Comments (7)
Hi @olliemelling,
I'm sorry that you got problems to install BLUES. I'm looking into it now.
Could you confirm that you got this issue on both MacOS and Linux?
Also could you attach your conda list of the environment created to install BLUES?
Thank you!
from blues.
Hi,
Thanks for looking into this. I can confirm that I got the same error both on MacOS and Linux.
Below is my conda list for the environment - this is after installing oeommtools and openeye-toolkits
# Name Version Build Channel
_libgcc_mutex 0.1 main
alabaster 0.7.12 py36_0
attrs 20.3.0 pyhd3eb1b0_0
babel 2.9.0 pyhd3eb1b0_0
blas 1.0 mkl
brotlipy 0.7.0 py36h27cfd23_1003
ca-certificates 2020.12.8 h06a4308_0
certifi 2020.12.5 py36h06a4308_0
cffi 1.14.4 py36h261ae71_0
chardet 4.0.0 py36h06a4308_1003
colorama 0.4.4 pyhd3eb1b0_0
cryptography 3.3.1 py36h3c74f83_0
cython 0.29.21 py36h2531618_0
docutils 0.16 py36_1
fftw3f 3.3.4 2 omnia
idna 2.10 py_0
imagesize 1.2.0 py_0
importlib-metadata 2.0.0 py_1
importlib_metadata 2.0.0 1
iniconfig 1.1.1 py_0
intel-openmp 2020.2 254
jinja2 2.11.2 py_0
ld_impl_linux-64 2.33.1 h53a641e_7
libedit 3.1.20191231 h14c3975_1
libffi 3.3 he6710b0_2
libgcc 7.2.0 h69d50b8_2
libgcc-ng 9.1.0 hdf63c60_0
libstdcxx-ng 9.1.0 hdf63c60_0
markupsafe 1.1.1 py36h7b6447c_0
mkl 2020.2 256
mkl-service 2.3.0 py36he8ac12f_0
mkl_fft 1.2.0 py36h23d657b_0
mkl_random 1.1.1 py36h0573a6f_0
more-itertools 8.6.0 pyhd3eb1b0_0
ncurses 6.2 he6710b0_1
numpy 1.19.2 py36h54aff64_0
numpy-base 1.19.2 py36hfa32c7d_0
numpydoc 1.1.0 pyhd3eb1b0_1
oeommtools 0.1.16 pypi_0 pypi
openeye-toolkits 2020.2.0 py36_0 openeye
openmm 7.4.2 py36_cuda101_rc_1 omnia
openssl 1.1.1i h27cfd23_0
packaging 20.8 pyhd3eb1b0_0
packmol 1.0.0 2 omnia
pandas 1.1.3 py36he6710b0_0
parmed 3.2.0 py36_0 omnia
pip 20.3.3 py36h06a4308_0
pluggy 0.13.1 py36_0
py 1.10.0 pyhd3eb1b0_0
pycparser 2.20 py_2
pygments 2.7.4 pyhd3eb1b0_0
pyopenssl 20.0.1 pyhd3eb1b0_1
pyparsing 2.4.7 py_0
pysocks 1.7.1 py36h06a4308_0
pytest 6.2.1 py36h06a4308_0
python 3.6.12 hcff3b4d_2
python-dateutil 2.8.1 py_0
pytz 2020.5 pyhd3eb1b0_0
readline 8.0 h7b6447c_0
requests 2.25.1 pyhd3eb1b0_0
setuptools 51.1.2 py36h06a4308_4
six 1.15.0 py36h06a4308_0
snowballstemmer 2.0.0 py_0
sphinx 3.4.3 pyhd3eb1b0_0
sphinxcontrib-applehelp 1.0.2 py_0
sphinxcontrib-devhelp 1.0.2 py_0
sphinxcontrib-htmlhelp 1.0.3 py_0
sphinxcontrib-jsmath 1.0.1 py_0
sphinxcontrib-qthelp 1.0.3 py_0
sphinxcontrib-serializinghtml 1.1.4 py_0
sqlite 3.33.0 h62c20be_0
tk 8.6.10 hbc83047_0
toml 0.10.1 py_0
urllib3 1.26.2 pyhd3eb1b0_0
wheel 0.36.2 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
zipp 3.4.0 pyhd3eb1b0_0
zlib 1.2.11 h7b6447c_3
Many thanks
from blues.
Hi @olliemelling,
I just tried it on my MacBook Pro and didn't have any issues. Below are what I did:
conda create -n blues python=3.6
conda activate blues
conda install -c mobleylab blues
Could you try it again with these command lines? I'm testing the Linux installation now.
Thanks!
from blues.
I have just tried running exactly that and unfortunately still ended up with the same error as before.
Maybe this is a problem with my conda setup somewhere given it is working for you! It just seemed strange that I'm getting the same error on both MacOS and Linux.
from blues.
Okay, that is strange. I also tried to install it on Linux system following the instructions on Github. Didn't get any problems either. So I don't know why it just cannot work for you. I plan to do more tests on different machines.
Have you tried to install it from source code (see following)? It works for me on a Linux system.
conda create -n blues python=3.6
conda activate blues
# Clone the BLUES repository
git clone https://github.com/MobleyLab/blues.git ./blues
# Install some dependencies
conda install -c omnia -c conda-forge openmmtools=0.15.0 openmm=7.4.2 numpy cython
# Optional: To use SideChainMove class, OpenEye toolkits and related tools are requried (requires OpenEye License)
conda install -c openeye/label/Orion -c omnia oeommtools
conda install -c openeye openeye-toolkits
# Install BLUES package from the top directory
pip install -e .
# To validate your BLUES installation run the tests (need pytest)
cd blues/tests
pytest -v -s
from blues.
Hi @olliemelling,
I tried to reproduce your errors in another Mac and here is how I resolved it:
conda create -n blues python=3.6
conda activate blues
conda install -c openeye/label/Orion -c omnia oeommtools
conda install -c openeye openeye-toolkits
conda install -c omnia -c conda-forge openmmtools=0.15.0 openmm=7.4.2 numpy cython
conda install -c mobleylab blues
Could you give it a try and see if it fixes your issue? For some reason I still don't see your errors in my own machine (both OSX and Linux). If you still cannot get it work, please try to install BLUES from source as I mentioned in my earlier message.
Please let me know if you still cannot get it work. Sorry again for the inconvenience.
from blues.
Hi @yunhuige
I have tried running with the above commands and it is now working on both MacOS and Linux!
I think it must have been because I hadn't previously been running:
conda install -c omnia -c conda-forge openmmtools=0.15.0 openmm=7.4.2 numpy cython
Maybe there were some version clashes with openmmtools or openmm that were causing the problem, so specifying the versions as 0.15.0 and 7.4.2 maybe solved it? Seems strange that it wasn't happening on your machine though.
Thanks for your help!
from blues.
Related Issues (20)
- oeommtools installation HOT 2
- Water translation & rotation HOT 2
- May ultimately need different handling of long range charge interactions HOT 2
- Tests fail with openmmtools=0.15.0 HOT 2
- Update conda packages HOT 1
- Multiple alchemical regions HOT 7
- Additions to YAML configuration file
- Update devdocs and package building instructions
- Installing from source via `setup.py` does not install required packages
- Give option for Logger to stream OR write to file. HOT 1
- TypeError with LoadParm Using "structure.restart" Property HOT 1
- Freezing water HOT 4
- Improve code readability and maintainability HOT 1
- Potential bug in syncing NCMC and MD simulation HOT 1
- Failing to deploy to anaconda cloud HOT 1
- Exception: Error compiling program when running system HOT 2
- Can BLUES perform multiple ligands rotate and move HOT 2
- protocol work turned nan after RandomLigandRotationMove HOT 3
- Acceptance Ratio: 0.0 HOT 4
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from blues.