022-12-01 12:19:27,298 run.py:234 INFO running cmd: ulimit -u 
== 2022-12-01 12:19:27,304 easyblock.py:2144 INFO Setting parallelism: 8
== 2022-12-01 12:19:27,354 easyblock.py:3774 INFO Running method make_builddir part of step ready
== 2022-12-01 12:19:27,354 easyblock.py:1072 INFO Found old directory /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0
== 2022-12-01 12:19:27,370 filetools.py:382 INFO Path /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0 successfully removed.
== 2022-12-01 12:19:27,370 easyblock.py:1080 INFO Removed old directory /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0
== 2022-12-01 12:19:27,370 filetools.py:1913 INFO Creating directory /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0 (parents: True, set_gid: False, sticky: False)
== 2022-12-01 12:19:27,370 easyblock.py:3774 INFO Running method reset_env part of step ready
== 2022-12-01 12:19:27,371 easyblock.py:3774 INFO Running method handle_iterate_opts part of step ready
== 2022-12-01 12:19:27,371 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,371 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', builddir='/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0', github_account='libjpeg-turbo', installdir='/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', parallel='8', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,371 build_log.py:265 INFO unpacking...
== 2022-12-01 12:19:27,375 easyblock.py:3766 INFO Starting source step
== 2022-12-01 12:19:27,375 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,375 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', builddir='/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0', github_account='libjpeg-turbo', installdir='/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', parallel='8', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,375 easyblock.py:3774 INFO Running method checksum_step part of step source
== 2022-12-01 12:19:27,385 easyblock.py:2353 INFO Checksum verification for /home/luke/.local/easybuild/sources/l/libjpeg-turbo/libjpeg-turbo-2.1.3.tar.gz using 467b310903832b033fe56cd37720d1b73a6a3bd0171dbf6ff0b620385f4f76d0 passed.
== 2022-12-01 12:19:27,385 easyblock.py:3774 INFO Running method extract_step part of step source
== 2022-12-01 12:19:27,386 easyblock.py:2446 INFO Unpacking source libjpeg-turbo-2.1.3.tar.gz
== 2022-12-01 12:19:27,386 run.py:234 INFO running cmd: tar xzf /home/luke/.local/easybuild/sources/l/libjpeg-turbo/libjpeg-turbo-2.1.3.tar.gz 
== 2022-12-01 12:19:27,451 build_log.py:265 INFO patching...
== 2022-12-01 12:19:27,455 easyblock.py:3766 INFO Starting patch step
== 2022-12-01 12:19:27,455 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,455 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', builddir='/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0', github_account='libjpeg-turbo', installdir='/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', parallel='8', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,455 easyblock.py:3774 INFO Running method patch_step part of step patch
== 2022-12-01 12:19:27,456 build_log.py:265 INFO preparing...
== 2022-12-01 12:19:27,459 easyblock.py:3766 INFO Starting prepare step
== 2022-12-01 12:19:27,460 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,460 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', builddir='/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0', github_account='libjpeg-turbo', installdir='/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', parallel='8', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,460 easyblock.py:3774 INFO Running method prepare_step part of step prepare
== 2022-12-01 12:19:27,460 modules.py:626 INFO Checking whether CMake/3.23.1-GCCcore-11.3.0 exists...
== 2022-12-01 12:19:27,460 modules.py:631 INFO Module CMake/3.23.1-GCCcore-11.3.0 exists (found in list of available modules)
== 2022-12-01 12:19:27,461 modules.py:654 INFO Result for existence check of CMake/3.23.1-GCCcore-11.3.0 module: True
== 2022-12-01 12:19:27,461 modules.py:626 INFO Checking whether binutils/2.38-GCCcore-11.3.0 exists...
== 2022-12-01 12:19:27,461 modules.py:631 INFO Module binutils/2.38-GCCcore-11.3.0 exists (found in list of available modules)
== 2022-12-01 12:19:27,461 modules.py:654 INFO Result for existence check of binutils/2.38-GCCcore-11.3.0 module: True
== 2022-12-01 12:19:27,461 modules.py:626 INFO Checking whether NASM/2.15.05-GCCcore-11.3.0 exists...
== 2022-12-01 12:19:27,461 modules.py:631 INFO Module NASM/2.15.05-GCCcore-11.3.0 exists (found in list of available modules)
== 2022-12-01 12:19:27,461 modules.py:654 INFO Result for existence check of NASM/2.15.05-GCCcore-11.3.0 module: True
== 2022-12-01 12:19:27,461 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists...
== 2022-12-01 12:19:27,462 modules.py:633 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'...
== 2022-12-01 12:19:27,524 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True
== 2022-12-01 12:19:27,753 environment.py:91 INFO Environment variable LD_LIBRARY_PATH set to /home/luke/.local/easybuild/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/XZ/5.2.5-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/cURL/7.83.0-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/OpenSSL/1.1/lib:/home/luke/.local/easybuild/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/zlib/1.2.12-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/ncurses/6.3-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib64 (previous value: '/home/luke/.local/easybuild/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/XZ/5.2.5-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/cURL/7.83.0-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/OpenSSL/1.1/lib:/home/luke/.local/easybuild/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/zlib/1.2.12-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/ncurses/6.3-GCCcore-11.3.0/lib')
== 2022-12-01 12:19:27,854 environment.py:91 INFO Environment variable LD_LIBRARY_PATH set to /home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/XZ/5.2.5-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/cURL/7.83.0-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/OpenSSL/1.1/lib:/home/luke/.local/easybuild/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/zlib/1.2.12-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/ncurses/6.3-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib64 (previous value: '/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib')
== 2022-12-01 12:19:27,948 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists...
== 2022-12-01 12:19:27,948 modules.py:633 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'...
== 2022-12-01 12:19:27,948 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True
== 2022-12-01 12:19:27,949 toolchain.py:760 INFO List of toolchain dependency modules and toolchain definition match!
== 2022-12-01 12:19:27,950 compiler.py:361 INFO _set_optimal_architecture: using march=native as optarch for x86_64.
== 2022-12-01 12:19:27,952 variables.py:201 WARNING flags_for_subdirs: directory /home/luke/.local/easybuild/software/CMake/3.23.1-GCCcore-11.3.0/include was not found
== 2022-12-01 12:19:27,952 variables.py:201 WARNING flags_for_subdirs: directory /home/luke/.local/easybuild/software/CMake/3.23.1-GCCcore-11.3.0/lib64 was not found
== 2022-12-01 12:19:27,952 variables.py:201 WARNING flags_for_subdirs: directory /home/luke/.local/easybuild/software/CMake/3.23.1-GCCcore-11.3.0/lib was not found
== 2022-12-01 12:19:27,952 variables.py:201 WARNING flags_for_subdirs: directory /home/luke/.local/easybuild/software/NASM/2.15.05-GCCcore-11.3.0/include was not found
== 2022-12-01 12:19:27,952 variables.py:201 WARNING flags_for_subdirs: directory /home/luke/.local/easybuild/software/NASM/2.15.05-GCCcore-11.3.0/lib64 was not found
== 2022-12-01 12:19:27,953 variables.py:201 WARNING flags_for_subdirs: directory /home/luke/.local/easybuild/software/NASM/2.15.05-GCCcore-11.3.0/lib was not found
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable CC set to gcc (previously undefined)
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable EBVARCC set to gcc (previously undefined)
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable CPPFLAGS set to -I/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/include (previously undefined)
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable EBVARCPPFLAGS set to -I/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/include (previously undefined)
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable CXX set to g++ (previously undefined)
== 2022-12-01 12:19:27,954 environment.py:91 INFO Environment variable EBVARCXX set to g++ (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable F77 set to gfortran (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable EBVARF77 set to gfortran (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable F90 set to gfortran (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable EBVARF90 set to gfortran (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,955 environment.py:91 INFO Environment variable FC set to gfortran (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable EBVARFC set to gfortran (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable FLIBS set to -lgfortran (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable LDFLAGS set to -L/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib -L/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib64 -L/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable EBVARLDFLAGS set to -L/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib -L/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib64 -L/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib (previously undefined)
== 2022-12-01 12:19:27,956 environment.py:91 INFO Environment variable LIBS set to -lm -lpthread (previously undefined)
== 2022-12-01 12:19:27,957 environment.py:91 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined)
== 2022-12-01 12:19:27,957 environment.py:91 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined)
== 2022-12-01 12:19:27,957 environment.py:91 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined)
== 2022-12-01 12:19:27,957 environment.py:91 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined)
== 2022-12-01 12:19:27,957 environment.py:91 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined)
== 2022-12-01 12:19:27,957 easyblock.py:2028 INFO Using /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0/libjpeg-turbo-2.1.3/ as start dir
== 2022-12-01 12:19:27,957 build_log.py:265 INFO configuring...
== 2022-12-01 12:19:27,961 easyblock.py:3766 INFO Starting configure step
== 2022-12-01 12:19:27,961 easyconfig.py:1686 INFO Generating template values...
== 2022-12-01 12:19:27,961 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='libjpeg-turbo', builddir='/home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0', github_account='libjpeg-turbo', installdir='/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0', module_name='libjpeg-turbo/2.1.3-GCCcore-11.3.0', name='libjpeg-turbo', nameletter='l', nameletterlower='l', namelower='libjpeg-turbo', parallel='8', toolchain_name='GCCcore', toolchain_version='11.3.0', version='2.1.3', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix=''
== 2022-12-01 12:19:27,961 easyblock.py:3774 INFO Running method configure_step part of step configure
== 2022-12-01 12:19:27,961 environment.py:91 INFO Environment variable CMAKE_INCLUDE_PATH set to /home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/include:/home/luke/.local/easybuild/software/libarchive/3.6.1-GCCcore-11.3.0/include:/home/luke/.local/easybuild/software/XZ/5.2.5-GCCcore-11.3.0/include:/home/luke/.local/easybuild/software/cURL/7.83.0-GCCcore-11.3.0/include:/home/luke/.local/easybuild/software/OpenSSL/1.1/include:/home/luke/.local/easybuild/software/bzip2/1.0.8-GCCcore-11.3.0/include:/home/luke/.local/easybuild/software/zlib/1.2.12-GCCcore-11.3.0/include:/home/luke/.local/easybuild/software/ncurses/6.3-GCCcore-11.3.0/include (previously undefined)
== 2022-12-01 12:19:27,961 environment.py:91 INFO Environment variable CMAKE_LIBRARY_PATH set to /home/luke/.local/easybuild/software/GCCcore/11.3.0/lib64:/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib:/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib64:/home/luke/.local/easybuild/software/binutils/2.38-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/XZ/5.2.5-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/cURL/7.83.0-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/OpenSSL/1.1/lib:/home/luke/.local/easybuild/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/zlib/1.2.12-GCCcore-11.3.0/lib:/home/luke/.local/easybuild/software/ncurses/6.3-GCCcore-11.3.0/lib (previous value: '/home/luke/.local/easybuild/software/GCCcore/11.3.0/lib64')
== 2022-12-01 12:19:27,962 environment.py:91 INFO Environment variable FC set to gfortran (previous value: 'gfortran')
== 2022-12-01 12:19:27,962 run.py:234 INFO running cmd:  cmake  -DCMAKE_INSTALL_PREFIX=/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF  -G"Unix Makefiles" -DWITH_JPEG8=1 /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0/libjpeg-turbo-2.1.3/ 
== 2022-12-01 12:19:28,024 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " cmake  -DCMAKE_INSTALL_PREFIX=/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF  -G"Unix Makefiles" -DWITH_JPEG8=1 /home/luke/.local/easybuild/build/libjpegturbo/2.1.3/GCCcore-11.3.0/libjpeg-turbo-2.1.3/" exited with exit code 1 and output:
cmake: /home/luke/.local/easybuild/software/GCCcore/11.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /usr/lib/libicuuc.so.72)
 (at easybuild/tools/run.py:641 in parse_cmd_output)
== 2022-12-01 12:19:28,024 filetools.py:2014 INFO Removing lock /home/luke/.local/easybuild/software/.locks/_home_luke_.local_easybuild_software_libjpeg-turbo_2.1.3-GCCcore-11.3.0.lock...
== 2022-12-01 12:19:28,024 filetools.py:382 INFO Path /home/luke/.local/easybuild/software/.locks/_home_luke_.local_easybuild_software_libjpeg-turbo_2.1.3-GCCcore-11.3.0.lock successfully removed.
== 2022-12-01 12:19:28,024 filetools.py:2018 INFO Lock removed: /home/luke/.local/easybuild/software/.locks/_home_luke_.local_easybuild_software_libjpeg-turbo_2.1.3-GCCcore-11.3.0.lock
== 2022-12-01 12:19:28,025 easyblock.py:4097 WARNING build failed (first 300 chars): cmd " cmake  -DCMAKE_INSTALL_PREFIX=/home/luke/.local/easybuild/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF  -G"Unix Makefiles" -DWITH_JPEG8=1 /home/luke/.local/easybuild
== 2022-12-01 12:19:28,025 easyblock.py:319 INFO Closing log for application name libjpeg-turbo version 2.1.3

This is not an answer to your question but it might help you as much: i have built a lot of scientific code in the past and even though i have little experience with easybuild, I do with spack. check it out if you do not know about it. — pattakosn, Nov 29 '22 at 16:23
Can you please show us a bigger part of the output that includes the error? — pattakosn, Nov 29 '22 at 16:26
I've included the full build log above. Note I had to delete some of the original question to meet the character limit. So I've looked more into it and the issue is that when `cmake` is run to configure `libjpeg`, it's using my system cmake, and not what I've specified for the build. However I've explicitly defined which cmake I want to use as builddependencies in all easyconfigs that I've written, and these easyconfigs only use the default easyconfigs that ship with easybuild. Any idea why that might be happening? Or any tips on diagnosing that? — lcleary, Dec 01 '22 at 10:21
Also I just checked the libjpeg easconfig file in `~/.local/easybuild/easyconfigs/l/libjpeg-turbo` and the GCCcore version has cmake as a build dependency, so I'm not sure why it's not being invoked properly — lcleary, Dec 01 '22 at 11:40

score 0 · Answer 1 · answered Nov 18 '22 at 06:31

The above error is telling me that it's /usr/lib/libicuuc.so.72 that needs the newer version.

Correct.

This is located outside of the easybuild environment, which I think is the cause of the issue.

Correct.

Everything within should be built against an older version of cmake.

There is no such thing as "built against version of cmake" -- cmake is a binary, and you haven't built anything with that binary yet.

Once you get this build environment working, anything built by that environment should be built against libraries in the easybuild environment. But you aren't there yet.

How do I figure out what's linked to libcuuc.so.72.

Run this command:

env LD_DEBUG=files ldd $(which cmake)

The output will look like this:

   3011146:     file=libarchive.so.13 [0];  needed by /usr/bin/cmake [0]
...
   3011146:     file=libxml2.so.2 [0];  needed by /lib/x86_64-linux-gnu/libarchive.so.13 [0]
...
   3011146:     file=libicuuc.so.71 [0];  needed by /lib/x86_64-linux-gnu/libxml2.so.2 [0]

This tells you that cmake directly depends on libarchive.so.13, which directly depends on libxml2.so.2, which directly depends on libicuuc.so.71 (on my system).

In your case, one (or more) of these libraries are coming from the system and not from easybuild.

You will probably need to fetch the older versions of these libraries into the easybuild environment.

Thanks this is a helpful tool, but the issue seems to be that easybuild is again using system cmake instead of the one I've specified for the build, which is actually the same error as before. I just need to figure out why... — lcleary, Dec 01 '22 at 10:14

How to properly diagnose a cmake GLIBC version error?

1 Answers1