Installation issues

[XuanZhou001]

When I run mamba env create -f environment.yaml,An error will be reported here.

Could not solve for environment specs
The following packages are incompatible
├─ tensorflow-base ==2.11.0 cuda112py310h52da4a5_0 is not installable because it requires
│  └─ __cuda, which is missing on the system;
├─ tensorflow-estimator ==2.11.0 cuda112py310h37add04_0 is not installable because it requires
│  └─ tensorflow-base 2.11.0 cuda112py310h52da4a5_0, which cannot be installed (as previously explained);
└─ tensorflow ==2.11.0 cuda112py310he87a039_0 is not installable because it requires
  └─ __cuda, which is missing on the system.

I would be very happy if you could provide some help. Thank you!

[r-krishna]

I think you might need to do this step on a node that has a GPU. Let me know if that works!

[Jnelen]

When I run mamba env create -f environment.yaml,An error will be reported here.

Could not solve for environment specs
The following packages are incompatible
├─ tensorflow-base ==2.11.0 cuda112py310h52da4a5_0 is not installable because it requires
│  └─ __cuda, which is missing on the system;
├─ tensorflow-estimator ==2.11.0 cuda112py310h37add04_0 is not installable because it requires
│  └─ tensorflow-base 2.11.0 cuda112py310h52da4a5_0, which cannot be installed (as previously explained);
└─ tensorflow ==2.11.0 cuda112py310he87a039_0 is not installable because it requires
  └─ __cuda, which is missing on the system.

I would be very happy if you could provide some help. Thank you!

Is cuda properly installed on your system? For example do the nvidia-smi and nvcc --version commands work? Either way if this is giving problems I would recommend to update your nvidia drivers.

[HBioquant]

I have encountered this problem too, but I've successfully resolved it. In fact, I noticed an inconsistency in the environment.yaml file, as the required CUDA version was 11.8, as shown below:

  - cuda-cudart=11.8.89=0
  - cuda-cupti=11.8.87=0
  - cuda-libraries=11.8.0=0
  - cuda-nvrtc=11.8.89=0
  - cuda-nvtx=11.8.86=0
  - cuda-runtime=11.8.0=0
  - cuda-version=11.8=h70ddcb2_3
  - cudatoolkit=11.8.0=h4ba93d1_13
  - cudnn=8.8.0.121=hcdd5f01_4

However, tensorFlow requires CUDA version 11.2, as indicated here:

  - tensorflow=2.11.0=cuda112py310he87a039_0
  - tensorflow-base=2.11.0=cuda112py310h52da4a5_0
  - tensorflow-estimator=2.11.0=cuda112py310h37add04_0

Therefore, you could consider modifying it to:

  - tensorflow=2.11.0
  - tensorflow-base=2.11.0
  - tensorflow-estimator=2.11.0

[ailiqiangCSU]

When I run mamba env create -f environment.yaml,An error will be reported here. nvidia/linux-64 ??.?MB @ ??.?MB/s 0 failed 6.0s predector/linux-64 ??.?MB @ ??.?MB/s 0 failed 6.0s pyg/linux-64 ??.?MB @ ??.?MB/s 0 failed 6.0s conda-forge/linux-64 ??.?MB @ ??.?MB/s 0 failed 6.0s

>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

Traceback (most recent call last):
  File "/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/lib/python3.10/site-packages/conda/exception_handler.py", line 17, in __call__
    return func(*args, **kwargs)
  File "/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/lib/python3.10/site-packages/conda_env/cli/main.py", line 56, in do_call
    exit_code = getattr(module, func_name)(arguments, parser)
  File "/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/lib/python3.10/site-packages/conda/notices/core.py", line 124, in wrapper
    return func(*args, **kwargs)
  File "/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/lib/python3.10/site-packages/conda_env/cli/main_create.py", line 164, in execute
    result[installer_type] = installer.install(
  File "/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/lib/python3.10/site-packages/mamba/mamba_env.py", line 54, in mamba_install
    index = load_channels(pool, channel_urls, repos, prepend=False)
  File "/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/lib/python3.10/site-packages/mamba/utils.py", line 126, in load_channels
    index = get_index(
  File "/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/lib/python3.10/site-packages/mamba/utils.py", line 107, in get_index
    is_downloaded = dlist.download(api.MAMBA_DOWNLOAD_FAILFAST)
RuntimeError: Download error (6) Couldn't resolve host name [https://conda.anaconda.org/bioconda/noarch/repodata.json]
Could not resolve host: conda.anaconda.org

$ /gpfs/hpc/home/duanranhui/share_group_folder/ENTER/bin/mamba create -f environment.yaml

environment variables: CIO_TEST= CONDA_AUTO_UPDATE_CONDA=false CONDA_DEFAULT_ENV=base CONDA_EXE=/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/bin/conda CONDA_PREFIX=/gpfs/hpc/home/duanranhui/share_group_folder/ENTER CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/bin/python CONDA_ROOT=/gpfs/hpc/home/duanranhui/share_group_folder/ENTER CONDA_SHLVL=1 CURL_CA_BUNDLE= LD_LIBRARY_PATH=/usr/local/cuda/lib64: LD_PRELOAD= PATH=/gpfs/hpc/home/duanranhui/share_group_folder/ENTER/bin:/gpfs/hpc/home/ duanranhui/share_group_folder/ENTER/condabin:/usr/local/cuda/bin:/usr/ lib64/qt- 3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/gpfs/hpc/ho me/duanranhui/ailiqiang/.local/bin:/gpfs/hpc/home/duanranhui/ailiqiang /bin QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : base
active env location : /gpfs/hpc/home/duanranhui/share_group_folder/ENTER
        shell level : 1
   user config file : /gpfs/hpc/home/duanranhui/ailiqiang/.condarc

populated config files : /gpfs/hpc/home/duanranhui/share_group_folder/ENTER/.condarc conda version : 23.11.0 conda-build version : not installed python version : 3.10.13.final.0 solver : libmamba (default) virtual packages : archspec=1=cascadelake conda=23.11.0=0 cuda=12.2=0 glibc=2.17=0 linux=3.10.0=0 unix=0=0 base environment : /gpfs/hpc/home/duanranhui/share_group_folder/ENTER (writable) conda av data dir : /gpfs/hpc/home/duanranhui/share_group_folder/ENTER/etc/conda conda av metadata url : None channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch package cache : /gpfs/hpc/home/duanranhui/share_group_folder/ENTER/pkgs /gpfs/hpc/home/duanranhui/ailiqiang/.conda/pkgs envs directories : /gpfs/hpc/home/duanranhui/share_group_folder/ENTER/envs /gpfs/hpc/home/duanranhui/ailiqiang/.conda/envs platform : linux-64 user-agent : conda/23.11.0 requests/2.31.0 CPython/3.10.13 Linux/3.10.0-1160.el7.x86_64 centos/7.9.2009 glibc/2.17 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.5 UID:GID : 32128:42040 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

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

[kochild]

Because your server session likely doesn't give you GPU access, you're going to face issues getting the CUDA requirements installed with conda. To get around this, you can make the conda/mamba environment ignore this issue by typing:

CONDA_OVERRIDE_CUDA="11.2" conda env create -f environment.yaml

This has been suggested by the conda-forge team

There's no need to modify the script after this.