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Broken Python3 on OpenSUSE, lib-dynload not correctly linked #39551

@DanielYang59

Description

@DanielYang59

Steps to reproduce the issue

Install py-pip (dependency of amdlibm) with [email protected]:

$ spack install py-pip %aocc
==> Warning: config:terminal_title has been replaced by install_status and is ignored
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/bzip2-1.0.8-q4pqsh3rxddsvyeuoc4umnhp4fbq3fcc
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/libmd-1.0.4-lp7x5tmamdnni6ccsick632krdghn4rl
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/ncurses-6.4-twp7yf3grnnzv3whbfr3fmccaml2s5ut
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/libiconv-1.17-xo2d4zaqgk4zq54eeic2sd6jxjhbxvuy
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/xz-5.4.1-huprvmsxzdvqjt4wiymsravg6ktpretm
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/zlib-ng-2.1.3-52s7eq32xbgfb2ecxnytevwzjfextkwo
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/zstd-1.5.5-knlbullsxnlliav3ee24osy35foxd26b
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/libffi-3.4.4-lqb7gtbxs7ugk2qj5z3eompbhiipra7k
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/libxcrypt-4.4.35-vyjg3panmbji2dy6oxo2iwvmvbm6tmr7
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/util-linux-uuid-2.38.1-p7rabtpzawmfnfxq5izkas34umhvtppj
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/libbsd-0.11.7-7cwjeplhcnehfrravoluexflx6rok44s
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/readline-8.2-so6tfuvqypsh7axma25ftc3kkroykzb4
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/pigz-2.7-rh55xrdkycsoipc7dlak6bgx2j3pmk3b
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/openssl-3.1.2-jufrpmzekubxplnjtioe3n4xri4zpjcr
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/libxml2-2.10.3-kcosc37y57aqexfzhvtjghvo2lxiwlve
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/expat-2.5.0-n3z6tlhhz3va2d2ympka6pz4jexp2sra
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/sqlite-3.42.0-ioreb5arslq7q7iy6m4bmyc6o4juiju4
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/gdbm-1.23-4rs5sb5jp4ohcu42kxqaqjcuijwm6wqe
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/tar-1.34-dztpp3xiyjxd4dthstdihajji24s7v4x
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/gettext-0.21.1-lvmu6twonklvtbhalkpccroswh6xtze2
[+] /home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp
==> Installing py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77 [22/22]
==> No binary for py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77 found: installing from source
Could not find platform dependent libraries <exec_prefix>
Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>]
==> Using cached archive: /var/tmp/yanghaoyu/spack-cache/_source-cache/archive/3e/3ef6ac33239e4027d9a5598a381b9d30880a1477e50039db2eac6e8a8f6d1b18
==> No patches needed for py-pip
==> py-pip: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
    '/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/bin/python3.10' '/tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-src/pip-23.1.2-py3-none-any.whl/pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77' '/tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-src/pip-23.1.2-py3-none-any.whl'
See build log for details:
  /tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-build-out.txt
$ spack spec -I py-pip
==> Warning: config:terminal_title has been replaced by install_status and is ignored
Input spec
--------------------------------
 -   py-pip

Concretized
--------------------------------
 -   [email protected]%[email protected] build_system=generic arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=0d98e93,7d40923,f2fd060 arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]~debug~pic+shared build_system=generic arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]+libbsd build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]                  ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2+tar+xz build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected] build_system=autotools libs=shared,static arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected]~python build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected] build_system=autotools zip=pigz arch=linux-opensusetumbleweed2.38-zen3
[+]                  ^[email protected]%[email protected] build_system=makefile arch=linux-opensusetumbleweed2.38-zen3
[+]                  ^[email protected]%[email protected]+programs build_system=makefile compression=none libs=shared,static arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]~obsolete_api build_system=autotools patches=4885da3 arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected]+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-opensusetumbleweed2.38-zen3
[+]                  ^[email protected]%[email protected]+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]~symlinks+termlib abi=none build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]~docs+shared build_system=generic certs=mozilla arch=linux-opensusetumbleweed2.38-zen3
[+]              ^ca-certificates-mozilla@2023-05-30%[email protected] build_system=generic arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools patches=bbf97f1 arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]~pic build_system=autotools libs=shared,static arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]+compat+opt build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
$ spack spec -I python
==> Warning: config:terminal_title has been replaced by install_status and is ignored
Input spec
--------------------------------
 -   python

Concretized
--------------------------------
[+]  [email protected]%[email protected]+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=0d98e93,7d40923,f2fd060 arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]~debug~pic+shared build_system=generic arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]+libbsd build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2+tar+xz build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools libs=shared,static arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]~python build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected] build_system=autotools zip=pigz arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected] build_system=makefile arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected]+programs build_system=makefile compression=none libs=shared,static arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]~obsolete_api build_system=autotools patches=4885da3 arch=linux-opensusetumbleweed2.38-zen3
[+]          ^[email protected]%[email protected]+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-opensusetumbleweed2.38-zen3
[+]              ^[email protected]%[email protected]+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]~symlinks+termlib abi=none build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]~docs+shared build_system=generic certs=mozilla arch=linux-opensusetumbleweed2.38-zen3
[+]          ^ca-certificates-mozilla@2023-05-30%[email protected] build_system=generic arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected] build_system=autotools patches=bbf97f1 arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected] build_system=autotools arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]~pic build_system=autotools libs=shared,static arch=linux-opensusetumbleweed2.38-zen3
[+]      ^[email protected]%[email protected]+compat+opt build_system=autotools arch=linux-opensusetumbleweed2.38-zen3

Error message

Error message
==> Installing py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77 [22/22]
==> No binary for py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77 found: installing from source
Could not find platform dependent libraries 
Consider setting $PYTHONHOME to [:]
==> Using cached archive: /var/tmp/yanghaoyu/spack-cache/_source-cache/archive/3e/3ef6ac33239e4027d9a5598a381b9d30880a1477e50039db2eac6e8a8f6d1b18
==> No patches needed for py-pip
==> py-pip: Executing phase: 'install'
==> Error: ProcessError: Command exited with status 1:
    '/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/bin/python3.10' '/tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-src/pip-23.1.2-py3-none-any.whl/pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77' '/tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-src/pip-23.1.2-py3-none-any.whl'
See build log for details:
  /tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-build-out.txt
Build Log
=> py-pip: Executing phase: 'install'
==> [2023-08-21-11:19:51.647349] '/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/bin/python3.10' '/tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-src/pip-23.1.2-py3-none-any.whl/pip' '-vvv' '--no-input' '--no-cache-dir' '--disable-pip-version-check' 'install' '--no-deps' '--ignore-installed' '--no-build-isolation' '--no-warn-script-location' '--no-index' '--prefix=/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77' '/tmp/yanghaoyu/spack-stage/spack-stage-py-pip-23.1.2-6j6wfgdu4xv4x6z5r56c4bdck3ekjs77/spack-src/pip-23.1.2-py3-none-any.whl'
Could not find platform dependent libraries 
Consider setting $PYTHONHOME to [:]
Traceback (most recent call last):
  File "", line 577, in _get_decompress_func
ModuleNotFoundError: No module named 'zlib'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "", line 625, in _get_data
  File "", line 580, in _get_decompress_func
zipimport.ZipImportError: can't decompress data; zlib not available

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/lib/python3.10/runpy.py", line 157, in _get_module_details
    code = loader.get_code(mod_name)
  File "", line 196, in get_code
  File "", line 759, in _get_module_code
  File "", line 627, in _get_data
zipimport.ZipImportError: can't decompress data; zlib not available

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/lib/python3.10/runpy.py", line 189, in _run_module_as_main
    mod_name, mod_spec, code = _get_main_module_details(_Error)
  File "/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/lib/python3.10/runpy.py", line 238, in _get_main_module_details
    return _get_module_details(main_name)
  File "/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/lib/python3.10/runpy.py", line 159, in _get_module_details
    raise error(format(e)) from e
ImportError: can't decompress data; zlib not available
Running Python3 Directly
$ which python3
/home/yanghaoyu/opt/spack/packages/linux-opensusetumbleweed2.38-zen3/aocc-4.1.0/python-3.10.12-fvclniug6pdjl475gjvkkcfjmh4cpnyp/bin/python3. 
$ python3
Could not find platform dependent libraries 
Consider setting $PYTHONHOME to [:]
Python 3.10.12 (main, Aug 21 2023, 10:11:54) [Clang 16.0.3 (CLANG: AOCC_4.1.0-Build#270 2023_07_10)] on linux
Type "help", "copyright", "credits" or "license" for more information.
Traceback (most recent call last):
  File "/etc/pythonstart", line 7, in 
    import readline
ModuleNotFoundError: No module named 'readline'

Information on your system

$ spack debug report:
* **Spack:** 0.21.0.dev0 (c9ec5fb9ac565033c7db643f0b51da5dc9315ac0)
* **Python:** 3.11.4
* **Platform:** linux-opensusetumbleweed2.38-zen3
==> Warning: config:terminal_title has been replaced by install_status and is ignored
* **Concretizer:** clingo

Additional information

Python maintainers:
@adamjstewart @scheibelp @skosukhin

py-pip maintainers:
@adamjstewart @pradyunsg

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

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