ExcitedStates / qfit-3.0

qFit: Automated and unbiased multi-conformer models from X-ray and EM maps.
MIT License
30 stars 11 forks source link

Installation in Fedora 39 not working? #401

Closed mysecondnameisdanger closed 2 months ago

mysecondnameisdanger commented 4 months ago

Not sure how to proceed. I am new to conda and all that.

(base) mysecondnameisdanger@fedora:~$ conda create --name qfit "python>=3.9"
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/mysecondnameisdanger/miniconda3/envs/qfit

  added / updated specs:
    - python[version='>=3.9']

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    expat-2.5.0                |       h6a678d5_0         172 KB
    openssl-3.0.13             |       h7f8727e_0         5.2 MB
    pip-23.3.1                 |  py312h06a4308_0         2.8 MB
    python-3.12.1              |       h996f2a0_0        35.2 MB
    setuptools-68.2.2          |  py312h06a4308_0         1.2 MB
    tzdata-2023d               |       h04d1e81_0         117 KB
    wheel-0.41.2               |  py312h06a4308_0         131 KB
    ------------------------------------------------------------
                                           Total:        44.8 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main 
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu 
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0 
  expat              pkgs/main/linux-64::expat-2.5.0-h6a678d5_0 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0 
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 
  openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_0 
  pip                pkgs/main/linux-64::pip-23.3.1-py312h06a4308_0 
  python             pkgs/main/linux-64::python-3.12.1-h996f2a0_0 
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 
  setuptools         pkgs/main/linux-64::setuptools-68.2.2-py312h06a4308_0 
  sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0 
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0 
  tzdata             pkgs/main/noarch::tzdata-2023d-h04d1e81_0 
  wheel              pkgs/main/linux-64::wheel-0.41.2-py312h06a4308_0 
  xz                 pkgs/main/linux-64::xz-5.4.5-h5eee18b_0 
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0 

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done                                                             
Verifying transaction: done                                                             
Executing transaction: done                                                             
#                                                                                       
# To activate this environment, use                                                     
#                                                                                       
#     $ conda activate qfit
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) mysecondnameisdanger@fedora:~$ conda activate qfit
(qfit) mysecondnameisdanger@fedora:~$ conda install -c anaconda mkl numpy=1.22
Channels:
 - anaconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: \ warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package numpy-1.22.3-py310h4f1e569_0 requires python >=3.10,<3.11.0a0, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ numpy 1.22**  is installable with the potential options
│  ├─ numpy 1.22.3 would require
│  │  └─ python >=3.10,<3.11.0a0 , which can be installed;
│  ├─ numpy 1.22.3 would require
│  │  └─ python >=3.11,<3.12.0a0 , which can be installed;
│  ├─ numpy 1.22.3 would require
│  │  └─ python >=3.8,<3.9.0a0 , which can be installed;
│  └─ numpy 1.22.3 would require
│     └─ python >=3.9,<3.10.0a0 , which can be installed;
└─ pin-1 is not installable because it requires
   └─ python 3.12.* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 3.12.* (labeled as 'pin-1')
blake-riley commented 4 months ago

Hi,

I'm not much of a conda person myself either. But reading your error message, it appears that your python has got stuck on 3.12, and that's incompatible with numpy 1.22. Try start from scratch, but rather than "python>=3.9", do "python>=3.9,<3.12". This would be my next step.

Please let us know if that works.

Good luck, Blake

mysecondnameisdanger commented 4 months ago

Output>

(base) mysecondnameisdanger@fedora:~$ conda create --name qfit-again "python>=3.9,<3.12"
Retrieving notices: ...working... done
Channels:
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/mysecondnameisdanger/miniconda3/envs/qfit-again

  added / updated specs:
    - python[version='>=3.9,<3.12']

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    python-3.11.7              |       h955ad1f_0        32.8 MB
    ------------------------------------------------------------
                                           Total:        32.8 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      pkgs/main/linux-64::_libgcc_mutex-0.1-main 
  _openmp_mutex      pkgs/main/linux-64::_openmp_mutex-5.1-1_gnu 
  bzip2              pkgs/main/linux-64::bzip2-1.0.8-h7b6447c_0 
  ca-certificates    pkgs/main/linux-64::ca-certificates-2023.12.12-h06a4308_0 
  ld_impl_linux-64   pkgs/main/linux-64::ld_impl_linux-64-2.38-h1181459_1 
  libffi             pkgs/main/linux-64::libffi-3.4.4-h6a678d5_0 
  libgcc-ng          pkgs/main/linux-64::libgcc-ng-11.2.0-h1234567_1 
  libgomp            pkgs/main/linux-64::libgomp-11.2.0-h1234567_1 
  libstdcxx-ng       pkgs/main/linux-64::libstdcxx-ng-11.2.0-h1234567_1 
  libuuid            pkgs/main/linux-64::libuuid-1.41.5-h5eee18b_0 
  ncurses            pkgs/main/linux-64::ncurses-6.4-h6a678d5_0 
  openssl            pkgs/main/linux-64::openssl-3.0.13-h7f8727e_0 
  pip                pkgs/main/linux-64::pip-23.3.1-py311h06a4308_0 
  python             pkgs/main/linux-64::python-3.11.7-h955ad1f_0 
  readline           pkgs/main/linux-64::readline-8.2-h5eee18b_0 
  setuptools         pkgs/main/linux-64::setuptools-68.2.2-py311h06a4308_0 
  sqlite             pkgs/main/linux-64::sqlite-3.41.2-h5eee18b_0 
  tk                 pkgs/main/linux-64::tk-8.6.12-h1ccaba5_0 
  tzdata             pkgs/main/noarch::tzdata-2023d-h04d1e81_0 
  wheel              pkgs/main/linux-64::wheel-0.41.2-py311h06a4308_0 
  xz                 pkgs/main/linux-64::xz-5.4.5-h5eee18b_0 
  zlib               pkgs/main/linux-64::zlib-1.2.13-h5eee18b_0 

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate qfit-again
#
# To deactivate an active environment, use
#
#     $ conda deactivate

(base) mysecondnameisdanger@fedora:~$ conda activate qfit-again
(qfit-again) mysecondnameisdanger@fedora:~$ conda install -c anaconda mkl numpy=1.22
Channels:
 - anaconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/mysecondnameisdanger/miniconda3/envs/qfit-again

  added / updated specs:
    - mkl
    - numpy=1.22

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    blas-1.0                   |         openblas          48 KB  anaconda
    intel-openmp-2023.1.0      |   hdb19cb5_46306        18.4 MB  anaconda
    libgfortran-ng-11.2.0      |       h00389a5_1          19 KB  anaconda
    libgfortran5-11.2.0        |       h1234567_1         5.0 MB  anaconda
    libopenblas-0.3.21         |       h043d6bf_0         9.7 MB  anaconda
    mkl-2023.1.0               |   h213fc3f_46344       197.2 MB  anaconda
    numpy-1.22.3               |  py311h5585df3_1          10 KB  anaconda
    numpy-base-1.22.3          |  py311hc9e7d78_1         7.9 MB  anaconda
    tbb-2021.8.0               |       hdb19cb5_0         1.8 MB  anaconda
    ------------------------------------------------------------
                                           Total:       240.0 MB

The following NEW packages will be INSTALLED:

  blas               anaconda/linux-64::blas-1.0-openblas 
  intel-openmp       anaconda/linux-64::intel-openmp-2023.1.0-hdb19cb5_46306 
  libgfortran-ng     anaconda/linux-64::libgfortran-ng-11.2.0-h00389a5_1 
  libgfortran5       anaconda/linux-64::libgfortran5-11.2.0-h1234567_1 
  libopenblas        anaconda/linux-64::libopenblas-0.3.21-h043d6bf_0 
  mkl                anaconda/linux-64::mkl-2023.1.0-h213fc3f_46344 
  numpy              anaconda/linux-64::numpy-1.22.3-py311h5585df3_1 
  numpy-base         anaconda/linux-64::numpy-base-1.22.3-py311hc9e7d78_1 
  tbb                anaconda/linux-64::tbb-2021.8.0-hdb19cb5_0 

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done                                                                       
Verifying transaction: done                                                                       
Executing transaction: done                                                                       
(qfit-again) mysecondnameisdanger@fedora:~$ conda install -c anaconda -c ibmdecisionoptimization cvxopt cplex
Channels:
 - anaconda                                                                                       
 - ibmdecisionoptimization
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: - warning  libmamba Added empty dependency for problem type SOLVER_RULE_UPDATE
failed

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides openssl >=1.1.1,<1.1.2.0a0 needed by python-2.7.15-h9bab390_2

Could not solve for environment specs
The following packages are incompatible
├─ cplex is installable with the potential options
│  ├─ cplex [12.7|12.8] would require
│  │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
│  ├─ cplex [12.7|12.8|12.9] would require
│  │  └─ python [2.7* |>=2.7,<2.8.0a0 ] with the potential options
│  │     ├─ python [2.7.13|2.7.14|...|2.7.18], which can be installed;
│  │     └─ python [2.7.15|3.6.7|3.7.1] would require
│  │        └─ openssl >=1.1.1,<1.1.2.0a0 , which does not exist (perhaps a missing channel);
│  ├─ cplex [12.10|12.7|12.8|12.9] would require
│  │  └─ python [3.6* |>=3.6,<3.7.0a0 ] with the potential options
│  │     ├─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
│  │     └─ python [3.6.10|3.6.12|...|3.6.9], which can be installed;
│  ├─ cplex [12.10|12.9|20.1|22.1] would require
│  │  └─ python >=3.7,<3.8.0a0  with the potential options
│  │     ├─ python [2.7.15|3.6.7|3.7.1], which cannot be installed (as previously explained);
│  │     └─ python [3.7.0|3.7.1|...|3.7.9], which can be installed;
│  ├─ cplex [20.1|22.1] would require
│  │  └─ python >=3.8,<3.9.0a0 , which can be installed;
│  ├─ cplex 22.1 would require
│  │  └─ python >=3.9,<3.10.0a0 , which can be installed;
│  └─ cplex 22.1 would require
│     └─ python >=3.10,<3.11.0a0 , which can be installed;
└─ pin-1 is not installable because it requires
   └─ python 3.11.* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 3.11.* (labeled as 'pin-1')
mysecondnameisdanger commented 2 months ago

Worked, after installing anaconda, then in anaconda-navigator created the environment, and... at least it runs to completion.