Hello,
I was attempting to activate the analysis3 environment & got stuck at conda init. I removed any previous conda things from my .bashrc file & logged out and back in again. The same steps I show below work for the hh5 version. Am I missing something? Any advice appreciated.
[xx@gadi-login-08 ~]$ module use /g/data/xp65/public/modules
[xx@gadi-login-08 ~]$ module load conda/analysis3
Loading conda/analysis3-25.03
Loading requirement: singularity
[xx@gadi-login-08 ~]$ conda activate analysis3
CondaError: Run 'conda init' before 'conda activate'
[xx@gadi-login-08 ~]$ conda init
Which gives an error (sorry it’s long)
/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/base/context.py:202: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3.
To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels:
conda config --add channels defaults
For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/exception_handler.py", line 18, in __call__
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/cli/main.py", line 61, in main_subshell
exit_code = do_call(args, parser)
^^^^^^^^^^^^^^^^^^^^^
File "/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/cli/conda_argparse.py", line 205, in do_call
result = getattr(module, func_name)(args, parser)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/cli/main_init.py", line 162, in execute
return initialize(
^^^^^^^^^^^
File "/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/core/initialize.py", line 139, in initialize
run_plan_elevated(plan2)
File "/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/core/initialize.py", line 852, in run_plan_elevated
result = subprocess_call(
^^^^^^^^^^^^^^^^
File "/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/lib/python3.11/site-packages/conda/gateways/subprocess.py", line 129, in subprocess_call
raise CalledProcessError(rc, command, output=formatted_output)
subprocess.CalledProcessError: Command '['sudo', '/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/bin/python', '-m', 'conda.core.initialize']' returned non-zero exit status 1.
`$ /g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/bin/conda init`
environment variables:
CIO_TEST=<not set>
CMAKE_PREFIX_PATH=/opt/conda/analysis3-25.03:/opt/conda/analysis3-25.03/x86_64-conda-
linux-gnu/sysroot/usr
CONDA_ALLOW_SOFTLINKS=false
CONDA_BASE=/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03
CONDA_BASE_ENV_PATH=/g/data/xp65/public/apps/med_conda
CONDA_BUILD_SYSROOT=/opt/conda/analysis3-25.03/x86_64-conda-linux-gnu/sysroot
CONDA_DEFAULT_ENV=/opt/conda/analysis3-25.03
CONDA_EXE=/g/data/xp65/public/apps/med_conda/bin/micromamba
CONDA_PREFIX=/opt/conda/analysis3-25.03
CONDA_PROMPT_MODIFIER=(/opt/conda/analysis3-25.03)
CONDA_PYTHONBREAKPOINT=
CONDA_ROOT=/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03
CONDA_SHLVL=1
CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
CONTAINER_OVERLAY_PATH=/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03.sqsh
CONTAINER_PATH=/g/data/xp65/public/apps/med_conda/etc/base.sif
CURL_CA_BUNDLE=<not set>
FPATH=/opt/Modules/v4.3.0/init/ksh-functions
GDAL_DRIVER_PATH=/opt/conda/analysis3-25.03/lib/gdalplugins
LD_LIBRARY_PATH=
LD_PRELOAD=<not set>
MANPATH=/opt/pbs/default/share/man:::/opt/pbs/default/share/man
MODULEPATH=/g/data/xp65/public/modules:/etc/scl/modulefiles:/apps/Modules/restric
# .bashrc
ted-modulefiles/matlab_melbourne:/opt/Modules/modulefiles:/opt/Modules
/v4.3.0/modulefiles:/apps/Modules/modulefiles
PATH=/opt/conda/analysis3-
25.03/bin:/g/data/xp65/public/apps/med_conda/envs/analysis3-
25.03/condabin:/home/581/mxr581/.local/bin:/home/581/mxr581/bin:/opt/p
bs/default/bin:/opt/nci/bin:/opt/bin:/opt/Modules/v4.3.0/bin:/opt/pbs/
default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/b
in
PKG_CONFIG_PATH=/half-root/usr/lib64/pkgconfig
PYTHONBREAKPOINT=ipdb.set_trace
REQUESTS_CA_BUNDLE=<not set>
SINGULARITY_BINARY_PATH=/opt/singularity/bin/singularity
SSL_CERT_FILE=<not set>
UDUNITS2_XML_PATH=/opt/conda/analysis3-25.03/share/udunits/udunits2.xml
USER_PATH=/g/data/xp65/public/apps/med_conda_scripts/analysis3-
25.03.d/bin:/home/581/mxr581/.local/bin:/home/581/mxr581/bin:/opt/pbs/
default/bin:/opt/nci/bin:/opt/bin:/opt/Modules/v4.3.0/bin:/bin:/usr/bi
n:/usr/local/sbin:/usr/sbin:/opt/pbs/default/bin:/opt/singularity/bin:
/bin:/usr/bin:/sbin:/usr/sbin:/usr/local/bin:/usr/local/sbin
active environment : /opt/conda/analysis3-25.03
active env location : /opt/conda/analysis3-25.03
shell level : 1
user config file : /home/581/mxr581/.condarc
populated config files :
conda version : 25.1.1
conda-build version : 25.1.2
python version : 3.11.11.final.0
solver : libmamba (default)
virtual packages : __archspec=1=cascadelake
__conda=25.1.1=0
__glibc=2.28=0
__linux=4.18.0=0
__unix=0=0
base environment : /g/data/xp65/public/apps/med_conda/envs/analysis3-25.03 (read only)
conda av data dir : /g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/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 : /g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/pkgs
/home/581/mxr581/.conda/pkgs
envs directories : /home/581/mxr581/.conda/envs
/g/data/xp65/public/apps/med_conda/envs/analysis3-25.03/envs
platform : linux-64
user-agent : conda/25.1.1 requests/2.32.3 CPython/3.11.11 Linux/4.18.0-553.34.1.el8.nci.x86_64 rocky/8.10 glibc/2.28 solver/libmamba conda-libmamba-solver/25.3.0 libmambapy/2.0.7
UID:GID : 10764:8086
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
