Installation of catalog builder

[Wen-hao-Dong]

I was trying to install the catalog builder following the instruction but ran into some issues:
conda install intakebuilder -c noaa-gfdl
Collecting package metadata (current_repodata.json): failed

ChannelNotAllowed: Channel not included in whitelist:
channel name: noaa-gfdl
channel url: https://conda.anaconda.org/noaa-gfdl

I then tried the alternative:
git clone https://github.com/aradhakrishnanGFDL/CatalogBuilder.git

conda env create -f environment_intake.yml

but got this message: EnvironmentFileNotFound: '/home/wnd/CatalogBuilder/environment_intake.yml' file not found

[Ciheim]

Hey Wenhao, the condo installation can be tricky. Try running this command conda config --add channels new_channel.

If you want to try the conda environment creation try running this: conda env create -f ./environment_intake.yml

Let me know if those work for you.

[aradhakrishnanGFDL]

Hi @Wen-hao-Dong and @Ciheim I think the following works

conda config --add channels noaa-gfdl
conda config --append channels conda-forge
conda install intakebuilder -c noaa-gfdl

[Wen-hao-Dong]

Hi Ciheim and Aparna, I was able to try your suggestions today but still ran into the same issue, see info below: wnd:/home/Wenhao.Dong> module load conda wnd:/home/Wenhao.Dong> conda config --add channels new_channel wnd:/home/Wenhao.Dong> conda install intakebuilder -c noaa-gfdl Collecting package metadata (current_repodata.json): failed ChannelNotAllowed: Channel not included in whitelist: channel name: noaa-gfdl channel url: https://conda.anaconda.org/noaa-gfdl wnd:/home/Wenhao.Dong> conda config --add channels noaa-gfdl wnd:/home/Wenhao.Dong> conda config --append channels conda-forge Warning: 'conda-forge' already in 'channels' list, moving to the bottom wnd:/home/Wenhao.Dong> conda install intakebuilder -c noaa-gfdl Collecting package metadata (current_repodata.json): failed ChannelNotAllowed: Channel not included in whitelist: channel name: noaa-gfdl channel url: https://conda.anaconda.org/noaa-gfdl Any further suggestions? I am testing on my workstation. Best, Wenhao

…

On Mon, Jul 1, 2024 at 4:15 PM Aparna Radhakrishnan < ***@***.***> wrote: Hi @Wen-hao-Dong <https://github.com/Wen-hao-Dong> and @Ciheim <https://github.com/Ciheim> I think the following works conda config --add channels noaa-gfdl conda config --append channels conda-forge conda install intakebuilder -c noaa-gfdl — Reply to this email directly, view it on GitHub <#136 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANBNRYC52ONILJIHS27JIC3ZKG2FLAVCNFSM6AAAAABJ6GJVC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBQHE2DMOJUGQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Wen-hao-Dong]

Thanks Aparna, I used your suggestion as well, see the last three commands in my previous email.

…

On Wed, Jul 3, 2024 at 15:18 Aparna Radhakrishnan ***@***.***> wrote: @Wen-hao-Dong <https://github.com/Wen-hao-Dong> make sure you try the following. In your commands, new_channel needs to be noaa-gfdl and we also need to append conga-forge. conda config --add channels noaa-gfdl conda config --append channels conda-forge conda install intakebuilder -c noaa-gfdl — Reply to this email directly, view it on GitHub <#136 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANBNRYEOTTG6TTHQ5UTESYDZKRFABAVCNFSM6AAAAABJ6GJVC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBXGAZDENZYHA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[aradhakrishnanGFDL]

Try this -

Make changes to your ~/.condarc file to reflect something like the following, mainly adding the channels to the whitelist.

whitelist_channels:
  - noaa-gfdl
  - conda-forge
  - anaconda
channels:
  - noaa-gfdl
  - conda-forge
  - anaconda

[aradhakrishnanGFDL]

@Wen-hao-Dong any luck?

[Wen-hao-Dong]

Hi Aparna, Yes, I made some suggestions after following your instructions, but ran into another issue (see below), looks like the intakebuilder-2.0.1 was not installed successfully: intakebuilder-2.0.1 | 47.9 MB | | 0% libpng-1.6.38 | 371 KB | ######################################################################################################################################################################## | 100% ChecksumMismatchError: Conda detected a mismatch between the expected content and downloaded content for url ' https://conda.anaconda.org/noaa-gfdl/noarch/intakebuilder-2.0.1-py_0.tar.bz2 '. download saved to: /home/Wenhao.Dong/.conda/pkgs/intakebuilder-2.0.1-py_0.tar.bz2 expected sha256: e26bad0f3cd668cd59e2ef487ab0854f6d06283167a1dc09ad057d700040284f actual sha256: 140531a6e7219dd77bbd70d906796f1168e8d4fd6bf422752e5e0235a216ad44 Any further suggestions? Best, Wenhao

…

On Wed, Jul 10, 2024 at 4:02 PM Aparna Radhakrishnan < ***@***.***> wrote: @Wen-hao-Dong <https://github.com/Wen-hao-Dong> any luck? — Reply to this email directly, view it on GitHub <#136 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANBNRYDSOQIJBYEHHZMT3UTZLWHLJAVCNFSM6AAAAABJ6GJVC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRRGMZDONBXGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Wen-hao-Dong]

Got a different message after another try:
Downloading and Extracting Packages
intakebuilder-2.0.1 | 47.9 MB | ######################################################################################################################################################################## | 100%
Preparing transaction: done
Verifying transaction: failed

EnvironmentNotWritableError: The current user does not have write permissions to the target environment.
environment location: /app/conda/miniconda
uid: 20398
gid: 77

[ceblanton]

That error means you need to tell conda to use directories you own to install the packages and environments into. If you're on the GFDL workstations, you can use /local2/home:

conda config --add pkgs_dirs /local2/home/conda/pkgs
conda config --add envs_dirs /local2/home/conda/envs

Then you should be able to install it into a new environment with:

conda create --name intakebuilder -c noaa-gfdl -c conda-forge intakebuilder

[Wen-hao-Dong]

Thank you all! It worked now! I was able to generate the data catalog as expected! --Wenhao

…

On Thu, Jul 11, 2024 at 4:01 PM Chris Blanton ***@***.***> wrote: That error means you need to tell conda to use directories you own to install the packages and environments into. If you're on the GFDL workstations, you can use /local2/home: conda config --add pkgs_dirs /local2/home/conda/pkgs conda config --add envs_dirs /local2/home/conda/envs Then you should be able to install it into a new environment with: conda create --name intakebuilder -c noaa-gfdl -c conda-forge intakebuilder — Reply to this email directly, view it on GitHub <#136 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANBNRYBI6ZMKIGIEG2VSPB3ZL3QCXAVCNFSM6AAAAABJ6GJVC6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRTHAZDGNJSGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>