patrickbryant1
error when creating the environment
hi again!
i was able to run it to predict 3 proteins-protein interactions for my project and it worked, thanks!! but then i wanted to do it again with more proteins and it passed the 2 first stages of the code but when it arrived at the stage 3 : "Predict" I got this error :
Running pred 1 out of 1 2024-05-02 22:56:04.344415: W external/org_tensorflow/tensorflow/tsl/platform/default/dso_loader.cc:66] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/share/lsf/10.1/linux3.10-glibc2.17-x86_64/lib:/apps/easybd/easybuild/software/snappy/1.1.9-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libpng/1.6.37-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/protobuf/3.17.3-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/nsync/1.24.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/LMDB/0.9.29-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libjpeg-turbo/2.0.6-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/JsonCpp/1.9.4-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ICU/69.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/giflib/5.2.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/flatbuffers/2.0.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/double-conversion/3.1.5-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/cURL/7.78.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/HDF5/1.12.1-gompi-2021b/lib:/apps/easybd/easybuild/software/Szip/2.1.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/numpy/core/lib:/apps/easybd/easybuild/software/Python/3.9.6-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libffi/3.4.2-GCCcore-11.2.0/lib64:/apps/easybd/easybuild/software/GMP/6.2.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/SQLite/3.36-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/Tcl/8.6.11-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libreadline/8.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ncurses/6.2-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib:/apps/easybd/easybuild/software/FFTW/3.3.10-gompi-2021b/lib:/apps/easybd/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib:/apps/easybd/easybuild/software/OpenBLAS/0.3.18-GCC-11.2.0/lib:/apps/easybd/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib:/apps/easybd/easybuild/software/PMIx/4.1.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/UCX/1.11.2-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libevent/2.1.12-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/OpenSSL/1.1/lib:/apps/easybd/easybuild/software/hwloc/2.5.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libpciaccess/0.16-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libxml2/2.9.10-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/XZ/5.2.5-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/numactl/2.0.14-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/binutils/2.37-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/zlib/1.2.11-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/GCCcore/11.2.0/lib64 2024-05-02 22:56:05.118459: W external/org_tensorflow/tensorflow/tsl/platform/default/dso_loader.cc:66] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/share/lsf/10.1/linux3.10-glibc2.17-x86_64/lib:/apps/easybd/easybuild/software/snappy/1.1.9-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libpng/1.6.37-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/protobuf/3.17.3-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/nsync/1.24.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/LMDB/0.9.29-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libjpeg-turbo/2.0.6-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/JsonCpp/1.9.4-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ICU/69.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/giflib/5.2.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/flatbuffers/2.0.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/double-conversion/3.1.5-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/cURL/7.78.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/HDF5/1.12.1-gompi-2021b/lib:/apps/easybd/easybuild/software/Szip/2.1.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/numpy/core/lib:/apps/easybd/easybuild/software/Python/3.9.6-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libffi/3.4.2-GCCcore-11.2.0/lib64:/apps/easybd/easybuild/software/GMP/6.2.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/SQLite/3.36-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/Tcl/8.6.11-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libreadline/8.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ncurses/6.2-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib:/apps/easybd/easybuild/software/FFTW/3.3.10-gompi-2021b/lib:/apps/easybd/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib:/apps/easybd/easybuild/software/OpenBLAS/0.3.18-GCC-11.2.0/lib:/apps/easybd/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib:/apps/easybd/easybuild/software/PMIx/4.1.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/UCX/1.11.2-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libevent/2.1.12-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/OpenSSL/1.1/lib:/apps/easybd/easybuild/software/hwloc/2.5.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libpciaccess/0.16-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libxml2/2.9.10-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/XZ/5.2.5-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/numactl/2.0.14-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/binutils/2.37-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/zlib/1.2.11-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/GCCcore/11.2.0/lib64 2024-05-02 22:56:05.155585: W external/org_tensorflow/tensorflow/tsl/platform/default/dso_loader.cc:66] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/share/lsf/10.1/linux3.10-glibc2.17-x86_64/lib:/apps/easybd/easybuild/software/snappy/1.1.9-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libpng/1.6.37-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/protobuf/3.17.3-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/nsync/1.24.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/LMDB/0.9.29-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libjpeg-turbo/2.0.6-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/JsonCpp/1.9.4-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ICU/69.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/giflib/5.2.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/flatbuffers/2.0.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/double-conversion/3.1.5-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/cURL/7.78.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/HDF5/1.12.1-gompi-2021b/lib:/apps/easybd/easybuild/software/Szip/2.1.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/SciPy-bundle/2021.10-foss-2021b/lib/python3.9/site-packages/numpy/core/lib:/apps/easybd/easybuild/software/Python/3.9.6-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libffi/3.4.2-GCCcore-11.2.0/lib64:/apps/easybd/easybuild/software/GMP/6.2.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/SQLite/3.36-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/Tcl/8.6.11-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libreadline/8.1-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ncurses/6.2-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/bzip2/1.0.8-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/ScaLAPACK/2.1.0-gompi-2021b-fb/lib:/apps/easybd/easybuild/software/FFTW/3.3.10-gompi-2021b/lib:/apps/easybd/easybuild/software/FlexiBLAS/3.0.4-GCC-11.2.0/lib:/apps/easybd/easybuild/software/OpenBLAS/0.3.18-GCC-11.2.0/lib:/apps/easybd/easybuild/software/OpenMPI/4.1.1-GCC-11.2.0/lib:/apps/easybd/easybuild/software/PMIx/4.1.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/UCX/1.11.2-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libevent/2.1.12-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/OpenSSL/1.1/lib:/apps/easybd/easybuild/software/hwloc/2.5.0-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libpciaccess/0.16-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/libxml2/2.9.10-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/XZ/5.2.5-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/numactl/2.0.14-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/binutils/2.37-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/zlib/1.2.11-GCCcore-11.2.0/lib:/apps/easybd/easybuild/software/GCCcore/11.2.0/lib64
and when i try to reinstall tensorflow i got :
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. tensorflow 2.8.4 requires keras<2.9,>=2.8.0rc0, but you have keras 2.12.0 which is incompatible. tensorflow 2.8.4 requires protobuf<3.20,>=3.9.2, but you have protobuf 4.25.3 which is incompatible. tensorflow 2.8.4 requires tensorboard<2.9,>=2.8, but you have tensorboard 2.12.3 which is incompatible. tensorflow 2.8.4 requires tensorflow-estimator<2.9,>=2.8, but you have tensorflow-estimator 2.12.0 which is incompatible. pythran 0.10.0 requires gast~=0.5.0, but you have gast 0.4.0 which is incompatible. beniget 0.4.1 requires gast~=0.5.0, but you have gast 0.4.0 which is incompatible. Successfully installed gast-0.4.0 google-auth-2.29.0 google-auth-oauthlib-1.0.0 grpcio-1.63.0 keras-2.12.0 numpy-1.22.4 protobuf-4.25.3 tensorboard-2.12.3 tensorboard-data-server-0.7.2 tensorflow-estimator-2.12.0 WARNING: You are using pip version 21.2.2; however, version 24.0 is available. You should consider upgrading via the '/apps/easybd/easybuild/software/Python/3.9.6-GCCcore-11.2.0/bin/python3.9 -m pip install --upgrade pip' command.
do you know how to manage this issue ?
thank you!!
hi it's still not working when i try to load the environment saying that there are some conflicts in the packages
I also get some conflicts
Could not solve for environment specs
The following packages are incompatible
├─ ambertools ==23.3 py312h1577c9a_6 is requested and can be installed;
└─ openmmforcefields ==0.11.2 pyhd8ed1ab_1 is not installable because it requires
└─ ambertools >=20.0,<23 , which conflicts with any installable versions previously reported.
Finally, the following configuration worked for me:
name: speed_ppi
channels:
- conda-forge
- defaults
dependencies:
- ambertools
- annotated-types=0.6.0
- anyio=4.1.0
- argon2-cffi=23.1.0
- argon2-cffi-bindings=21.2.0
- arpack
- arrow=1.3.0
- asttokens=2.4.1
- astunparse=1.6.3
- async-lru=2.0.4
- attrs=23.1.0
- babel=2.14.0
- beautifulsoup4=4.12.2
- blas=1.0=mkl
- bleach=6.1.0
- blosc=1.21.5
- brotli=1.1.0
- brotli-bin=1.1.0
- brotli-python=1.1.0
- bson=0.5.9=py_0
- bzip2=1.0.8
- cairo=1.18.0
- cffi=1.16.0
- charset-normalizer=3.3.2
- chex=0.1.85
- colorama=0.4.6
- comm=0.1.4
- contourpy=1.2.0
- cuda-version=11.8
- cudatoolkit=11.8.0
- cudnn=8.9.2.26
- cycler=0.12.1
- debugpy=1.8.0
- decorator=5.1.1
- defusedxml=0.7.1
- dm-tree=0.1.7
- entrypoints=0.4
- exceptiongroup=1.2.0
- executing=2.0.1
- expat=2.5.0
- font-ttf-ubuntu=0.83
- fontconfig=2.14.2
- fonttools=4.46.0
- fqdn=1.5.1
- freetype=2.12.1
- freetype-py=2.3.0
- hdf4=4.2.15
- hdf5=1.14.3
- icu=73.2=h59595ed_0
- idna=3.6
- ipykernel=6.26.0
- ipython=8.18.1
- ipywidgets=8.1.1
- isoduration=20.11.0
- jedi=0.19.1
- jinja2=3.1.2=pyhd8ed1ab_1
- joblib=1.3.2
- json5=0.9.14
- jsonpointer=2.4=py312h7900ff3_3
- jsonschema=4.20.0
- jsonschema-specifications=2023.11.2
- jsonschema-with-format-nongpl=4.20.0
- jupyter-lsp=2.2.1
- jupyter_client=8.6.0
- jupyter_core=5.5.0=py312h7900ff3_0
- jupyter_events=0.9.0
- jupyter_server=2.12.1
- jupyter_server_terminals=0.5.0
- jupyterlab=4.0.9
- jupyterlab_pygments=0.3.0
- jupyterlab_server=2.25.2
- jupyterlab_widgets=3.0.9
- keyutils=1.6.1
- kiwisolver=1.4.5
- krb5=1.21.2
- lcms2=2.16
- ld_impl_linux-64=2.38
- lerc=4.0.0
- lxml=4.9.3
- lz4-c=1.9.4
- lzo=2.10
- notebook
- notebook-shim
- numpy
- overrides=7.4.0
- packaging=23.2
- packmol=20.010
- pandas=2.1.4
- pandocfilters=1.5.0
- panedr=0.7.2
- parmed
- parso=0.8.3
- pbr=6.0.0
- pcre2=10.42
- pdbfixer=1.9
- perl=5.32.1
- pexpect=4.8.0
- pickleshare=0.7.5
- pillow=10.1.0
- pint=0.21
- pip
- pixman=0.42.2
- pkgutil-resolve-name=1.3.10
- platformdirs=4.1.0
- prometheus_client=0.19.0
- prompt-toolkit=3.0.42
- psutil=5.9.7
- pthread-stubs=0.4
- ptyprocess=0.7.0
- pure_eval=0.2.2
- py-cpuinfo=9.0.0
- pycairo=1.25.1
- pycparser=2.21
- pydantic=2.5.2
- pydantic-core=2.14.5
- pyedr=0.7.2
- pygments=2.17.2
- pyparsing=3.1.1
- pysocks=1.7.1
- python_abi
- pytz=2023.3.post1
- pyyaml=6.0.1
- pyzmq=25.1.2
- rdkit=2023.09.3
- re2=2023.06.02
- readline=8.2
- referencing=0.32.0
- reportlab=4.0.7
- requests=2.31.0
- rfc3339-validator=0.1.4
- rfc3986-validator=0.1.1
- rlpycairo=0.2.0
- rpds-py=0.13.2
- scipy=1.11.4
- send2trash=1.8.2
- setuptools=68.0.0
- six=1.16.0
- smirnoff99frosst=1.1.0
- snappy=1.1.10
- sniffio=1.3.0
- soupsieve=2.5
- sqlalchemy=2.0.23
- sqlite=3.41.2
- stack_data=0.6.2
- tbb=2021.8.0
- terminado=0.18.0
- tinycss2=1.2.1
- tinydb=4.8.0
- tk=8.6.13
- tomli=2.0.1
- toolz=0.12.0
- tornado=6.3.3
- tqdm=4.66.1
- traitlets=5.14.0
- types-python-dateutil=2.8.19.14
- typing-extensions=4.9.0
- typing_extensions=4.9.0
- typing_utils=0.1.0
- tzdata
- widgetsnbextension
- zstd
- pip
Followed by
pip install biopython==1.81 click etils fsspec google-auth h5py ml-collections markdown mmpbsa-py==16.0 svgwrite wrapt tf-keras-nightly pdb4amber protobuf rich rsa sander
For me, neither sander nor mmpbsa can be found anymore with either pip or conda.
