Unable to install MDTF from the current main branch
Closed this issue · 5 comments
Bug Severity
2 = Major problem that affects overall functionality, but that does not occur for all users (e.g., problems installing the framework with a specific Conda version, a framework option that causes one or more PODs to fail, or missing/incompatible Python modules).
Describe the bug
I started developing my POD few months ago. I was able to do the installation before. However, since I merged the latest commits on main branch, when I do installation, I encounter an error related to mamba installation.
Steps To Reproduce
The setup failed both on Linux and Mac (which previous version worked before). I executed:
$ ./src/conda/conda_env_setup.sh --all --conda_root /home/[username]/miniconda3 --env_dir /home/[username]/miniconda3/envsand then I encountered the error No module named 'conda.cliconda' from mamba installation. See "Log information and/or terminal output" for the error output from linux. The error from Mac is also the same (No module named 'conda.cliconda').
Environment
I have MDTF installed on both (1) my local Mac machine and (2) remote linux machine.
(1) Mac environment
- OS: iMac 3 GHz 6-Core Intel Core i5
- Conda version:
active environment : base
active env location : /Users/[username]/miniconda3
shell level : 1
user config file : /Users/[username]/.condarc
populated config files :
conda version : 23.5.2
conda-build version : not installed
python version : 3.11.4.final.0
virtual packages : __archspec=1=x86_64
__osx=10.16=0
__unix=0=0
base environment : /Users/[username]/miniconda3 (writable)
conda av data dir : /Users/[username]/miniconda3/etc/conda
conda av metadata url : None
channel URLs : 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/[username]/miniconda3/pkgs
/Users/[username]/.conda/pkgs
envs directories : /Users/[username]/miniconda3/envs
/Users/[username]/.conda/envs
platform : osx-64
user-agent : conda/23.5.2 requests/2.29.0 CPython/3.11.4 Darwin/22.6.0 OSX/10.16
UID:GID : 501:20
netrc file : None
offline mode : False
- branch name:
main
(2) Linux environment
- OS: Ubuntu 18.04
- Conda version:
active environment : base
active env location : /home/[username]/miniconda3
shell level : 1
user config file : /home/[username]/.condarc
populated config files :
conda version : 4.10.3
conda-build version : not installed
python version : 3.7.6.final.0
virtual packages : __cuda=12.0=0
__linux=4.15.0=0
__glibc=2.27=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/[username]/miniconda3 (writable)
conda av data dir : /home/[username]/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/[username]/miniconda3/pkgs
/home/[username]/.conda/pkgs
envs directories : /home/[username]/miniconda3/envs
/home/[username]/.conda/envs
platform : linux-64
user-agent : conda/4.10.3 requests/2.28.1 CPython/3.7.6 Linux/4.15.0-214-generic ubuntu/18.04.6 glibc/2.27
UID:GID : 1001:1001
netrc file : None
offline mode : False
- branch name:
main
Log information and/or terminal output
$ ./src/conda/conda_env_setup.sh --all --conda_root /home/[username]/miniconda3 --env_dir /home/[username]/miniconda3/envs
WARNING: user supplied CONDA_ROOT so unsetting existing CONDA_EXE
CONDA_ROOT set from command line
Looking for conda executable in /home/[username]/miniconda3
Found CONDA_EXE
_CONDA_EXE=/home/[username]/miniconda3/bin/conda
_CONDA_ROOT=/home/[username]/miniconda3
Installing envs into /home/[username]/miniconda3/envs
To use envs interactively, run "conda config --append envs_dirs /home/[username]/miniconda3/envs"
Couldn't find mamba executable; installing in temp environment.
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/[username]/miniconda3/envs/_MDTF_install_temp
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/[username]/miniconda3/envs/_MDTF_install_temp
added / updated specs:
- mamba
The following NEW packages will be INSTALLED:
_libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
_openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu
archspec conda-forge/noarch::archspec-0.2.2-pyhd8ed1ab_0
boltons conda-forge/noarch::boltons-23.0.0-pyhd8ed1ab_0
brotli-python conda-forge/linux-64::brotli-python-1.1.0-py312h30efb56_1
bzip2 conda-forge/linux-64::bzip2-1.0.8-hd590300_5
c-ares conda-forge/linux-64::c-ares-1.23.0-hd590300_0
ca-certificates conda-forge/linux-64::ca-certificates-2023.11.17-hbcca054_0
certifi conda-forge/noarch::certifi-2023.11.17-pyhd8ed1ab_0
cffi conda-forge/linux-64::cffi-1.16.0-py312hf06ca03_0
charset-normalizer conda-forge/noarch::charset-normalizer-3.3.2-pyhd8ed1ab_0
colorama conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
conda conda-forge/linux-64::conda-23.11.0-py312h7900ff3_1
conda-libmamba-so~ conda-forge/noarch::conda-libmamba-solver-23.11.1-pyhd8ed1ab_0
conda-package-han~ conda-forge/noarch::conda-package-handling-2.2.0-pyh38be061_0
conda-package-str~ conda-forge/noarch::conda-package-streaming-0.9.0-pyhd8ed1ab_0
distro conda-forge/noarch::distro-1.8.0-pyhd8ed1ab_0
fmt conda-forge/linux-64::fmt-10.1.1-h00ab1b0_1
icu conda-forge/linux-64::icu-73.2-h59595ed_0
idna conda-forge/noarch::idna-3.6-pyhd8ed1ab_0
jsonpatch conda-forge/noarch::jsonpatch-1.33-pyhd8ed1ab_0
jsonpointer conda-forge/linux-64::jsonpointer-2.4-py312h7900ff3_3
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
krb5 conda-forge/linux-64::krb5-1.21.2-h659d440_0
ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0
libarchive conda-forge/linux-64::libarchive-3.7.2-h039dbb9_0
libcurl conda-forge/linux-64::libcurl-8.4.0-hca28451_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libexpat conda-forge/linux-64::libexpat-2.5.0-hcb278e6_1
libffi conda-forge/linux-64::libffi-3.4.2-h7f98852_5
libgcc-ng conda-forge/linux-64::libgcc-ng-13.2.0-h807b86a_3
libgomp conda-forge/linux-64::libgomp-13.2.0-h807b86a_3
libiconv conda-forge/linux-64::libiconv-1.17-h166bdaf_0
libmamba conda-forge/linux-64::libmamba-1.5.4-had39da4_0
libmambapy conda-forge/linux-64::libmambapy-1.5.4-py312hd9e9ff6_0
libnghttp2 conda-forge/linux-64::libnghttp2-1.58.0-h47da74e_0
libnsl conda-forge/linux-64::libnsl-2.0.1-hd590300_0
libsolv conda-forge/linux-64::libsolv-0.7.27-hfc55251_0
libsqlite conda-forge/linux-64::libsqlite-3.44.2-h2797004_0
libssh2 conda-forge/linux-64::libssh2-1.11.0-h0841786_0
libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.2.0-h7e041cc_3
libuuid conda-forge/linux-64::libuuid-2.38.1-h0b41bf4_0
libxml2 conda-forge/linux-64::libxml2-2.11.6-h232c23b_0
libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5
lz4-c conda-forge/linux-64::lz4-c-1.9.4-hcb278e6_0
lzo conda-forge/linux-64::lzo-2.10-h516909a_1000
mamba conda-forge/linux-64::mamba-1.5.4-py312h9460a1c_0
menuinst conda-forge/linux-64::menuinst-2.0.0-py312h7900ff3_1
ncurses conda-forge/linux-64::ncurses-6.4-h59595ed_2
openssl conda-forge/linux-64::openssl-3.2.0-hd590300_1
packaging conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
pip conda-forge/noarch::pip-23.3.1-pyhd8ed1ab_0
platformdirs conda-forge/noarch::platformdirs-4.1.0-pyhd8ed1ab_0
pluggy conda-forge/noarch::pluggy-1.3.0-pyhd8ed1ab_0
pybind11-abi conda-forge/noarch::pybind11-abi-4-hd8ed1ab_3
pycosat conda-forge/linux-64::pycosat-0.6.6-py312h98912ed_0
pycparser conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
pysocks conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
python conda-forge/linux-64::python-3.12.0-hab00c5b_0_cpython
python_abi conda-forge/linux-64::python_abi-3.12-4_cp312
readline conda-forge/linux-64::readline-8.2-h8228510_1
reproc conda-forge/linux-64::reproc-14.2.4.post0-hd590300_1
reproc-cpp conda-forge/linux-64::reproc-cpp-14.2.4.post0-h59595ed_1
requests conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
ruamel.yaml conda-forge/linux-64::ruamel.yaml-0.18.5-py312h98912ed_0
ruamel.yaml.clib conda-forge/linux-64::ruamel.yaml.clib-0.2.7-py312h98912ed_2
setuptools conda-forge/noarch::setuptools-68.2.2-pyhd8ed1ab_0
tk conda-forge/linux-64::tk-8.6.13-noxft_h4845f30_101
tqdm conda-forge/noarch::tqdm-4.66.1-pyhd8ed1ab_0
truststore conda-forge/noarch::truststore-0.8.0-pyhd8ed1ab_0
tzdata conda-forge/noarch::tzdata-2023c-h71feb2d_0
urllib3 conda-forge/noarch::urllib3-2.1.0-pyhd8ed1ab_0
wheel conda-forge/noarch::wheel-0.42.0-pyhd8ed1ab_0
xz conda-forge/linux-64::xz-5.2.6-h166bdaf_0
yaml-cpp conda-forge/linux-64::yaml-cpp-0.8.0-h59595ed_0
zstandard conda-forge/linux-64::zstandard-0.22.0-py312hd58854c_0
zstd conda-forge/linux-64::zstd-1.5.5-hfc55251_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
No module named 'conda.cliconda'
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/[username]/miniconda3/envs/_MDTF_install_temp/lib/python3.12/site-packages/conda/exception_handler.py", line 17, in __call__
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/home/[username]/miniconda3/envs/_MDTF_install_temp/lib/python3.12/site-packages/mamba/mamba.py", line 956, in exception_converter
raise e
File "/home/[username]/miniconda3/envs/_MDTF_install_temp/lib/python3.12/site-packages/mamba/mamba.py", line 949, in exception_converter
exit_code = _wrapped_main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/[username]/miniconda3/envs/_MDTF_install_temp/lib/python3.12/site-packages/mamba/mamba.py", line 895, in _wrapped_main
result = do_call(parsed_args, p)
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/[username]/miniconda3/envs/_MDTF_install_temp/lib/python3.12/site-packages/mamba/mamba.py", line 758, in do_call
exit_code = clean(args, parser)
^^^^^^^^^^^^^^^^^^^
File "/home/[username]/miniconda3/envs/_MDTF_install_temp/lib/python3.12/site-packages/mamba/mamba.py", line 701, in clean
module = import_module("conda.cli" + relative_mod, __name__.rsplit(".", 1)[0])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/[username]/miniconda3/envs/_MDTF_install_temp/lib/python3.12/importlib/__init__.py", line 90, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1381, in _gcd_import
File "<frozen importlib._bootstrap>", line 1354, in _find_and_load
File "<frozen importlib._bootstrap>", line 1304, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1381, in _gcd_import
File "<frozen importlib._bootstrap>", line 1354, in _find_and_load
File "<frozen importlib._bootstrap>", line 1304, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 488, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1381, in _gcd_import
File "<frozen importlib._bootstrap>", line 1354, in _find_and_load
File "<frozen importlib._bootstrap>", line 1318, in _find_and_load_unlocked
ModuleNotFoundError: No module named 'conda.cliconda'
`$ /home/[username]/miniconda3/envs/_MDTF_install_temp/bin/mamba clean -qi`
environment variables:
CIO_TEST=<not set>
CONDA_DEFAULT_ENV=_MDTF_install_temp
CONDA_EXE=/home/[username]/miniconda3/bin/conda
CONDA_PREFIX=/home/[username]/miniconda3/envs/_MDTF_install_temp
CONDA_PREFIX_1=/home/[username]/miniconda3
CONDA_PROMPT_MODIFIER=(_MDTF_install_temp)
CONDA_PYTHON_EXE=/home/[username]/miniconda3/bin/python
CONDA_ROOT=/home/[username]/miniconda3/envs/_MDTF_install_temp
CONDA_SHLVL=2
CURL_CA_BUNDLE=<not set>
LD_PRELOAD=<not set>
PATH=/home/[username]/miniconda3/envs/_MDTF_install_temp/bin:/home/[username]/minicon
da3/condabin:/home/[username]/.local/bin:/home/[username]/miniconda3/bin:/home/c
lare/miniconda3/condabin:/home/[username]/spark-2.4.4-bin-hadoop2.7/bin:/us
r/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/
usr/local/games:/usr/lib/jvm/jdk-
11.0.3/bin:/snap/bin:/usr/lib/jvm/java-11-
oracle/bin:/usr/lib/jvm/java-11-
oracle/db/bin:/home/[username]/bin:/home/[username]/jdk1.8.0_221/bin
PYTHONPATH=:/home/[username]/Dropbox/GitHub-siying/plurk_posting
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : base
active env location : /home/[username]/miniconda3/envs/_MDTF_install_temp
shell level : 2
user config file : /home/[username]/.condarc
populated config files :
conda version : 23.11.0
conda-build version : not installed
python version : 3.12.0.final.0
solver : libmamba (default)
virtual packages : __archspec=1=zen
__conda=23.11.0=0
__cuda=12.0=0
__glibc=2.27=0
__linux=4.15.0=0
__unix=0=0
base environment : /home/[username]/miniconda3/envs/_MDTF_install_temp (writable)
conda av data dir : /home/[username]/miniconda3/envs/_MDTF_install_temp/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/[username]/miniconda3/envs/_MDTF_install_temp/pkgs
/home/[username]/.conda/pkgs
envs directories : /home/[username]/miniconda3/envs/_MDTF_install_temp/envs
/home/[username]/.conda/envs
platform : linux-64
user-agent : conda/23.11.0 requests/2.31.0 CPython/3.12.0 Linux/4.15.0-214-generic ubuntu/18.04.6 glibc/2.27 solver/libmamba conda-libmamba-solver/23.11.1 libmambapy/1.5.4
UID:GID : 1001:1001
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If you suspect this error is being caused by a malfunctioning plugin,
consider using the --no-plugins option to turn off plugins.
Example: conda --no-plugins install <package>
Alternatively, you can set the CONDA_NO_PLUGINS environment variable on
the command line to run the command without plugins enabled.
Example: CONDA_NO_PLUGINS=true conda install <package>
@yihungkuo Thank you for the discussion this evening! Here's the ticket I created for the installation issue.
@csyhuang After looking at some stack overflow posts, it looks like there is an issue with the PYTHONPATH environment variable or there is a collision between the Python version update and the version of miniconda3 on your machine(s). You can try resetting PYTHONPATH, or uninstalling miniconda3 and installing latest version of miniconda3 (or uninstall/reinstall the latest version if you are already using it). I'm not sure if you can do the latter on your workstation if you are relying a central installation maintained by your institution, but you can try it on your personal Mac. See this thread for the full details.
@wrongkindofdoctor thanks for the reply. I tried on my Mac completely uninstalling miniconda, reinstall the latest version and then rerun the MDTF setup (as stated above) but still got the same error unfortunately.
The latest miniconda release is in python 3.11:
https://docs.conda.io/projects/miniconda/en/latest/
while the installation of MDTF involves python 3.12 (python conda-forge/linux-64::python-3.12.0-hab00c5b_0_cpython) - I wonder if this is related to the error.
(Given no success on my Mac machine, I am not doing this on the linux machine for now)
FYI, printing out my sys path gives
>> sys.path
['', '/Users/username/miniconda3/lib/python311.zip', '/Users/username/miniconda3/lib/python3.11', '/Users/username/miniconda3/lib/python3.11/lib-dynload', '/Users/username/miniconda3/lib/python3.11/site-packages']
@csyhuang Are you able to install mamba in your conda base environment:
conda activate base
conda install -c conda-forge mamba
If so, then you can just activate the base environment before running conda_env_setup.sh and the installer will skip installing mamba in the temp environment. If neither of these solve the problem, you can try installing the the environments that you need using the conda command directly:
conda env create --force -q -p=$conda_prefix -f=$env_file
where $conda_prefix = $CONDA_ROOT/envs and $env_file = $MDTF_INSTALL_ROOT_PATH/mdtf/MDTF-diagnostics/src/conda/[env file name].yml
You can then create your own mdtf executable file [MDTF_ROOT_PATH]/mdtf/MDTF-diagnostics/mdtf
with the following linew, substituting the appropriate paths for MDTF_ROOT_PATH and PATH TO MINICONDA3 INSTALLATION:
#!/usr/bin/env bash
# This wrapper script is generated by conda_env_setup.sh.
_mdtf="[MDTF_ROOT_PATH]/mdtf/MDTF-diagnostics"
source "${_mdtf}/src/conda/conda_init.sh" -q "[PATH TO MINICONDA3 INSTALLATION]/miniconda3"
conda activate [PATH TO MINICONDA3 INSTALLATION]/miniconda3/envs/_MDTF_base
"${_mdtf}/mdtf_framework.py" "$@"
exit $?
This will take longer, but will likely be more manageable on your Mac since it is not using a shared file system.
You can also try installing micromamba, and using the corresponding build scripts and runtime configurations indicated in the documentation. Make sure to set the "micromamba_exe" path in your runtime config file if you build with micromamba.
As a last resort, you may have to check out the tag or commit of the last version that worked for you and use that instead of the latest version.
Also, I noticed that the installation paths include "/home/username" in the prefix. I don't know if this necessarily affects the installation, but "username" is meant to be substituted with your user name on the systems you are trying to build on (e.g., /home/csyhuang/...).
@wrongkindofdoctor Hi Jess, thank you for the instructions! Sorry for not getting back earlier as I was traveling and not able to access my linux machine. After pulling the latest commits today, I was able to run the conda installation properly without changing any of my machine settings. The issue has been fixed so this ticket can be closed.