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mpiexec Missing on MacOS 12.0 #8

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langmm opened this issue Jan 5, 2023 · 4 comments
Closed
1 task done

mpiexec Missing on MacOS 12.0 #8

langmm opened this issue Jan 5, 2023 · 4 comments
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@langmm
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langmm commented Jan 5, 2023

Solution to issue cannot be found in the documentation.

  • I checked the documentation.

Issue

In testing an installation on Github Actions (example job), I have encountered an issue where after installing mpi via conda on a job running the MacOS 12.0 image, the mpi executables (mpiexec, mpicc, etc.) cannot be located. conda reports that mpi is installed (along with mpich by default), but inspection of the conda bin directory confirms that they are not present. This problem does not occur on the MacOS 11.0 image and occurs with both mpich and openmpi when specified explicitly. I am not sure if this is an issue with the runner image or the conda installation and will redirect if this is not the right place to report, but I am starting here as I believe this metapackage is used by both mpich and openmpi. Thanks! - Meagan

Installed packages

# packages in environment at /usr/local/miniconda/envs/test:
#
# Name                    Version                   Build  Channel
_r-mutex                  1.0.1               anacondar_1    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
brotli                    1.0.9                hb7f2c08_8    conda-forge
brotli-bin                1.0.9                hb7f2c08_8    conda-forge
brotlipy                  0.7.0           py37h69ee0a8_1004    conda-forge
bwidget                   1.9.14               h694c41f_1    conda-forge
bzip2                     1.0.8                h0d85af4_4    conda-forge
ca-certificates           2022.9.24            h033912b_0    conda-forge
cairo                     1.16.0            hec6a9b0_1003    conda-forge
ccache                    4.3                  hfceccdb_1    conda-forge
cctools                   949.0.1              h22b1bf0_0    conda-forge
cctools_osx-64            949.0.1              h5ba7a2e_0    conda-forge
certifi                   2022.9.24          pyhd8ed1ab_0    conda-forge
cffi                      1.15.1           py37h7346b73_1    conda-forge
charset-normalizer        2.1.1              pyhd8ed1ab_0    conda-forge
chevron                   0.14.0             pyhd3deb0d_1    conda-forge
clang                     9.0.1           default_ha9b4ba2_5    conda-forge
clang-9                   9.0.1           default_hf139c7e_5    conda-forge
clang_osx-64              9.0.1                h05bbb7f_2    conda-forge
clangxx                   9.0.1           default_he082bbe_5    conda-forge
clangxx_osx-64            9.0.1                h05bbb7f_2    conda-forge
click                     8.1.3            py37hf985489_0    conda-forge
cmake                     3.17.0               hd28f656_0    conda-forge
codecov                   2.1.11             pyhd3deb0d_0    conda-forge
compiler-rt               9.0.1                h6a512c6_3    conda-forge
compiler-rt_osx-64        9.0.1                h99342c6_3    conda-forge
coverage                  6.5.0            py37h8052db5_0    conda-forge
cryptography              38.0.2           py37h1818b49_1    conda-forge
curl                      7.68.0               h8754def_0    conda-forge
cycler                    0.11.0             pyhd8ed1ab_0    conda-forge
czmq                      4.2.1                h3dbecb7_4    conda-forge
exceptiongroup            1.0.4              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                hf0c8a7f_0    conda-forge
flake8                    5.0.4              pyhd8ed1ab_0    conda-forge
flaky                     3.7.0              pyh9f0ad1d_0    conda-forge
flask                     2.2.2              pyhd8ed1ab_0    conda-forge
fontconfig                2.13.1            h10f422b_1005    conda-forge
fonttools                 4.38.0           py37h8052db5_0    conda-forge
fortran-compiler          1.1.2                hcc3dc05_0    conda-forge
freetype                  2.12.1               h3f81eb7_0    conda-forge
fribidi                   1.0.10               hbcb3906_0    conda-forge
gettext                   0.21.1               h8a4c099_0    conda-forge
gfortran_impl_osx-64      7.5.0               hdadd0f8_23    conda-forge
gfortran_osx-64           7.5.0               h18f7dce_15    conda-forge
git                       2.38.1          pl5321h00ebd2c_1    conda-forge
gitdb                     4.0.9              pyhd8ed1ab_0    conda-forge
gitpython                 3.1.29             pyhd8ed1ab_0    conda-forge
glib                      2.74.1               hbc0c0cd_1    conda-forge
glib-tools                2.74.1               hbc0c0cd_1    conda-forge
gmp                       6.2.1                h2e338ed_0    conda-forge
gmpy2                     2.1.2            py37h60f582e_0    conda-forge
graphite2                 1.3.13            h2e338ed_1001    conda-forge
gsl                       2.5                  ha2d443c_1    conda-forge
harfbuzz                  2.4.0                hd8d2a14_3    conda-forge
icu                       64.2                 h6de7cb9_1    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
importlib-metadata        4.11.4           py37hf985489_0    conda-forge
importlib_metadata        4.11.4               hd8ed1ab_0    conda-forge
iniconfig                 1.1.1              pyh9f0ad1d_0    conda-forge
isl                       0.22.1               hb1e8313_2    conda-forge
itsdangerous              2.1.2              pyhd8ed1ab_0    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jpeg                      9e                   hac89ed1_2    conda-forge
jsonschema                3.2.0              pyhd8ed1ab_3    conda-forge
kiwisolver                1.4.4            py37h229a17a_0    conda-forge
krb5                      1.16.4               h1752a42_0    conda-forge
lcms2                     2.14                 h90f4b2a_0    conda-forge
ld64                      530                           0    conda-forge
ld64_osx-64               530                  h3c32e8a_0    conda-forge
lerc                      4.0.0                hb486fe8_0    conda-forge
libblas                   3.9.0                8_openblas    conda-forge
libbrotlicommon           1.0.9                hb7f2c08_8    conda-forge
libbrotlidec              1.0.9                hb7f2c08_8    conda-forge
libbrotlienc              1.0.9                hb7f2c08_8    conda-forge
libcblas                  3.9.0                8_openblas    conda-forge
libclang-cpp9             9.0.1           default_hf139c7e_5    conda-forge
libcurl                   7.68.0               h709d2b2_0    conda-forge
libcxx                    14.0.6               hccf4f1f_0    conda-forge
libdeflate                1.14                 hb7f2c08_0    conda-forge
libedit                   3.1.20191231         h0678c8f_2    conda-forge
libffi                    3.4.2                h0d85af4_5    conda-forge
libgfortran               4.0.0           7_5_0_h1a10cd1_23    conda-forge
libgfortran-devel_osx-64  7.5.0               h1a10cd1_23    conda-forge
libgfortran4              7.5.0               h1a10cd1_23    conda-forge
libglib                   2.74.1               h4c723e1_1    conda-forge
libiconv                  1.17                 hac89ed1_0    conda-forge
liblapack                 3.9.0                8_openblas    conda-forge
libllvm9                  9.0.1           default_h2671707_7    conda-forge
libopenblas               0.3.12          openmp_h63d9170_1    conda-forge
libpng                    1.6.38               ha978bb4_0    conda-forge
libsodium                 1.0.18               hbcb3906_1    conda-forge
libsqlite                 3.40.0               ha978bb4_0    conda-forge
libssh2                   1.10.0               h7535e13_3    conda-forge
libtiff                   4.4.0                hdb44e8a_4    conda-forge
libuuid                   2.32.1            h35c211d_1000    conda-forge
libuv                     1.44.2               hac89ed1_0    conda-forge
libwebp-base              1.2.4                h775f41a_0    conda-forge
libxcb                    1.13              h0d85af4_1004    conda-forge
libxml2                   2.9.10               h53d96d6_0    conda-forge
libzlib                   1.2.13               hfd90126_4    conda-forge
llvm-openmp               15.0.5               h61d9ccf_0    conda-forge
llvm-tools                9.0.1           default_h2671707_7    conda-forge
lz4                       4.0.0            py37hf9031b7_2    conda-forge
lz4-c                     1.9.3                he49afe7_1    conda-forge
make                      4.3                  h22f3db7_1    conda-forge
markupsafe                2.1.1            py37h69ee0a8_1    conda-forge
matplotlib-base           3.5.3            py37h3748cd6_2    conda-forge
mccabe                    0.7.0              pyhd8ed1ab_0    conda-forge
mpc                       1.2.1                hbb51d92_0    conda-forge
mpfr                      4.1.0                h0f52abe_1    conda-forge
mpi                       1.0                       mpich    conda-forge
mpi4py                    3.1.3            py37h483e1c3_2    conda-forge
mpich                     4.0.3                external_0    conda-forge
mpmath                    1.2.1              pyhd8ed1ab_0    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncurses                   6.3                  h96cf925_1    conda-forge
nose                      1.3.7                   py_1006    conda-forge
numpy                     1.21.6           py37h345d48f_0    conda-forge
openjpeg                  2.5.0                h5d0d7b0_1    conda-forge
openssl                   1.1.1s               hfd90126_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.3.5            py37h5b83a90_0    conda-forge
pango                     1.42.4               haa940fe_4    conda-forge
pcre                      8.45                 he49afe7_0    conda-forge
pcre2                     10.40                h1c4e4bc_0    conda-forge
perl                      5.32.1          2_h0d85af4_perl5    conda-forge
pillow                    9.2.0            py37ha6ba2b9_2    conda-forge
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pixman                    0.38.0            h01d97ff_1003    conda-forge
pluggy                    1.0.0            py37hf985489_3    conda-forge
psutil                    5.9.3            py37h8052db5_0    conda-forge
pthread-stubs             0.4               hc929b4f_1001    conda-forge
pycodestyle               2.9.1              pyhd8ed1ab_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyflakes                  2.5.0              pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyopenssl                 22.1.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyperf                    2.4.1            py37hf985489_0    conda-forge
pyrsistent                0.18.1           py37h69ee0a8_1    conda-forge
pysocks                   1.7.1            py37hf985489_5    conda-forge
pytest                    7.2.0            py37hf985489_0    conda-forge
pytest-cov                4.0.0              pyhd8ed1ab_0    conda-forge
pytest-mpi                0.6                pyhd8ed1ab_0    conda-forge
pytest-repeat             0.9.1              pyhd8ed1ab_0    conda-forge
pytest-rerunfailures      10.2               pyhd8ed1ab_0    conda-forge
pytest-timeout            2.1.0              pyhd8ed1ab_0    conda-forge
python                    3.7.12          haf480d7_100_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-rapidjson          1.9              py37hac51a3e_0    conda-forge
python_abi                3.7                     2_cp37m    conda-forge
pytz                      2022.6             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0              py37h69ee0a8_4    conda-forge
pyzmq                     24.0.1           py37haa7bc41_0    conda-forge
r-base                    3.5.1             hc03ab29_1012    conda-forge
r-bit                     1.1_15.2          r35h17f1fa6_0    conda-forge
r-bit64                   0.9_7           r35h159158b_1001    conda-forge
r-jsonlite                1.6.1             r35h17f1fa6_0    conda-forge
r-lattice                 0.20_41           r35h17f1fa6_1    conda-forge
r-matrix                  1.2_18            r35h26f5615_2    conda-forge
r-r6                      2.4.1             r35h6115d3f_0    conda-forge
r-rappdirs                0.3.1           r35h17f1fa6_1003    conda-forge
r-rcpp                    1.0.4.6           r35hc5da6b9_0    conda-forge
r-reticulate              1.15              r35hc5da6b9_0    conda-forge
r-units                   0.6_6             r35hc5da6b9_0    conda-forge
r-zeallot                 0.1.0           r35h6115d3f_1001    conda-forge
readline                  8.1.2                h3899abd_0    conda-forge
requests                  2.28.1             pyhd8ed1ab_1    conda-forge
rhash                     1.4.3                hac89ed1_0    conda-forge
scipy                     1.5.3            py37h04d6967_0    conda-forge
setuptools                59.8.0           py37hf985489_1    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     3.0.5              pyh44b312d_0    conda-forge
sqlite                    3.40.0               h9ae0607_0    conda-forge
sympy                     1.10.1           py37hf985489_1    conda-forge
sysv_ipc                  1.1.0            py37h69ee0a8_4    conda-forge
tapi                      1000.10.8            h879752b_4    conda-forge
tk                        8.6.12               h5dbffcc_0    conda-forge
tktable                   2.10                 h49f0cf7_3    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
trimesh                   3.16.4             pyhd8ed1ab_0    conda-forge
typing-extensions         4.4.0                hd8ed1ab_0    conda-forge
typing_extensions         4.4.0              pyha770c72_0    conda-forge
udunits2                  2.2.28               h06ef574_0    conda-forge
unicodedata2              14.0.0           py37h69ee0a8_1    conda-forge
unyt                      2.8.0                      py_0    conda-forge
urllib3                   1.26.11            pyhd8ed1ab_0    conda-forge
werkzeug                  2.2.2              pyhd8ed1ab_0    conda-forge
wheel                     0.38.4             pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.9                h35c211d_0    conda-forge
xorg-libxdmcp             1.1.3                h35c211d_0    conda-forge
xz                        5.2.6                h775f41a_0    conda-forge
yaml                      0.2.5                h0d85af4_2    conda-forge
yggdrasil                 1.8.4           py37r35hae5c3c8_0    file://usr/local/miniconda/conda-bld
zeromq                    4.3.4                he49afe7_1    conda-forge
zipp                      3.10.0             pyhd8ed1ab_0    conda-forge
zlib                      1.2.13               hfd90126_4    conda-forge
zstd                      1.5.2                hfa58983_4    conda-forge

Environment info

active environment : test
    active env location : /usr/local/miniconda/envs/test
            shell level : 2
       user config file : /Users/runner/.condarc
 populated config files : /Users/runner/.condarc
          conda version : 22.11.1
    conda-build version : 3.23.3
         python version : 3.9.15.final.0
       virtual packages : __archspec=1=x86_64
                          __osx=12.6.2=0
                          __unix=0=0
       base environment : /usr/local/miniconda  (writable)
      conda av data dir : /usr/local/miniconda/etc/conda
  conda av metadata url : None
           channel URLs : file://usr/local/miniconda/conda-bld/osx-64
                          file://usr/local/miniconda/conda-bld/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /Users/runner/conda_pkgs_dir
       envs directories : /usr/local/miniconda/envs
                          /Users/runner/.conda/envs
               platform : osx-64
             user-agent : conda/22.11.1 requests/2.28.1 CPython/3.9.15 Darwin/21.6.0 OSX/12.6.2
                UID:GID : 501:20
             netrc file : None
           offline mode : False
@langmm langmm added the bug Something isn't working label Jan 5, 2023
@langmm
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langmm commented Jan 6, 2023

An update, I was mistaken, the same issue also occurs on the MacOS 11.0 image

@langmm
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langmm commented Jan 6, 2023

I looks like this is an issue with the image modifying the Python path and is not specific to MPI.

@langmm langmm closed this as completed Jan 6, 2023
@leofang
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leofang commented Jan 6, 2023

@langmm This is the wrong repo to report to. The mpi package here is just a mutex, to ensure you only have either openmpi or mpich installed, as they cannot coexist.

The issue in your env is this

mpich                     4.0.3                external_0    conda-forge

for some reason you installed the "empty" mpich package (note the build string says "external"). It does not come with the actual library or executable. It's there only to satisfy the conda solver requirement, so that users can use their local MPICH installation. You should reinstall your mpich.

@langmm
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langmm commented Jan 6, 2023

@leofang Thank you for the help! I had not realized it was the empty version

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