CDT packages are broken for s390x

[pradghos]

There couple of issues in CDT packages for s390x platform -

1. Link broken for java-1.8.0-openjdk-headless-cos7-s390x

conda install java-1.8.0-openjdk-headless-cos7-s390x
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.11.0
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /opt/miniconda3/envs/debug

  added / updated specs:
    - java-1.8.0-openjdk-headless-cos7-s390x


The following NEW packages will be INSTALLED:

  copy-jdk-configs-~ pkgs/main/noarch::copy-jdk-configs-cos7-s390x-3.3-2
  java-1.8.0-openjd~ pkgs/main/noarch::java-1.8.0-openjdk-headless-cos7-s390x-1.8.0.242.b08-2


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(699): An error occurred while installing package 'defaults::java-1.8.0-openjdk-headless-cos7-s390x-1.8.0.242.b08-2'.
Rolling back transaction: done

[Errno 2] No such file or directory: '/opt/miniconda3/pkgs/java-1.8.0-openjdk-headless-cos7-s390x-1.8.0.242.b08-2/s390x-conda-linux-gnu/sysroot/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-1.el7.s390x/jre/lib/tzdb.dat'
()


ls -l /opt/miniconda3/pkgs/java-1.8.0-openjdk-headless-cos7-s390x-1.8.0.242.b08-2/s390x-conda-linux-gnu/sysroot/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-1.el7.s390x/jre/lib/tzdb.dat
lrwxrwxrwx. 1 root root 30 Jan 29  2021 /opt/miniconda3/pkgs/java-1.8.0-openjdk-headless-cos7-s390x-1.8.0.242.b08-2/s390x-conda-linux-gnu/sysroot/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.242.b08-1.el7.s390x/jre/lib/tzdb.dat -> /usr/share/javazi-1.8/tzdb.dat

2. SYSROOT path issue for CDT package -

Let take an example for java-1.8.0-openjdk-devel-cos7-s390x

Install java-1.8.0-openjdk-devel-cos7-s390x -

Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.11.0
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /opt/miniconda3/envs/debug

  added / updated specs:
    - java-1.8.0-openjdk-devel-cos7-s390x


The following NEW packages will be INSTALLED:

  chkconfig-cos7-s3~ pkgs/main/noarch::chkconfig-cos7-s390x-1.7.4-2
  java-1.8.0-openjd~ pkgs/main/noarch::java-1.8.0-openjdk-devel-cos7-s390x-1.8.0.242.b08-2


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

After installation :-

[root@infare1 jvm]# pwd
/opt/miniconda3/envs/debug/s390x-conda-linux-gnu/sysroot/usr/lib/jvm
[root@infare1 jvm]# ls
java-1.8.0-openjdk-1.8.0.242.b08-1.el7.s390x
[root@infare1 jvm]#

Scenario -

During any package build when CDT and toolchain both coexists in same build environment -

As part of the toolchain installation binutils_impl_linux-s390x will get installed

conda install binutils_impl_linux-s390x
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.11.0
  latest version: 4.12.0

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /opt/miniconda3/envs/debug

  added / updated specs:
    - binutils_impl_linux-s390x


The following NEW packages will be INSTALLED:

  binutils_impl_lin~ pkgs/main/linux-s390x::binutils_impl_linux-s390x-2.33.1-hb8c1d61_19
  kernel-headers_li~ pkgs/main/noarch::kernel-headers_linux-s390x-3.10.0-hc325423_10
  sysroot_linux-s39~ pkgs/main/noarch::sysroot_linux-s390x-2.17-h7ca9e3a_10


Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Both the packages installed successfully -

conda list java-1.8.0-openjdk-devel
# packages in environment at /opt/miniconda3/envs/debug:
#
# Name                    Version                   Build  Channel
java-1.8.0-openjdk-devel-cos7-s390x 1.8.0.242.b08                 2
conda list binutils_impl_linux
# packages in environment at /opt/miniconda3/envs/debug:
#
# Name                    Version                   Build  Channel
binutils_impl_linux-s390x 2.33.1              hb8c1d61_19

However, lib is now linked to lib64

ls -l /opt/miniconda3/envs/debug/s390x-conda-linux-gnu/sysroot/usr/lib/jvm
ls: cannot access '/opt/miniconda3/envs/debug/s390x-conda-linux-gnu/sysroot/usr/lib/jvm': No such file or directory

ls -l
total 12
drwxr-xr-x.  2 root root  205 Apr 13 04:58 bin
drwxr-xr-x. 32 root root 4096 Apr 13 04:58 include
lrwxrwxrwx.  1 root root    5 Apr 13 04:58 lib -> lib64
drwxr-xr-x.  5 root root 4096 Apr 13 04:58 lib64
drwxr-xr-x.  3 root root   21 Apr 13 04:58 libexec
drwxr-xr-x.  2 root root  181 Apr 13 04:58 sbin
drwxr-xr-x. 13 root root  163 Apr 13 04:58 share

So jvm and other related directory related to java-1.8.0-openjdk-devel went missing.

[pradghos]

JFYI @potula-chandra @ravigumm

[potula-chandra]

This is an important yet urgent issue that needs a quick help in fixing the SYSROOT path of a package and at the same time feedstock (like binutils above) should not override the folder or directory which already populated (in this case lib directory)

[pradghos]

@chenghlee @katietz : Could you please have a look ? Thank you very much !

[Moises1200]

Hello Team,

Wanted to touch base to check if we had an update on this GH issue.