Steps to reproduce
Installing this small spack environment entirely from buildcache results in some packages depending on ghost specs. What I mean by "ghost" spec here is that some specs get installed which depend on non-installed dependency specs! This creates issues with generated module files, for instance, where loading dependents of the ghost spec results in attempts to load the non-existent dependency's modulefile.
I've wiped out my spack install entirely and re-installed the environment here a couple times. The first time there was a ghost glibc. The second attempt at wiping+re-installing resulted in the prior missing glibc now being installed, but now there was a ghost libxml2.
For instance, here is how I installed this environment:
$> spack -e . concretize -f | tee concretize.log
$> spack -e . env depfile -o Makefile
$> export SPACK_INSTALL_FLAGS=--cache-only
$> spack -e . buildcache keys -it
$> make -j -k SPACK_COLOR=always --output-sync=recurse
The concretization log shows four libxml2's in the DAG:
$> grep "\^libxml2 concretize.log
- 3juct62 ^libxml2@2.13.5%gcc@10.5.0~http+pic~python+shared build_system=autotools arch=linux-centos7-x86_64_v3
- etomzyn ^libxml2@2.13.5%gcc@10.5.0~http+pic~python+shared build_system=autotools arch=linux-centos7-x86_64_v3
- qxbwyas ^libxml2@2.13.5%gcc@10.5.0~http+pic~python+shared build_system=autotools arch=linux-centos7-x86_64_v3
- lmh2pr7 ^libxml2@2.13.4%gcc@10.5.0+pic~python+shared build_system=autotools arch=linux-centos7-x86_64_v3
With the environment installed, only three of these libxml2's were installed:
$> spack find -l libxml2
-- linux-centos7-x86_64_v3 / gcc@10.5.0 -------------------------
lmh2pr7 libxml2@2.13.4 qxbwyas libxml2@2.13.5 3juct62 libxml2@2.13.5
==> 3 installed packages
Note above we are missing libxml2 /etomzyn. But libxml2 /etomzyn has installed dependents!
$> spack dependents -i /etomzyn
==> Dependents of libxml2@2.13.5%gcc@=10.5.0/etomzyn
-- linux-centos7-x86_64_v3 / gcc@10.5.0 -------------------------
trjllzb gettext@0.23.1 drqlymo hwloc@2.11.1 j3ch2pk llvm@17.0.6 xxonzxz llvm@19.1.7
Thus, if I generate modules and then try module load for one of the dependents of this ghost libxml2, we see the following errors:
$> module load llvm/19.1.7
Lmod has detected the following error: The following module(s) are unknown: "libxml2/2.13.5-etomzyn"
Please check the spelling or version number. Also try "module spider ..."
It is also possible your cache file is out-of-date; it may help to try:
$ module --ignore_cache load "libxml2/2.13.5-etomzyn"
Also make sure that all modulefiles written in TCL start with the string #%Module
Executing this command requires loading "libxml2/2.13.5-etomzyn" which failed while processing the following module(s):
Module fullname Module Filename
--------------- ---------------
hwloc/2.11.1-drqlymo /storage/upack/spack-tools/spack/share/spack/lmod-modules/linux-centos7-x86_64/Core/hwloc/2.11.1-drqlymo.lua
llvm/19.1.7 /storage/upack/spack-tools/spack/share/spack/lmod-modules/linux-centos7-x86_64/Core/llvm/19.1.7.luaExecuting this command requires loading "libxml2/2.13.5-etomzyn" which failed while processing the following module(s):
Module fullname Module Filename
--------------- ---------------
llvm/19.1.7 /storage/upack/spack-tools/spack/share/spack/lmod-modules/linux-centos7-x86_64/Core/llvm/19.1.7.lua
Oddly, if I query Spack for the installed dependencies of llvm@19.1.7 it shows libxml /etomzyn as installed!
$> spack dependencies -i llvm@19.1.7
... etomzyn libxml2@2.13.5 ...
Spack environment:
spack:
view: false
config:
install_tree:
projections:
all: '{name}-{version}-{hash:5}'
concretizer:
reuse: true
unify: when_possible
packages:
all:
require: '%gcc target=x86_64_v3'
mirrors:
bootstrap:
url: https://cache.e4s.io/spack-universal-bootstrap/x86_64_v3-glibc2.17
specs:
- ccache
- cmake
- environment-modules
- gcc@11:11.9
- gcc@12:12.9
- gcc@13:13.9
- gcc@14:14.9
- gcc
- git
- gmake
- gnupg
- libtree
- llvm@17:17.9
- llvm@18:18.9
- llvm@19:19.9 +flang
- llvm
- lmod
- ninja
- patchelf
Concretization
==> Concretized 19 specs:
- nv2nyfn ccache@4.10.2%gcc@10.5.0~ipo+redis build_system=cmake build_type=Release generator=make arch=linux-centos7-x86_64_v3
- p6uh33b ^cmake@3.31.4%gcc@10.5.0~doc+ncurses+ownlibs~qtgui build_system=generic build_type=Release arch=linux-centos7-x86_64_v3
- hep2cnf ^gcc-runtime@10.5.0%gcc@10.5.0 build_system=generic arch=linux-centos7-x86_64_v3
[e] 27tc2cv ^glibc@2.17%gcc@10.5.0 build_system=autotools patches=be65fec,e179c43 arch=linux-centos7-x86_64_v3
- zuvciju ^hiredis@1.1.0%gcc@10.5.0~ipo~ssl~test~test_async~test_ssl build_system=cmake build_type=Release generator=make arch=linux-centos7-x86_64_v3
- az6bfca ^pkgconf@2.3.0%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- j5wi5dt ^zstd@1.5.6%gcc@10.5.0+programs build_system=makefile compression=none libs=shared,static arch=linux-centos7-x86_64_v3
- icxh7cl cmake@3.31.5%gcc@10.5.0~doc+ncurses+ownlibs~qtgui build_system=generic build_type=Release arch=linux-centos7-x86_64_v3
- blxzpb6 ^curl@8.11.1%gcc@10.5.0~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-centos7-x86_64_v3
- bf4snhu ^nghttp2@1.64.0%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- npwsgyq ^ncurses@6.5%gcc@10.5.0~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-centos7-x86_64_v3
- gg6etkq ^zlib-ng@2.2.3%gcc@10.5.0+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-centos7-x86_64_v3
- mdimoi7 environment-modules@5.5.0%gcc@10.5.0+X build_system=generic arch=linux-centos7-x86_64_v3
- dkla36w ^less@668%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 3os3byy ^tcl@8.6.12%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- qgjvcnh ^util-linux@2.40.2%gcc@10.5.0~bash build_system=autotools patches=040a650 arch=linux-centos7-x86_64_v3
- zazgzwm ^libxcrypt@4.4.35%gcc@10.5.0~obsolete_api build_system=autotools patches=4885da3 arch=linux-centos7-x86_64_v3
- nng3iaa gcc@11.5.0%gcc@10.5.0~binutils+bootstrap~graphite~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages='c,c++,fortran' arch=linux-centos7-x86_64_v3
- dh6ncbe ^diffutils@3.10%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- i63gger ^libiconv@1.17%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- qrbpzae ^gawk@5.3.1%gcc@10.5.0~nls build_system=autotools arch=linux-centos7-x86_64_v3
- whztj2l ^libsigsegv@2.14%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- g63ir3j ^readline@8.2%gcc@10.5.0 build_system=autotools patches=1ea4349,24f587b,3d9885e,5911a5b,622ba38,6c8adf8,758e2ec,79572ee,a177edc,bbf97f1,c7b45ff,e0013d9,e065038 arch=linux-centos7-x86_64_v3
- sjeha5y ^gcc-runtime@10.5.0%gcc@10.5.0 build_system=generic arch=linux-centos7-x86_64_v3
- x36dbpd ^gmake@4.4.1%gcc@10.5.0~guile build_system=generic arch=linux-centos7-x86_64_v3
- mfqwymx ^gmp@6.3.0%gcc@10.5.0+cxx build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- h2qh6w2 ^autoconf@2.72%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- wpecwcu ^automake@1.16.5%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- cokv7ku ^m4@1.4.19%gcc@10.5.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-centos7-x86_64_v3
- lkssnb4 ^libtool@2.4.7%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- es32djr ^findutils@4.10.0%gcc@10.5.0 build_system=autotools patches=440b954 arch=linux-centos7-x86_64_v3
- ci2rgez ^mpc@1.3.1%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- eud6xo6 ^mpfr@4.2.1%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- wtqikvz ^autoconf-archive@2023.02.20%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- ymbyxkm ^perl@5.40.0%gcc@10.5.0+cpanm+opcode+open+shared+threads build_system=generic arch=linux-centos7-x86_64_v3
- jg2tcz6 ^berkeley-db@18.1.40%gcc@10.5.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-centos7-x86_64_v3
- kk4yfzc ^bzip2@1.0.8%gcc@10.5.0~debug~pic+shared build_system=generic arch=linux-centos7-x86_64_v3
- n5vjg4o ^gdbm@1.23%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- dn3waoi ^texinfo@7.1%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- mlabqye ^gettext@0.23.1%gcc@10.5.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-centos7-x86_64_v3
- 3juct62 ^libxml2@2.13.5%gcc@10.5.0~http+pic~python+shared build_system=autotools arch=linux-centos7-x86_64_v3
- k5kixla ^tar@1.35%gcc@10.5.0 build_system=autotools zip=pigz arch=linux-centos7-x86_64_v3
- uoke7ey ^pigz@2.8%gcc@10.5.0 build_system=makefile arch=linux-centos7-x86_64_v3
- hb7sdbq ^xz@5.4.6%gcc@10.5.0~pic build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- t2bvzdo ^ncurses@6.5%gcc@10.5.0~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-centos7-x86_64_v3
- nbn5uw7 ^pkgconf@2.3.0%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- zshmpvf ^zlib-ng@2.2.3%gcc@10.5.0+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-centos7-x86_64_v3
- irvproe ^zstd@1.5.6%gcc@10.5.0+programs build_system=makefile compression=none libs=shared,static arch=linux-centos7-x86_64_v3
- 3kdik75 gcc@12.4.0%gcc@10.5.0~binutils+bootstrap~graphite~mold~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages='c,c++,fortran' arch=linux-centos7-x86_64_v3
- pfthnhd ^diffutils@3.10%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- gy76bph ^gawk@5.3.1%gcc@10.5.0~nls build_system=autotools arch=linux-centos7-x86_64_v3
- 36sbhpd ^libsigsegv@2.14%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- hxvxqf7 ^readline@8.2%gcc@10.5.0 build_system=autotools patches=1ea4349,24f587b,3d9885e,5911a5b,622ba38,6c8adf8,758e2ec,79572ee,a177edc,bbf97f1,c7b45ff,e0013d9,e065038 arch=linux-centos7-x86_64_v3
- dsxg4mw ^gmp@6.3.0%gcc@10.5.0+cxx build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- necuzxw ^libtool@2.4.7%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 5cbih2i ^findutils@4.10.0%gcc@10.5.0 build_system=autotools patches=440b954 arch=linux-centos7-x86_64_v3
- 33kivvi ^mpc@1.3.1%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- e3a4kfe ^mpfr@4.2.1%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- l7q3nxb ^autoconf-archive@2023.02.20%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- r4v65ar ^perl@5.40.0%gcc@10.5.0+cpanm+opcode+open+shared+threads build_system=generic arch=linux-centos7-x86_64_v3
- 4uxwdlo ^berkeley-db@18.1.40%gcc@10.5.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-centos7-x86_64_v3
- acxlsss ^bzip2@1.0.8%gcc@10.5.0~debug~pic+shared build_system=generic arch=linux-centos7-x86_64_v3
- x4ld3s4 ^gdbm@1.23%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 5x6rzhs ^texinfo@7.1%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 6ui5fcm gcc@13.3.0%gcc@10.5.0~binutils+bootstrap~graphite~mold~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages='c,c++,fortran' arch=linux-centos7-x86_64_v3
- yr3rkj4 ^diffutils@3.10%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- ipzxe4m ^libiconv@1.17%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- hc3lbyh ^gawk@5.3.1%gcc@10.5.0~nls build_system=autotools arch=linux-centos7-x86_64_v3
- rsn4g4s ^libsigsegv@2.14%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- nyetdo6 ^readline@8.2%gcc@10.5.0 build_system=autotools patches=1ea4349,24f587b,3d9885e,5911a5b,622ba38,6c8adf8,758e2ec,79572ee,a177edc,bbf97f1,c7b45ff,e0013d9,e065038 arch=linux-centos7-x86_64_v3
- penejcy ^gcc-runtime@10.5.0%gcc@10.5.0 build_system=generic arch=linux-centos7-x86_64_v3
[e] aqxq2if ^glibc@2.17%gcc@10.5.0 build_system=autotools patches=be65fec,e179c43 arch=linux-centos7-x86_64_v3
- k4vjuxx ^gmake@4.4.1%gcc@10.5.0~guile build_system=generic arch=linux-centos7-x86_64_v3
- 23xkd3b ^gmp@6.3.0%gcc@10.5.0+cxx build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- 4w7gddn ^autoconf@2.72%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- xkhlzzq ^automake@1.16.5%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- u7qe7s5 ^m4@1.4.19%gcc@10.5.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-centos7-x86_64_v3
- 4v5dp44 ^libtool@2.4.7%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 5luujln ^findutils@4.10.0%gcc@10.5.0 build_system=autotools patches=440b954 arch=linux-centos7-x86_64_v3
- ivu277h ^mpc@1.3.1%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- 5to42p6 ^mpfr@4.2.1%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- vsujrbn ^autoconf-archive@2023.02.20%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- hhwndes ^perl@5.40.0%gcc@10.5.0+cpanm+opcode+open+shared+threads build_system=generic arch=linux-centos7-x86_64_v3
- b3nd6kn ^berkeley-db@18.1.40%gcc@10.5.0+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-centos7-x86_64_v3
- kg4jek7 ^bzip2@1.0.8%gcc@10.5.0~debug~pic+shared build_system=generic arch=linux-centos7-x86_64_v3
- u2e6fkz ^gdbm@1.23%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 2lye2fq ^texinfo@7.1%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- zritpaw ^gettext@0.23.1%gcc@10.5.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-centos7-x86_64_v3
- mdtxhyr ^tar@1.35%gcc@10.5.0 build_system=autotools zip=pigz arch=linux-centos7-x86_64_v3
- rjc4jyv ^pigz@2.8%gcc@10.5.0 build_system=makefile arch=linux-centos7-x86_64_v3
- 2muvkhf ^zlib-ng@2.2.3%gcc@10.5.0+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-centos7-x86_64_v3
- ob2urpy ^zstd@1.5.6%gcc@10.5.0+programs build_system=makefile compression=none libs=shared,static arch=linux-centos7-x86_64_v3
- kyh762i gcc@14.2.0%gcc@10.5.0~binutils+bootstrap~graphite~mold~nvptx~piclibs~profiled~strip build_system=autotools build_type=RelWithDebInfo languages='c,c++,fortran' arch=linux-centos7-x86_64_v3
- aofffrz git@2.47.0%gcc@10.5.0+man+nls+perl+subtree~svn~tcltk build_system=autotools arch=linux-centos7-x86_64_v3
- uy2sjoe ^autoconf@2.72%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- qxbfrmi ^automake@1.16.5%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 62a7wu6 ^expat@2.6.4%gcc@10.5.0+libbsd build_system=autotools arch=linux-centos7-x86_64_v3
- 7qkhovz ^libbsd@0.12.2%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- rjvj2vz ^libmd@1.0.4%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- trjllzb ^gettext@0.23.1%gcc@10.5.0+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-centos7-x86_64_v3
- rhzijzz ^tar@1.35%gcc@10.5.0 build_system=autotools zip=pigz arch=linux-centos7-x86_64_v3
- dwhahri ^pigz@2.8%gcc@10.5.0 build_system=makefile arch=linux-centos7-x86_64_v3
- gwcsp4a ^libiconv@1.17%gcc@10.5.0 build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- 26j7axb ^libidn2@2.3.7%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- lmuuwfx ^libunistring@1.2%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- u6azsks ^m4@1.4.19%gcc@10.5.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-centos7-x86_64_v3
- nyyfanm ^openssh@9.9p1%gcc@10.5.0+gssapi build_system=autotools arch=linux-centos7-x86_64_v3
- mtkbcuf ^krb5@1.21.3%gcc@10.5.0+shared build_system=autotools arch=linux-centos7-x86_64_v3
- 226347m ^bison@3.8.2%gcc@10.5.0~color build_system=autotools arch=linux-centos7-x86_64_v3
- jjw6w6t ^openssl@3.4.0%gcc@10.5.0~docs+shared build_system=generic certs=mozilla arch=linux-centos7-x86_64_v3
- zg4xzox ^ca-certificates-mozilla@2023-05-30%gcc@10.5.0 build_system=generic arch=linux-centos7-x86_64_v3
- vimukie ^pcre2@10.44%gcc@10.5.0~jit+multibyte+pic build_system=autotools arch=linux-centos7-x86_64_v3
- fcrzh2t gmake@4.4.1%gcc@10.5.0~guile build_system=generic arch=linux-centos7-x86_64_v3
- ezf4uxo gnupg@2.5.3%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- ln23n55 ^libassuan@3.0.1%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- ghqolrv ^libgcrypt@1.11.0%gcc@10.5.0 build_system=autotools patches=4e308ba arch=linux-centos7-x86_64_v3
- 6myligw ^libgpg-error@1.51%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 5cfgng4 ^libksba@1.6.7%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- vajq3nz ^npth@1.7%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
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- 2v4ptaf ^lua@5.3.6%gcc@10.5.0+shared build_system=makefile fetcher=curl arch=linux-centos7-x86_64_v3
- tkgioxu ^unzip@6.0%gcc@10.5.0 build_system=makefile patches=881d2ed,f6f6236 arch=linux-centos7-x86_64_v3
- rrs5ilq ^ncurses@6.5%gcc@10.5.0~symlinks+termlib abi=none build_system=autotools patches=7a351bc arch=linux-centos7-x86_64_v3
- v6mgemm ^ninja@1.12.1%gcc@10.5.0+re2c build_system=generic patches=93f4bb3 arch=linux-centos7-x86_64_v3
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- b6stjba ^perl-data-dumper@2.173%gcc@10.5.0 build_system=perl arch=linux-centos7-x86_64_v3
- t2plv3v ^pkgconf@2.3.0%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- 25yp3su ^python@3.13.1%gcc@10.5.0+bz2+ctypes+dbm~debug+libxml2+lzma~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic arch=linux-centos7-x86_64_v3
- nvjx7p5 ^expat@2.6.4%gcc@10.5.0+libbsd build_system=autotools arch=linux-centos7-x86_64_v3
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- nvhh32m ^openssl@3.4.0%gcc@10.5.0~docs+shared build_system=generic certs=mozilla arch=linux-centos7-x86_64_v3
- pj65pzk ^ca-certificates-mozilla@2023-05-30%gcc@10.5.0 build_system=generic arch=linux-centos7-x86_64_v3
- 7zmhyt7 ^sqlite@3.46.0%gcc@10.5.0+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-centos7-x86_64_v3
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- mqcnefx ^swig@4.1.1%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- vtoomjb ^pcre2@10.44%gcc@10.5.0~jit+multibyte+pic build_system=autotools arch=linux-centos7-x86_64_v3
- wz6ojms ^xz@5.4.6%gcc@10.5.0~pic build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
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- dqu6akt ^bc@1.07.1%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- rw5dnwd ^ed@1.4%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- kjnuq2t ^lua-luafilesystem@1.8.0%gcc@10.5.0 build_system=lua arch=linux-centos7-x86_64_v3
- asaw4rl ^lua-luaposix@36.1%gcc@10.5.0 build_system=lua arch=linux-centos7-x86_64_v3
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- ehxnxlt ^python@3.13.0%gcc@10.5.0+bz2+ctypes+dbm~debug+libxml2+lzma~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic arch=linux-centos7-x86_64_v3
- smdwikc ^bzip2@1.0.8%gcc@10.5.0~debug~pic+shared build_system=generic arch=linux-centos7-x86_64_v3
- u4jjvmn ^diffutils@3.10%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
- zwfwkqr ^expat@2.6.4%gcc@10.5.0+libbsd build_system=autotools arch=linux-centos7-x86_64_v3
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- f2nlsha ^xz@5.4.6%gcc@10.5.0~pic build_system=autotools libs=shared,static arch=linux-centos7-x86_64_v3
- fm5dtgi ^zlib-ng@2.2.1%gcc@10.5.0+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-centos7-x86_64_v3
- ousz6wb ^re2c@3.1%gcc@10.5.0 build_system=autotools arch=linux-centos7-x86_64_v3
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@kftsehk @becker33 @alalazo @haampie
Error message
No response
Information on your system
- Spack: 0.24.0.dev0 (6b13017)
- Python: 3.6.8
- Platform: linux-rhel8-cascadelake
General information
Steps to reproduce
Installing this small spack environment entirely from buildcache results in some packages depending on ghost specs. What I mean by "ghost" spec here is that some specs get installed which depend on non-installed dependency specs! This creates issues with generated module files, for instance, where loading dependents of the ghost spec results in attempts to load the non-existent dependency's modulefile.
I've wiped out my spack install entirely and re-installed the environment here a couple times. The first time there was a ghost glibc. The second attempt at wiping+re-installing resulted in the prior missing glibc now being installed, but now there was a ghost libxml2.
For instance, here is how I installed this environment:
The concretization log shows four
libxml2's in the DAG:With the environment installed, only three of these
libxml2's were installed:Note above we are missing
libxml2 /etomzyn. Butlibxml2 /etomzynhas installed dependents!Thus, if I generate modules and then try
module loadfor one of the dependents of this ghostlibxml2, we see the following errors:Oddly, if I query Spack for the installed dependencies of
llvm@19.1.7it showslibxml /etomzynas installed!Spack environment:
Concretization
@kftsehk @becker33 @alalazo @haampie
Error message
No response
Information on your system
General information
spack debug reportand reported the version of Spack/Python/Platform