Installation issue: bazel (JUSUF)
Summary
| Summary | Spack package build failure |
| Package info | bazel |
| System | JUSUF |
| Related |
Steps to reproduce the issue
$ spack env activate <ebrains-env>
$ spack spec -lI bazel@5.4.0
Input spec
--------------------------------
- bazel@5.4.0
Concretized
--------------------------------
- ol4n7oc bazel@5.4.0%gcc@12.3.0+nodepfail build_system=generic patches=0f6940d,3e6448a,53ca269,604423c,af73a49,dbbf38b arch=linux-rocky8-zen2
[^] n2qjcd2 ^binutils@2.40%gcc@12.3.0~gas+gold~gprofng+headers~interwork+ld~libiberty~lto~nls~pgo+plugins build_system=autotools compress_debug_sections=zlib libs=shared,static arch=linux-rocky8-zen2
[^] ulk5n5w ^openjdk@11.0.17_8%gcc@12.3.0 build_system=generic arch=linux-rocky8-zen2
[^] zqjqxiw ^python@3.10.10%gcc@12.3.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tix+tkinter+uuid+zlib build_system=generic patches=0d98e93,f2fd060 arch=linux-rocky8-zen2
[^] rkpncyj ^bzip2@1.0.8%gcc@12.3.0~debug~pic+shared build_system=generic arch=linux-rocky8-zen2
[^] c4nkaa7 ^diffutils@3.9%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] fkkxyng ^expat@2.5.0%gcc@12.3.0+libbsd build_system=autotools arch=linux-rocky8-zen2
[^] yxlo7m7 ^libbsd@0.11.7%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] b5yqrv4 ^libmd@1.0.4%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] ph3g3jl ^gdbm@1.23%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] bve5u47 ^gettext@0.21.1%gcc@12.3.0+bzip2+curses+git~libunistring+libxml2+tar+xz build_system=autotools arch=linux-rocky8-zen2
[^] ifjhave ^libiconv@1.17%gcc@12.3.0 build_system=autotools libs=shared,static arch=linux-rocky8-zen2
[^] s4degss ^libxml2@2.10.3%gcc@12.3.0~python build_system=autotools arch=linux-rocky8-zen2
[^] udgip6g ^tar@1.34%gcc@12.3.0 build_system=autotools zip=pigz arch=linux-rocky8-zen2
[^] ji6on2f ^pigz@2.7%gcc@12.3.0 build_system=makefile arch=linux-rocky8-zen2
[^] t52wh4s ^zstd@1.5.5%gcc@12.3.0+programs build_system=makefile compression=none libs=shared,static arch=linux-rocky8-zen2
[^] fe7bgrb ^libffi@3.3%gcc@12.3.0 build_system=autotools patches=26f26c6 arch=linux-rocky8-zen2
[^] vvzjsvv ^libxcrypt@4.4.33%gcc@12.3.0~obsolete_api build_system=autotools arch=linux-rocky8-zen2
[^] e7wit4z ^perl@5.36.0%gcc@12.3.0+cpanm+open+shared+threads build_system=generic arch=linux-rocky8-zen2
[^] hjd7kv5 ^berkeley-db@18.1.40%gcc@12.3.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-rocky8-zen2
[^] anbhe3x ^ncurses@6.4%gcc@12.3.0~symlinks+termlib abi=none build_system=autotools arch=linux-rocky8-zen2
[^] 5or3mbc ^openssl@1.1.1t%gcc@12.3.0~docs~shared build_system=generic certs=mozilla arch=linux-rocky8-zen2
[^] fzi3ysm ^ca-certificates-mozilla@2023-01-10%gcc@12.3.0 build_system=generic arch=linux-rocky8-zen2
[^] kvbvcpk ^pkgconf@1.9.5%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] 3yhuhib ^readline@8.2%gcc@12.3.0 build_system=autotools patches=bbf97f1 arch=linux-rocky8-zen2
[^] 7lmvl6k ^sqlite@3.40.1%gcc@12.3.0+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-rocky8-zen2
[^] z6l4ymo ^tcl@8.6.12%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] m2b55hp ^tk@8.6.11%gcc@12.3.0+xft+xss build_system=autotools arch=linux-rocky8-zen2
[^] q7rcpt4 ^libx11@1.8.4%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] jsvwj4z ^inputproto@2.3.2%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] l6u6rjc ^kbproto@1.0.7%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] yltfv3u ^libxcb@1.14%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] 7enmlzm ^libpthread-stubs@0.4%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] j7d3nej ^libxau@1.0.8%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] nhk5i2i ^libxdmcp@1.1.4%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] httiq7y ^xcb-proto@1.15.2%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] se6mptl ^util-macros@1.19.3%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] nzc3e6o ^xextproto@7.3.0%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] gxix5ar ^xproto@7.0.31%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] vmmmeko ^xtrans@1.4.0%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] rvwnv7o ^libxft@2.3.2%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] cllghe2 ^fontconfig@2.13.1%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] gtacjut ^font-util@1.4.0%gcc@12.3.0 build_system=autotools fonts=encodings,font-adobe-100dpi,font-adobe-75dpi,font-adobe-utopia-100dpi,font-adobe-utopia-75dpi,font-adobe-utopia-type1,font-alias,font-arabic-misc,font-bh-100dpi,font-bh-75dpi,font-bh-lucidatypewriter-100dpi,font-bh-lucidatypewriter-75dpi,font-bh-type1,font-bitstream-100dpi,font-bitstream-75dpi,font-bitstream-speedo,font-bitstream-type1,font-cronyx-cyrillic,font-cursor-misc,font-daewoo-misc,font-dec-misc,font-ibm-type1,font-isas-misc,font-jis-misc,font-micro-misc,font-misc-cyrillic,font-misc-ethiopic,font-misc-meltho,font-misc-misc,font-mutt-misc,font-schumacher-misc,font-screen-cyrillic,font-sun-misc,font-winitzki-cyrillic,font-xfree86-type1 arch=linux-rocky8-zen2
[^] yap3ah7 ^autoconf@2.69%gcc@12.3.0 build_system=autotools patches=35c4492,7793209,a49dd5b arch=linux-rocky8-zen2
[^] y2uuwbg ^m4@1.4.19%gcc@12.3.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rocky8-zen2
[^] uz6jrx2 ^libsigsegv@2.14%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] 6gvor5w ^automake@1.16.5%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] dy5o5xi ^bdftopcf@1.1%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] sbcc6gh ^fontsproto@2.1.3%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] devf5pp ^libxfont@1.5.4%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] v3qc2hj ^mkfontdir@1.0.7%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] 4a4t37d ^mkfontscale@1.2.2%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] yphtcqx ^libfontenc@1.1.7%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] o3qeujq ^gperf@3.1%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] kucimyf ^freetype@2.11.1%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] vvyrmeu ^libpng@1.6.39%gcc@12.3.0~ipo build_system=cmake build_type=Release generator=make libs=shared,static arch=linux-rocky8-zen2
[^] uzvhveq ^cmake@3.26.3%gcc@12.3.0~doc+ncurses+ownlibs~qt build_system=generic build_type=Release arch=linux-rocky8-zen2
[^] fsr7bux ^gmake@4.4.1%gcc@12.3.0~guile build_system=autotools arch=linux-rocky8-zen2
[^] njhdrce ^libxrender@0.9.10%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] clvvmqk ^renderproto@0.11.1%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] erfiram ^libxscrnsaver@1.2.2%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] bicmcp3 ^libxext@1.3.3%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] 6mlv5cq ^scrnsaverproto@1.2.2%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] vfltdd4 ^util-linux-uuid@2.38.1%gcc@12.3.0 build_system=autotools arch=linux-rocky8-zen2
[^] nibnzqv ^xz@5.4.1%gcc@12.3.0~pic build_system=autotools libs=shared,static arch=linux-rocky8-zen2
[^] s46ief3 ^zlib@1.2.13%gcc@12.3.0+optimize+pic+shared build_system=makefile arch=linux-rocky8-zen2
[^] ud7756a ^zip@3.0%gcc@12.3.0 build_system=makefile patches=14dc880,3bc30ba,5068e7c,51f48db,66ab4ce,a92fc4e,a95ed93,eb83fc8,f7d0bc4,fa8312c arch=linux-rocky8-zen2
$ spack install --fresh --test root
...Error message
ERROR: /tmp/bazel_hutSAowo/out/external/com_google_protobuf/BUILD:354:15: Generating upb protos for :descriptor_proto failed: (Exit 1): protoc failed: error executing command
(cd /tmp/bazel_hutSAowo/out/execroot/io_bazel && \
exec env - \
bazel-out/host/bin/external/com_google_protobuf/protoc '--upb_out=bazel-out/k8-opt/bin/external/com_google_protobuf' '--plugin=protoc-gen-upb=bazel-out/host/bin/external/upb/upbc/protoc-gen-upb' '--descriptor_set_in=bazel-out/k8-opt/bin/external/com_google_protobuf/descriptor_proto-descriptor-set.proto.bin' google/protobuf/descriptor.proto)
# Configuration: 06da92ffbe24d802c285aaef2c79bccfdcdf7b80f7ac8d166c3c81b48d0df40c
# Execution platform: //:default_host_platform
/tmp/bazel_hutSAowo/out/execroot/io_bazel/bazel-out/host/bin/external/com_google_protobuf/protoc: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /tmp/bazel_hutSAowo/out/execroot/io_bazel/bazel-out/host/bin/external/com_google_protobuf/protoc)Information on your system
Additional information
Activity
added build-error label
There was a similar error while installing the last release (EBRAINS 23.06), that was fixed with (I think) !384 (merged), !387 (merged), !385 (merged).
So just to be complete (i.e. lift the information from EBRAINS Rocket.Chat to here): Build env looks fine, i.e. the "StdEnv/2024` thingy from the compiler settings is correctly applied to the build environment:
LD_LIBRARY_PATH=\ # … /p/software/jusuf/stages/2024/software/binutils/2.40-GCCcore-12.3.0/lib /p/software/jusuf/stages/2024/software/GCCcore/12.3.0/lib64 # …and there's:
$ ls /p/software/jusuf/stages/2024/software/GCCcore/12.3.0/lib64/libstdc++* libstdc++.so libstdc++.so.6 libstdc++.so.6.0.30 libstdc++.so.6.0.30-gdb.pyLooks like
bazelis droppingLD_LIBRARY_PATH? Ah, and we had theGCC_HOST_COMPILER_PREFIXmodification before… but it's still active, right?Edited by Eric Mülleryes: bazel_package.py
sure, I pushed them here (temporarily - we probably want to keep the config files in different subdirs for different stages)
hopefully solved by !504 (merged) … (the requirement to build on the login node might be lifted by a recent [upstream change]https://github.com/spack/spack/commit/fe4a4ddcf9123eff97181b9d0b2bacf7054a19f9)
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