Linking fails with "command substitution: ignored null byte in input"

[chrisburr]

Running micromamba create --name test python on a ppc64le machine is failing with a bunch of messages of the form:

Linking _libgcc_mutex-0.1-conda_forge
/tmp/mambafdkxcsXRzEe: line 44: warning: command substitution: ignored null byte in input
/tmp/mambafdkxcsXRzEe: line 5: /m100/home/userexternal/cburr000/micromamba/envs/test//._libgcc_mutex-post-link.sh: No such file or directory

Linking ld_impl_linux-ppc64le-2.36.1-ha35d02b_2
/tmp/mambafbjLq9OjFa4: line 44: warning: command substitution: ignored null byte in input
/tmp/mambafbjLq9OjFa4: line 5: /m100/home/userexternal/cburr000/micromamba/envs/test//.ld_impl_linux-ppc64le-post-link.sh: No such file or directory

before eventually ending with:

Linking wheel-0.37.1-pyhd8ed1ab_0
Clobberwarning: $CONDA_PREFIX//python3.10/site-packages/wheel-0.37.1-py3.8.egg-info/PKG-INFO
warning  Clobberwarning: $CONDA_PREFIX/
critical Directory not empty: '/m100/home/userexternal/cburr000/micromamba/envs/test/

So far when debugging I've found that the PATH variable from micromamba shell is having three null bytes inserted (at approximately position 0x49):

$ micromamba shell --shell bash activate /m100/home/userexternal/cburr000/envs/test1 | hexdump -C
00000000  50 53 31 3d 27 28 74 65  73 74 31 29 20 27 0a 65  |PS1='(test1) '.e|
00000010  78 70 6f 72 74 20 50 41  54 48 3d 27 2f 6d 31 30  |xport PATH='/m10|
00000020  30 2f 68 6f 6d 65 2f 75  73 65 72 65 78 74 65 72  |0/home/userexter|
00000030  6e 61 6c 2f 63 62 75 72  72 30 30 30 2f 65 6e 76  |nal/cburr000/env|
00000040  73 2f 74 65 73 74 31 2f  00 00 00 3a 2f 6d 31 30  |s/test1/...:/m10|
00000050  30 2f 68 6f 6d 65 2f 75  73 65 72 65 78 74 65 72  |0/home/userexter|
00000060  6e 61 6c 2f 63 62 75 72  72 30 30 30 2f 6d 69 63  |nal/cburr000/mic|
00000070  72 6f 6d 61 6d 62 61 2f  63 6f 6e 64 61 62 69 6e  |romamba/condabin|
00000080  3a 2f 6d 31 30 30 2f 68  6f 6d 65 2f 75 73 65 72  |:/m100/home/user|

I see the same if I use a different directory or --name test.

Any ideas?

[wolfv]

can you post what you have in $MAMBA_ROOT_PREFIX and $HOME

Also I am wondering -- did you install micromamba using conda or mamba? -- i.e. was the prefix replaced?

And maybe you can show thte output of micromamba info?

[chrisburr]

Changing $HOME to be an empty directory and cleaning the environment doesn't help.

Also I am wondering -- did you install micromamba using conda or mamba? -- i.e. was the prefix replaced?

Indeed it was installed with mamba. https://micromamba.snakepit.net/api/micromamba/linux-ppc64le/latest works without issue.

From mamba

[cburr000@login01 ~]$ /m100/home/userexternal/cburr000/.local/bin/micromamba info

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/


            environment : None (not found)
           env location : -
      user config files : /tmp/cburr/.mambarc
 populated config files :
       libmamba version : 0.21.2
     micromamba version : 0.21.2
           curl version : libcurl/7.81.0 OpenSSL/1.1.1l zlib/1.2.11 libssh2/1.10.0 nghttp2/1.46.0
     libarchive version : libarchive 3.3.3 zlib/1.2.11 liblzma/5.2.5 bz2lib/1.0.8 liblz4/1.9.2 libzstd/1.4.5
       virtual packages : __unix=0=0
                          __linux=4.18.0=0
                          __glibc=2.28=0
                          __archspec=1=ppc64le
                          __cuda=11.0=0
               channels :
       base environment : /tmp/cburr/micromamba
               platform : linux-ppc64le
[cburr000@login01 ~]$ /m100/home/userexternal/cburr000/.local/bin/micromamba shell --shell bash activate /m100/home/userexternal/cburr000/envs/test1 | hexdump -C | head -n6
00000000  50 53 31 3d 27 28 74 65  73 74 31 29 20 27 0a 65  |PS1='(test1) '.e|
00000010  78 70 6f 72 74 20 50 41  54 48 3d 27 2f 6d 31 30  |xport PATH='/m10|
00000020  30 2f 68 6f 6d 65 2f 75  73 65 72 65 78 74 65 72  |0/home/userexter|
00000030  6e 61 6c 2f 63 62 75 72  72 30 30 30 2f 65 6e 76  |nal/cburr000/env|
00000040  73 2f 74 65 73 74 31 2f  00 00 00 3a 2f 74 6d 70  |s/test1/...:/tmp|
00000050  2f 63 62 75 72 72 2f 6d  69 63 72 6f 6d 61 6d 62  |/cburr/micromamb|

From micromamba.snakepit.net

[cburr000@login01 ~]$ bin/micromamba info

                                           __
          __  ______ ___  ____ _____ ___  / /_  ____ _
         / / / / __ `__ \/ __ `/ __ `__ \/ __ \/ __ `/
        / /_/ / / / / / / /_/ / / / / / / /_/ / /_/ /
       / .___/_/ /_/ /_/\__,_/_/ /_/ /_/_.___/\__,_/
      /_/


            environment : None (not found)
           env location : -
      user config files : /tmp/cburr/.mambarc
 populated config files :
       libmamba version : 0.21.2
     micromamba version : 0.21.2
           curl version : libcurl/7.81.0 OpenSSL/1.1.1l zlib/1.2.11 libssh2/1.10.0 nghttp2/1.46.0
     libarchive version : libarchive 3.3.3 zlib/1.2.11 liblzma/5.2.5 bz2lib/1.0.8 liblz4/1.9.2 libzstd/1.4.5
       virtual packages : __unix=0=0
                          __linux=4.18.0=0
                          __glibc=2.28=0
                          __archspec=1=ppc64le
                          __cuda=11.0=0
               channels :
       base environment : /tmp/cburr/micromamba
               platform : linux-ppc64le
[cburr000@login01 ~]$ bin/micromamba shell --shell bash activate /m100/home/userexternal/cburr000/envs/test1 | hexdump -C | head -n6
00000000  50 53 31 3d 27 28 74 65  73 74 31 29 20 27 0a 65  |PS1='(test1) '.e|
00000010  78 70 6f 72 74 20 50 41  54 48 3d 27 2f 6d 31 30  |xport PATH='/m10|
00000020  30 2f 68 6f 6d 65 2f 75  73 65 72 65 78 74 65 72  |0/home/userexter|
00000030  6e 61 6c 2f 63 62 75 72  72 30 30 30 2f 65 6e 76  |nal/cburr000/env|
00000040  73 2f 74 65 73 74 31 2f  62 69 6e 3a 2f 74 6d 70  |s/test1/bin:/tmp|
00000050  2f 63 62 75 72 72 2f 6d  69 63 72 6f 6d 61 6d 62  |/cburr/micromamb|

[wolfv]

I think we need to prevent conda/mamba to replace the prefix in the micromamba executable :/ sorry for the trouble.

[hmaarrfk]

Do you know which package this occurs in?

[chrisburr]

I've only seen it in conda-forge/linux-ppc64le/micromamba-0.21.2-0.

[hmaarrfk]

is there somewhere in the source where string concatenatenation happens at a macro level (#define)?

[hmaarrfk]

somewhere when the prefix is passed in as a macro duing a test?

[wolfv]

@chrisburr I am assuming this is fixed now, right?

@hmaarrfk to be honest I don't really know where we have a hardcoded prefix ...

[chrisburr]

I am assuming this is fixed now, right?

Yup 👍