installation issues - scripts/install_third_party_dependencies.sh

[chewyalvin]

I face multiple errors during installation on an ubuntu workstation: Ubuntu 22.04.1 LTS 5.15.0-58-generic #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux NVIDIA-SMI 520.61.05 Driver Version: 520.61.05 CUDA Version: 11.8

Snippet of Error messages, please advice on how to resolve them? Successfully built nvidia-pyindex Installing collected packages: nvidia-pyindex Successfully installed nvidia-pyindex-1.0.9 Collecting package metadata (repodata.json): done Solving environment: / Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed /
Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed |

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libcblas conflicts for: pytorch::pytorch=1.12 -> blas=[build=mkl] -> libcblas[version='3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.8.0|3.9.0',build='4_mkl|7_mkl|10_mkl|11_mkl|12_mkl|13_mkl|14_mkl|15_mkl|19_mkl|6_mkl|7_mkl|10_mkl|12_linux64_mkl|14_linux64_mkl|15_linux64_mkl|16_linux64_mkl|13_linux64_mkl|11_linux64_mkl|9_mkl|8_mkl|5_mkl|21_mkl|20_mkl|18_mkl|16_mkl|9_mkl|8_mkl|6_mkl|5_mkl'] conda-forge::pdbfixer -> numpy -> libcblas[version='>=3.8.0,<4.0a0|>=3.9.0,<4.0a0'] conda-forge::openmm=7.5.1 -> numpy -> libcblas[version='>=3.8.0,<4.0a0|>=3.9.0,<4.0a0']

Package pypy3.9 conflicts for: pytorch::pytorch=1.12 -> python[version='>=3.9,<3.10.0a0'] -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.'] conda-forge::setuptools=59.5.0 -> python[version='>=3.9,<3.10.0a0'] -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.'] conda-forge::pip -> python[version='>=3.7'] -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.|>=7.3.9|>=7.3.8'] conda-forge::pdbfixer -> numpy -> pypy3.9[version='7.3.11.|>=7.3.11|>=7.3.9|>=7.3.8|7.3.9.|7.3.8.'] conda-forge::openmm=7.5.1 -> numpy -> pypy3.9[version='7.3.11.|>=7.3.11|>=7.3.9|>=7.3.8|7.3.9.|7.3.8.'] bioconda::hhsuite==3.3.0 -> python[version='>=3.9,<3.10.0a0'] -> pypy3.9[version='7.3.11.|7.3.9.|7.3.8.']

Package pip conflicts for: conda-forge|conda-forge::pip conda-forge::openmm=7.5.1 -> python[version='>=3.7,<3.8.0a0'] -> pip pytorch::pytorch=1.12 -> python[version='>=3.7,<3.8.0a0'] -> pip conda-forge::python=3.7 -> pip bioconda::hhsuite==3.3.0 -> python[version='>=3.10,<3.11.0a0'] -> pip conda-forge::pdbfixer -> python[version='>=3.6'] -> pip conda-forge::setuptools=59.5.0 -> python[version='>=3.9,<3.10.0a0'] -> pip

Package llvm-openmp conflicts for: bioconda::hhsuite==3.3.0 -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='8.0.0|8.0.0|8.0.1|>=9.0.1',build='hc9558a2_0|hc9558a2_0|hc9558a2_1'] pytorch::pytorch=1.12 -> blas=[build=mkl] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=15.0.7|>=15.0.6|>=14.0.3|>=9.0.1']

Package _openmp_mutex conflicts for: pytorch::pytorch=1.12 -> blas=[build=mkl] -> _openmp_mutex[version='|>=4.5',build=_llvm] bioconda::hhsuite==3.3.0 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5'] conda-forge::openmm=7.5.1 -> libgcc-ng[version='>=7.5.0'] -> _openmp_mutex[version='>=4.5'] bioconda::hhsuite==3.3.0 -> _openmp_mutex[version='>=4.5'] bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5'] conda-forge::python=3.7 -> libgcc-ng[version='>=9.4.0'] -> _openmp_mutex[version='>=4.5'] bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']

Package pypy3.6 conflicts for: conda-forge::pip -> setuptools -> pypy3.6[version='7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.1|>=7.3.2|>=7.3.3'] conda-forge::openmm=7.5.1 -> numpy -> pypy3.6[version='7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.1|>=7.3.2|>=7.3.3'] conda-forge::pdbfixer -> numpy -> pypy3.6[version='7.3.0.|7.3.1.|7.3.2.|7.3.3.|>=7.3.1|>=7.3.2|>=7.3.3'] bioconda::hhsuite==3.3.0 -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.0.|7.3.1.|7.3.2.|7.3.3.']

Package libstdcxx-ng conflicts for: bioconda::hhsuite==3.3.0 -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.3.0|>=4.9|>=7.2.0'] conda-forge::cudatoolkit=11.3 -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0'] pytorch::pytorch=1.12 -> cudatoolkit[version='>=11.3,<11.4'] -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=11.2.0|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0'] conda-forge::pdbfixer -> numpy -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=7.3.0|>=4.9|>=11.2.0|>=7.5.0|>=9.3.0|>=7.2.0'] conda-forge::openmm=7.5.1 -> libstdcxx-ng[version='>=7.5.0'] conda-forge::python=3.7 -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0'] conda-forge::pip -> python[version='>=3.7'] -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0'] bioconda::hhsuite==3.3.0 -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0'] conda-forge::openmm=7.5.1 -> cudatoolkit[version='11.0|11.0.*'] -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] bioconda::hmmer==3.3.2 -> libstdcxx-ng[version='>=10.3.0|>=9.3.0|>=7.5.0'] conda-forge::setuptools=59.5.0 -> python[version='>=3.9,<3.10.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=9.3.0|>=7.3.0|>=9.4.0|>=4.9|>=7.2.0'] conda-forge::python=3.7 -> libffi[version='>=3.4.2,<3.5.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.2.0']

Package ca-certificates conflicts for: conda-forge::python=3.7 -> openssl[version='>=1.1.1l,<1.1.2a'] -> ca-certificates conda-forge::pip -> python -> ca-certificates bioconda::hhsuite==3.3.0 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates

Package setuptools conflicts for: conda-forge|conda-forge::setuptools=59.5.0 conda-forge::pip -> setuptools conda-forge::pdbfixer -> setuptools conda-forge::setuptools=59.5.0 conda-forge::python=3.7 -> pip -> setuptools

Package libgcc-ng conflicts for: conda-forge::python=3.7 -> libffi[version='>=3.4.2,<3.5.0a0'] -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=12|>=7.2.0'] conda-forge::openmm=7.5.1 -> libgcc-ng[version='>=7.5.0'] conda-forge::openmm=7.5.1 -> cudatoolkit[version='11.0|11.0.'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] bioconda::hhsuite==3.3.0 -> perl[version='>=5.32.1,<5.33.0a0',build=_perl5] -> libgcc-ng[version='>=11.2.0|>=7.3.0|>=4.9|>=7.2.0'] conda-forge::setuptools=59.5.0 -> python[version='>=3.9,<3.10.0a0'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=11.2.0|>=7.3.0|>=4.9|>=7.2.0'] bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.5.0'] conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0'] bioconda::hhsuite==3.3.0 -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0'] conda-forge::pdbfixer -> numpy -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] conda-forge::pip -> python[version='>=3.7'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0'] pytorch::pytorch=1.12 -> blas=[build=mkl] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=11.2.0|>=4.9|>=7.2.0'] conda-forge::python=3.7 -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0'] bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.5.0|>=4.9']

Package mkl conflicts for: pytorch::pytorch=1.12 -> mkl[version='>=2018'] pytorch::pytorch=1.12 -> blas=[build=mkl] -> mkl

Package _libgcc_mutex conflicts for: conda-forge::openmm=7.5.1 -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='|0.1|0.1',build='conda_forge|main|main'] bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] conda-forge::python=3.7 -> libgcc-ng[version='>=9.4.0'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main'] bioconda::hhsuite==3.3.0 -> _openmp_mutex[version='>=4.5'] -> _libgcc_mutex[version='|0.1',build='conda_forge|main|main']

Package expat conflicts for: conda-forge::python=3.7 -> pypy3.7=7.3.7 -> expat[version='>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0'] conda-forge::openmm=7.5.1 -> pypy3.7[version='>=7.3.4'] -> expat[version='>=2.3.0,<3.0a0|>=2.4.1,<3.0a0'] conda-forge::setuptools=59.5.0 -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.4.1,<3.0a0']

Package cudatoolkit conflicts for: conda-forge::openmm=7.5.1 -> cudatoolkit[version='10.0|10.0.|10.1|10.1.|10.2|10.2.|11.0|11.0.|11.1|11.1.|>=11.2,<12.0a0|9.2|9.2.'] pytorch::pytorch=1.12 -> cudatoolkit[version='>=10.2,<10.3|>=11.3,<11.4|>=11.6,<11.7'] conda-forge::cudatoolkit=11.3 conda-forge::pdbfixer -> openmm[version='>=7.6'] -> cudatoolkit[version='10.0|10.0.|10.1|10.1.|10.2|10.2.|11.0|11.0.|11.1|11.1.|>=11.2,<12|9.2|9.2.|>=11.2,<12.0a0']

Package certifi conflicts for: conda-forge::pdbfixer -> setuptools -> certifi[version='>=2016.09|>=2016.9.26'] conda-forge::pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']

Package wheel conflicts for: conda-forge::python=3.7 -> pip -> wheel conda-forge::pip -> wheel

Package openmm conflicts for: conda-forge|conda-forge::openmm=7.5.1 conda-forge::pdbfixer -> openmm[version='>=7.5|>=7.6'] conda-forge::openmm=7.5.1The following specifications were found to be incompatible with your system:

• feature:/linux-64::__glibc==2.35=0
• feature:|@/linux-64::__glibc==2.35=0
• bioconda::hhsuite==3.3.0 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
• bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
• bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
• conda-forge::openmm=7.5.1 -> __glibc[version='>=2.17']
• conda-forge::openmm=7.5.1 -> cudatoolkit[version='11.0|11.0.*'] -> __glibc[version='>=2.17,<3.0.a0']
• conda-forge::pdbfixer -> openmm[version='>=7.6'] -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
• conda-forge::python=3.7 -> libgcc-ng[version='>=9.4.0'] -> __glibc[version='>=2.17']
• pytorch::pytorch=1.12 -> cudatoolkit[version='>=11.3,<11.4'] -> __glibc[version='>=2.17,<3.0.a0']

Your installed version is: 2.35

Note that strict channel priority may have removed packages required for satisfiability.

EnvironmentNameNotFound: Could not find conda environment: openfold_venv You can list all discoverable environments with conda info --envs.

[chewyalvin]

the installations ends with the following missing file:

gzip: tests/test_data/sample_feats.pickle.gz: No such file or directory

[gezmi]

I also have similar problems. When trying to solve the environment, conda comes up with a very long list of conflicts. I am installing it on debian 11. Any ideas which package versions could be removed safely, so that conda has higher chance of solving the environment?

Package python conflicts for:
pytorch::pytorch=1.12 -> typing_extensions -> python[version='>=2.7,<2.8.0a0|>=3.5|>=3.6|>=3.7|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.11,<3.12.0a0']
conda-forge::openmm=7.5.1 -> numpy -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.5,<3.6.0a0|3.4.*|3.7.*|3.9.*|3.8.*']
conda-forge::setuptools=59.5.0 -> python_abi=3.9[build=*_cp39] -> python[version='3.10.*|3.7.*|3.9.*|3.8.*']
bioconda::hhsuite==3.3.0 -> python[version='>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.6,<3.7.0a0']
conda-forge::openmm=7.5.1 -> python[version='>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0']
pytorch::pytorch=1.12 -> python[version='>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0']
conda-forge::pip -> setuptools -> python[version='!=3.0,!=3.1,!=3.2,!=3.3,!=3.4|>=3.10,<3.11.0a0|>=3.8|>=3.9,<3.10.0a0|>=3.11,<3.12.0a0|2.7.*|>=3.6']
conda-forge::setuptools=59.5.0 -> python[version='>=3.10,<3.11.0a0|>=3.7,<3.8.0a0|>=3.9,<3.10.0a0|>=3.8,<3.9.0a0']
conda-forge::pip -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.8,<3.9.0a0|>=3|>=3.6|>=3.7|>=3.6,<3.7.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0|3.4.*']
conda-forge::pdbfixer -> python[version='>=3.6']
conda-forge::pdbfixer -> numpy -> python[version='2.7.*|3.5.*|3.6.*|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.*|>=3.7|>=3.8']
bioconda::hhsuite==3.3.0 -> python_abi=3.10[build=*_cp310] -> python[version='2.7.*|3.10.*|3.8.*|3.7.*|3.9.*|3.6.*']


Package libstdcxx-ng conflicts for:
conda-forge::openmm=7.5.1 -> cudatoolkit[version='11.0|11.0.*'] -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
conda-forge::pip -> python[version='>=3.7'] -> libstdcxx-ng[version='>=11.2.0|>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0|>=7.2.0']
conda-forge::cudatoolkit=11.3 -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0']
conda-forge::python=3.7 -> libffi[version='>=3.4.2,<3.5.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.2.0']
bioconda::hhsuite==3.3.0 -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.3.0|>=4.9|>=7.2.0']
bioconda::hhsuite==3.3.0 -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0']
conda-forge::openmm=7.5.1 -> libstdcxx-ng[version='>=7.5.0']
conda-forge::pdbfixer -> numpy -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=7.3.0|>=4.9|>=11.2.0|>=7.5.0|>=9.3.0|>=7.2.0']
conda-forge::python=3.7 -> libstdcxx-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0']
conda-forge::setuptools=59.5.0 -> python[version='>=3.9,<3.10.0a0'] -> libstdcxx-ng[version='>=11.2.0|>=7.5.0|>=9.3.0|>=7.3.0|>=9.4.0|>=4.9|>=7.2.0']
bioconda::hmmer==3.3.2 -> libstdcxx-ng[version='>=10.3.0|>=9.3.0|>=7.5.0']
pytorch::pytorch=1.12 -> cudatoolkit[version='>=11.3,<11.4'] -> libstdcxx-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=11.2.0|>=7.5.0|>=7.3.0|>=4.9|>=7.2.0']

Package libgcc-ng conflicts for:
conda-forge::openmm=7.5.1 -> cudatoolkit[version='11.0|11.0.*'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
conda-forge::pip -> python[version='>=3.7'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.5.0|>=4.9']
conda-forge::python=3.7 -> libffi[version='>=3.4.2,<3.5.0a0'] -> libgcc-ng[version='>=10.3.0|>=11.2.0|>=12|>=7.2.0']
conda-forge::openmm=7.5.1 -> libgcc-ng[version='>=7.5.0']
conda-forge::python=3.7 -> libgcc-ng[version='>=4.9|>=7.3.0|>=7.5.0|>=9.3.0|>=9.4.0']
conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0']
conda-forge::pdbfixer -> numpy -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=4.9|>=11.2.0|>=7.2.0']
bioconda::hhsuite==3.3.0 -> perl[version='>=5.32.1,<5.33.0a0',build=*_perl5] -> libgcc-ng[version='>=11.2.0|>=7.3.0|>=4.9|>=7.2.0']
bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0|>=9.3.0|>=7.5.0']
conda-forge::setuptools=59.5.0 -> python[version='>=3.9,<3.10.0a0'] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=11.2.0|>=7.3.0|>=4.9|>=7.2.0']
pytorch::pytorch=1.12 -> blas=[build=mkl] -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0|>=7.3.0|>=11.2.0|>=4.9|>=7.2.0']
bioconda::hhsuite==3.3.0 -> libgcc-ng[version='>=10.3.0|>=12|>=9.4.0|>=9.3.0|>=7.5.0']

Package expat conflicts for:
conda-forge::setuptools=59.5.0 -> pypy3.7[version='>=7.3.7'] -> expat[version='>=2.4.1,<3.0a0']
conda-forge::python=3.7 -> pypy3.7=7.3.7 -> expat[version='>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0']
conda-forge::openmm=7.5.1 -> pypy3.7[version='>=7.3.4'] -> expat[version='>=2.3.0,<3.0a0|>=2.4.1,<3.0a0']

Package openmm conflicts for:
conda-forge::openmm=7.5.1
conda-forge|conda-forge::openmm=7.5.1
conda-forge::pdbfixer -> openmm[version='>=7.5|>=7.6']

Package pypy3.6 conflicts for:
conda-forge::pip -> setuptools -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
conda-forge::openmm=7.5.1 -> numpy -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']
bioconda::hhsuite==3.3.0 -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*']
conda-forge::pdbfixer -> numpy -> pypy3.6[version='7.3.0.*|7.3.1.*|7.3.2.*|7.3.3.*|>=7.3.1|>=7.3.2|>=7.3.3']

Package cudatoolkit conflicts for:
conda-forge::openmm=7.5.1 -> cudatoolkit[version='10.0|10.0.*|10.1|10.1.*|10.2|10.2.*|11.0|11.0.*|11.1|11.1.*|>=11.2,<12.0a0|9.2|9.2.*']
conda-forge::cudatoolkit=11.3
pytorch::pytorch=1.12 -> cudatoolkit[version='>=10.2,<10.3|>=11.3,<11.4|>=11.6,<11.7']
conda-forge::pdbfixer -> openmm[version='>=7.6'] -> cudatoolkit[version='10.0|10.0.*|10.1|10.1.*|10.2|10.2.*|11.0|11.0.*|11.1|11.1.*|>=11.2,<12|9.2|9.2.*|>=11.2,<12.0a0']
conda-forge|conda-forge::cudatoolkit=11.3

Package _libgcc_mutex conflicts for:
bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='*|0.1',build='main|main|conda_forge']
bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0'] -> _libgcc_mutex[version='*|0.1',build='main|main|conda_forge']
bioconda::hhsuite==3.3.0 -> _openmp_mutex[version='>=4.5'] -> _libgcc_mutex[version='*|0.1',build='main|main|conda_forge']
conda-forge::openmm=7.5.1 -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='*|0.1|0.1',build='main|main|conda_forge']
conda-forge::python=3.7 -> libgcc-ng[version='>=9.4.0'] -> _libgcc_mutex[version='*|0.1',build='main|main|conda_forge']
conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=12'] -> _libgcc_mutex[version='*|0.1',build='main|main|conda_forge']

Package pypy3.8 conflicts for:
bioconda::hhsuite==3.3.0 -> python[version='>=3.8,<3.9.0a0'] -> pypy3.8[version='7.3.11.*|7.3.9.*|7.3.8.*']
conda-forge::openmm=7.5.1 -> numpy -> pypy3.8[version='7.3.11.*|>=7.3.11|>=7.3.9|>=7.3.8|7.3.9.*|7.3.8.*']
conda-forge::setuptools=59.5.0 -> python[version='>=3.8,<3.9.0a0'] -> pypy3.8[version='7.3.11.*|7.3.9.*|7.3.8.*']
conda-forge::pdbfixer -> numpy -> pypy3.8[version='7.3.11.*|>=7.3.11|>=7.3.9|>=7.3.8|7.3.9.*|7.3.8.*']
conda-forge::pip -> python[version='>=3.7'] -> pypy3.8[version='7.3.11.*|7.3.9.*|7.3.8.*|>=7.3.9|>=7.3.8']
pytorch::pytorch=1.12 -> python[version='>=3.8,<3.9.0a0'] -> pypy3.8[version='7.3.11.*|7.3.9.*|7.3.8.*']

Package llvm-openmp conflicts for:
pytorch::pytorch=1.12 -> blas=[build=mkl] -> llvm-openmp[version='>=10.0.0|>=11.0.0|>=11.0.1|>=11.1.0|>=12.0.1|>=13.0.1|>=14.0.4|>=15.0.7|>=15.0.6|>=14.0.3|>=9.0.1']
bioconda::hhsuite==3.3.0 -> _openmp_mutex[version='>=4.5'] -> llvm-openmp[version='8.0.0|8.0.0|8.0.1|>=9.0.1',build='hc9558a2_0|hc9558a2_1|hc9558a2_0']

Package setuptools conflicts for:
conda-forge|conda-forge::setuptools=59.5.0
conda-forge::pip -> setuptools
conda-forge::pdbfixer -> setuptools
conda-forge::setuptools=59.5.0

Package _openmp_mutex conflicts for:
bioconda::hhsuite==3.3.0 -> _openmp_mutex[version='>=4.5']
bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']
conda-forge::openmm=7.5.1 -> libgcc-ng[version='>=7.5.0'] -> _openmp_mutex[version='>=4.5']
bioconda::hhsuite==3.3.0 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex
pytorch::pytorch=1.12 -> blas=[build=mkl] -> _openmp_mutex[version='*|>=4.5',build=*_llvm]
conda-forge::python=3.7 -> libgcc-ng[version='>=9.4.0'] -> _openmp_mutex[version='>=4.5']
conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0'] -> _openmp_mutex[version='>=4.5']

Package blas conflicts for:
conda-forge::pdbfixer -> numpy -> blas[version='*|*|1.0|1.1|1.0',build='openblas|openblas|mkl|openblas|mkl']
conda-forge::openmm=7.5.1 -> numpy -> blas[version='*|*|1.0|1.1|1.0',build='openblas|openblas|mkl|openblas|mkl']
pytorch::pytorch=1.12 -> blas=[build=mkl]

Package wheel conflicts for:
conda-forge::pip -> wheel
conda-forge::python=3.7 -> pip -> wheel

Package certifi conflicts for:
conda-forge::pdbfixer -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
conda-forge::pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']

Package ca-certificates conflicts for:
conda-forge::pip -> python -> ca-certificates
bioconda::hhsuite==3.3.0 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
conda-forge::python=3.7 -> openssl[version='>=1.1.1l,<1.1.2a'] -> ca-certificatesThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.31=0
  - feature:|@/linux-64::__glibc==2.31=0
  - bioconda::hhsuite==3.3.0 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::hmmer==3.3.2 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - bioconda::kalign2==2.04 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - conda-forge::cudatoolkit=11.3 -> __glibc[version='>=2.17,<3.0.a0']
  - conda-forge::cudatoolkit=11.3 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']
  - conda-forge::openmm=7.5.1 -> __glibc[version='>=2.17']
  - conda-forge::openmm=7.5.1 -> cudatoolkit[version='11.0|11.0.*'] -> __glibc[version='>=2.17,<3.0.a0']
  - conda-forge::pdbfixer -> openmm[version='>=7.6'] -> __glibc[version='>=2.17|>=2.17,<3.0.a0']
  - pytorch::pytorch=1.12 -> cudatoolkit[version='>=11.3,<11.4'] -> __glibc[version='>=2.17,<3.0.a0']

Your installed version is: 2.31

[Pellarin]

Hello I had the same error as @chewyalvin

gzip: tests/test_data/sample_feats.pickle.gz: No such file or directory

and during unit-tests I had the same error

I guess the installation gunzipped the original file, so it is not found. As a quick fix you can

cd tests/test_data/
gzip sample_feats.pickle

Now unit-tests using that file pass.