Installation issue: libx11 (`spack/lib/spack/env/cpp` points to wrong gcc toolchain?)

Question

Installation issue: libx11 (`spack/lib/spack/env/cpp` points to wrong gcc toolchain?)

BenWibking opened this issue a month ago · comments

Steps to reproduce the issue

$ spack spec -I libx11
Input spec
--------------------------------
 -   libx11

Concretized
--------------------------------
 -   libx11@1.8.7%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^gcc-runtime@11.3.1%gcc@11.3.1 build_system=generic arch=linux-rocky9-sapphirerapids
[e]      ^glibc@2.34%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^gmake@4.4.1%gcc@11.3.1~guile build_system=generic arch=linux-rocky9-sapphirerapids
[+]      ^inputproto@2.3.2%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^kbproto@1.0.7%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^libxcb@1.16%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]          ^libpthread-stubs@0.5%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]          ^libxau@1.0.11%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]          ^libxdmcp@1.1.4%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]              ^libbsd@0.12.1%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]                  ^libmd@1.0.4%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]          ^python@3.8.18%gcc@11.3.1+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=0d98e93,4c24573,ebdca64,f2fd060 arch=linux-rocky9-sapphirerapids
[+]              ^bzip2@1.0.8%gcc@11.3.1~debug~pic+shared build_system=generic arch=linux-rocky9-sapphirerapids
[+]                  ^diffutils@3.10%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]              ^expat@2.6.2%gcc@11.3.1+libbsd build_system=autotools arch=linux-rocky9-sapphirerapids
[+]              ^gdbm@1.23%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]              ^gettext@0.22.4%gcc@11.3.1+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rocky9-sapphirerapids
[+]                  ^libxml2@2.10.3%gcc@11.3.1+pic~python+shared build_system=autotools arch=linux-rocky9-sapphirerapids
[+]                  ^tar@1.34%gcc@11.3.1 build_system=autotools zip=pigz arch=linux-rocky9-sapphirerapids
[+]                      ^pigz@2.8%gcc@11.3.1 build_system=makefile arch=linux-rocky9-sapphirerapids
[+]                      ^zstd@1.5.6%gcc@11.3.1+programs build_system=makefile compression=none libs=shared,static arch=linux-rocky9-sapphirerapids
[+]              ^libffi@3.4.6%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]              ^libxcrypt@4.4.35%gcc@11.3.1~obsolete_api build_system=autotools patches=4885da3 arch=linux-rocky9-sapphirerapids
[e]                  ^perl@5.32.1%gcc@11.3.1~cpanm+opcode+open+shared+threads build_system=generic arch=linux-rocky9-sapphirerapids
[+]              ^ncurses@6.4%gcc@11.3.1~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-rocky9-sapphirerapids
[+]              ^openssl@3.2.1%gcc@11.3.1~docs+shared build_system=generic certs=mozilla arch=linux-rocky9-sapphirerapids
[+]                  ^ca-certificates-mozilla@2023-05-30%gcc@11.3.1 build_system=generic arch=linux-rocky9-sapphirerapids
[+]              ^readline@8.2%gcc@11.3.1 build_system=autotools patches=bbf97f1 arch=linux-rocky9-sapphirerapids
[+]              ^sqlite@3.43.2%gcc@11.3.1+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-rocky9-sapphirerapids
[+]              ^util-linux-uuid@2.38.1%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]              ^xz@5.4.6%gcc@11.3.1~pic build_system=autotools libs=shared,static arch=linux-rocky9-sapphirerapids
[+]              ^zlib-ng@2.1.6%gcc@11.3.1+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky9-sapphirerapids
[+]          ^xcb-proto@1.16.0%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[e]      ^perl@5.32.1%gcc@11.3.1~cpanm+opcode+open+shared+threads build_system=generic arch=linux-rocky9-sapphirerapids
[+]      ^pkgconf@1.9.5%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^util-macros@1.19.3%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^xextproto@7.3.0%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^xproto@7.0.31%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids
[+]      ^xtrans@1.5.0%gcc@11.3.1 build_system=autotools arch=linux-rocky9-sapphirerapids

Error message

==> Installing libx11-1.8.7-ofxuo2csmnpwm5ominoi4m4f3ajhkc6i [37/37]
==> No binary for libx11-1.8.7-ofxuo2csmnpwm5ominoi4m4f3ajhkc6i found: installing from source
==> Using cached archive: /scratch/02661/bwibking/spack/var/spack/cache/_source-cache/archive/79/793ebebf569f12c864b77401798d38814b51790fce206e01a431e5feb982e20b.tar.gz
==> No patches needed for libx11
==> libx11: Executing phase: 'autoreconf'
==> libx11: Executing phase: 'configure'
==> Error: ProcessError: Command exited with status 1:
    '/tmp/bwibking/spack-stage/spack-stage-libx11-1.8.7-ofxuo2csmnpwm5ominoi4m4f3ajhkc6i/spack-src/configure' '--prefix=/scratch/02661/bwibking/spack/opt/spack/linux-rocky9-sapphirerapids/gcc-11.3.1/libx11-1.8.7-ofxuo2csmnpwm5ominoi4m4f3ajhkc6i'

4 errors found in build log:
     133    checking for xmlto... no
     134    configure: WARNING: xmlto not found - documentation targets will be skipped
     135    checking for xsltproc... /usr/bin/xsltproc
     136    checking for X.Org SGML entities >= 1.10... no
     137    checking how to run the C preprocessor... /scratch/02661/bwibking/spack/lib/spack/env/gcc/gcc -E
     138    checking for cpp... /scratch/02661/bwibking/spack/lib/spack/env/cpp
  >> 139    checking if /scratch/02661/bwibking/spack/lib/spack/env/cpp requires -undef... /opt/apps/gcc/13.2.0/libexec/gcc/x86_64-
            pc-linux-gnu/13.2.0/cc1: error while loading shared libraries: libisl.so.15: cannot open shared object file: No such fi
            le or directory
  >> 140    /opt/apps/gcc/13.2.0/libexec/gcc/x86_64-pc-linux-gnu/13.2.0/cc1: error while loading shared libraries: libisl.so.15: ca
            nnot open shared object file: No such file or directory
  >> 141    /opt/apps/gcc/13.2.0/libexec/gcc/x86_64-pc-linux-gnu/13.2.0/cc1: error while loading shared libraries: libisl.so.15: ca
            nnot open shared object file: No such file or directory
  >> 142    configure: error: /scratch/02661/bwibking/spack/lib/spack/env/cpp defines unix with or without -undef.  I don't know wh
            at to do.

Information on your system

Spack: 0.22.0.dev0 (a1f34ec)
Python: 3.9.18
Platform: linux-rocky9-sapphirerapids
Concretizer: clingo

Additional information

spack-build-out.txt
spack-build-env.txt

@wdconinc

General information

I have run spack debug report and reported the version of Spack/Python/Platform
I have run spack maintainers <name-of-the-package> and @mentioned any maintainers
I have uploaded the build log and environment files
I have searched the issues of this repo and believe this is not a duplicate