Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Alphaflow not working. #31

Open
johnny-rodriguez opened this issue Aug 29, 2024 · 8 comments
Open

Alphaflow not working. #31

johnny-rodriguez opened this issue Aug 29, 2024 · 8 comments

Comments

@johnny-rodriguez
Copy link

I installed alphaflow as described on the github page. I used a .csv file whose format looks exactly as the atlas example. I get the following error:
python predict.py --mode esmfold --input_csv /data/AI_tools/alphaflow/test/protein.csv --weights /data/AI_tools/alphaflow/weights/esmflow_md_base_202402.pt --samples 10 --outpdb /data/AI_tools/alphaflow/test/output
2024-08-29 12:27:56,173 [ip-10-10-32-206:1533012] [INFO] Loading the model
2024-08-29 12:29:34,063 [ip-10-10-32-206:1533012] [INFO] Model has been loaded
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 10/10 [03:16<00:00, 19.68s/it]

Traceback (most recent call last):
File "/data/AI_tools/alphaflow/predict.py", line 178, in
main()
File "/data/anaconda3/envs/alphaflow/lib/python3.9/site-packages/torch/autograd/grad_mode.py", line 27, in decorate_context
return func(*args, **kwargs)
File "/data/AI_tools/alphaflow/predict.py", line 153, in main
chains = pd.concat(chains)
File "/data/anaconda3/envs/alphaflow/lib/python3.9/site-packages/pandas/util/_decorators.py", line 331, in wrapper
return func(*args, **kwargs)
File "/data/anaconda3/envs/alphaflow/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 368, in concat
op = _Concatenator(
File "/data/anaconda3/envs/alphaflow/lib/python3.9/site-packages/pandas/core/reshape/concat.py", line 425, in init
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate

These are the packages I have in the environment:

packages in environment at /data/anaconda3/envs/alphaflow:

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
absl-py 2.1.0 pyhd8ed1ab_0 conda-forge
aiohappyeyeballs 2.4.0 pypi_0 pypi
aiohttp 3.10.5 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
appdirs 1.4.4 pyh9f0ad1d_0 conda-forge
astor 0.8.1 pyh9f0ad1d_0 conda-forge
async-timeout 4.0.3 pypi_0 pypi
attrs 24.2.0 pypi_0 pypi
biopandas 0.4.0 pypi_0 pypi
biopython 1.79 py39hb9d737c_3 conda-forge
blosc 1.21.5 hc2324a3_1 conda-forge
brotli-python 1.1.0 py39h3d6467e_1 conda-forge
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.33.1 heb4867d_0 conda-forge
ca-certificates 2024.7.4 hbcca054_0 conda-forge
certifi 2024.7.4 pyhd8ed1ab_0 conda-forge
cffi 1.17.0 py39h49a4b6b_0 conda-forge
charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
contextlib2 21.6.0 pypi_0 pypi
cuda 11.3.0 h3b286be_0 nvidia
cuda-command-line-tools 11.3.0 h3b286be_0 nvidia
cuda-compiler 11.3.0 h3b286be_0 nvidia
cuda-cudart 11.3.58 hc1aae59_0 nvidia
cuda-cuobjdump 11.3.58 hc78e225_0 nvidia
cuda-cupti 11.3.58 h9a3dd33_0 nvidia
cuda-cuxxfilt 11.3.58 he670d9e_0 nvidia
cuda-gdb 11.3.58 h531059a_0 nvidia
cuda-libraries 11.3.0 h3b286be_0 nvidia
cuda-libraries-dev 11.3.0 h3b286be_0 nvidia
cuda-memcheck 11.3.58 h8711ecb_0 nvidia
cuda-nvcc 11.3.58 h2467b9f_0 nvidia
cuda-nvdisasm 11.3.58 hd2ea46e_0 nvidia
cuda-nvml-dev 12.6.37 2 nvidia
cuda-nvprof 11.3.58 h860cd9e_0 nvidia
cuda-nvprune 11.3.58 hb917323_0 nvidia
cuda-nvrtc 11.3.58 he300756_0 nvidia
cuda-nvtx 11.3.58 h3fa534a_0 nvidia
cuda-nvvp 11.3.58 hd16380c_0 nvidia
cuda-runtime 11.3.0 h3b286be_0 nvidia
cuda-samples 11.6.101 h8efea70_0 nvidia
cuda-sanitizer-api 11.3.58 h58da6c8_0 nvidia
cuda-thrust 11.3.58 h7b74f08_0 nvidia
cuda-toolkit 11.3.0 h3b286be_0 nvidia
cuda-tools 11.3.0 h3b286be_0 nvidia
cuda-version 12.6 3 nvidia
cuda-visual-tools 11.3.0 h3b286be_0 nvidia
dm-tree 0.1.6 py39h1832856_1 conda-forge
docker-pycreds 0.4.0 py_0 conda-forge
einops 0.8.0 pyhd8ed1ab_0 conda-forge
fair-esm 2.0.0 pypi_0 pypi
filelock 3.15.4 pypi_0 pypi
frozenlist 1.4.1 pypi_0 pypi
fsspec 2024.6.1 pypi_0 pypi
gitdb 4.0.11 pyhd8ed1ab_0 conda-forge
gitpython 3.1.43 pyhd8ed1ab_0 conda-forge
h2 4.1.0 pyhd8ed1ab_0 conda-forge
hdf5 1.14.0 nompi_hb72d44e_103 conda-forge
hpack 4.0.0 pyh9f0ad1d_0 conda-forge
hyperframe 6.0.1 pyhd8ed1ab_0 conda-forge
idna 3.8 pyhd8ed1ab_0 conda-forge
ihm 1.3 py39hcd6043d_0 conda-forge
jinja2 3.1.4 pypi_0 pypi
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.3 h659f571_0 conda-forge
ld_impl_linux-64 2.40 hf3520f5_7 conda-forge
libabseil 20240116.2 cxx17_he02047a_1 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libblas 3.9.0 20_linux64_openblas conda-forge
libcblas 3.9.0 20_linux64_openblas conda-forge
libcublas 11.4.2.10064 h8a72295_0 nvidia
libcufft 10.4.2.58 h58ccd86_0 nvidia
libcurand 10.2.4.58 h99380db_0 nvidia
libcurl 8.8.0 hca28451_1 conda-forge
libcusolver 11.1.1.58 hec68242_0 nvidia
libcusparse 11.5.0.58 hf5aa513_0 nvidia
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.1.0 h77fa898_1 conda-forge
libgcc-ng 14.1.0 h69a702a_1 conda-forge
libgfortran 14.1.0 h69a702a_1 conda-forge
libgfortran-ng 14.1.0 h69a702a_1 conda-forge
libgfortran5 14.1.0 hc5f4f2c_1 conda-forge
libgomp 14.1.0 h77fa898_1 conda-forge
liblapack 3.9.0 20_linux64_openblas conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnpp 11.3.3.44 h8df316f_0 nvidia
libnsl 2.0.1 hd590300_0 conda-forge
libnvjpeg 11.4.1.58 h3d06750_0 nvidia
libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge
libprotobuf 4.25.3 h08a7969_0 conda-forge
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx 14.1.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.1.0 h4852527_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
lightning-utilities 0.11.6 pypi_0 pypi
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 hd590300_1001 conda-forge
markupsafe 2.1.5 pypi_0 pypi
mdtraj 1.9.4 py39h1dbbcdb_2 conda-forge
ml-collections 0.1.0 pypi_0 pypi
modelcif 0.7 pyhd8ed1ab_0 conda-forge
mpmath 1.3.0 pypi_0 pypi
msgpack-python 1.0.8 py39h95fdab5_0 conda-forge
multidict 6.0.5 pypi_0 pypi
ncurses 6.5 he02047a_1 conda-forge
networkx 3.2.1 pypi_0 pypi
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.10.0 py39he85e4be_100 conda-forge
numpy 1.21.2 py39hdbf815f_0 conda-forge
nvidia-cublas-cu12 12.1.3.1 pypi_0 pypi
nvidia-cuda-cupti-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-nvrtc-cu12 12.1.105 pypi_0 pypi
nvidia-cuda-runtime-cu12 12.1.105 pypi_0 pypi
nvidia-cudnn-cu12 9.1.0.70 pypi_0 pypi
nvidia-cufft-cu12 11.0.2.54 pypi_0 pypi
nvidia-curand-cu12 10.3.2.106 pypi_0 pypi
nvidia-cusolver-cu12 11.4.5.107 pypi_0 pypi
nvidia-cusparse-cu12 12.1.0.106 pypi_0 pypi
nvidia-nccl-cu12 2.20.5 pypi_0 pypi
nvidia-nvjitlink-cu12 12.6.20 pypi_0 pypi
nvidia-nvtx-cu12 12.1.105 pypi_0 pypi
openfold 1.0.1 pypi_0 pypi
openssl 3.3.1 hb9d3cd8_3 conda-forge
packaging 24.1 pyhd8ed1ab_0 conda-forge
pandas 1.5.3 py39h2ad29b5_1 conda-forge
pip 24.2 pyhd8ed1ab_0 conda-forge
platformdirs 4.2.2 pyhd8ed1ab_0 conda-forge
protobuf 4.25.3 py39h1be52a0_0 conda-forge
psutil 6.0.0 py39hd3abc70_0 conda-forge
pycparser 2.22 pyhd8ed1ab_0 conda-forge
pyparsing 3.1.4 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
pytables 3.7.0 py39hf8baa48_4 conda-forge
python 3.9.19 h0755675_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python_abi 3.9 5_cp39 conda-forge
pytorch-lightning 2.0.4 pypi_0 pypi
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyyaml 6.0.2 py39hcd6043d_0 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.32.3 pyhd8ed1ab_0 conda-forge
scipy 1.7.1 py39hee8e79c_0 conda-forge
sentry-sdk 2.13.0 pyhd8ed1ab_0 conda-forge
setproctitle 1.3.3 py39hd1e30aa_0 conda-forge
setuptools 72.2.0 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
smmap 5.0.0 pyhd8ed1ab_0 conda-forge
snappy 1.2.1 ha2e4443_0 conda-forge
sympy 1.13.2 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
torch 1.12.1+cu113 pypi_0 pypi
torchmetrics 1.4.1 pypi_0 pypi
tqdm 4.66.5 pypi_0 pypi
triton 3.0.0 pypi_0 pypi
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024a h8827d51_1 conda-forge
urllib3 2.2.2 pyhd8ed1ab_1 conda-forge
wandb 0.16.6 pyhd8ed1ab_1 conda-forge
wheel 0.44.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
yarl 1.9.4 pypi_0 pypi
zlib 1.2.13 h4ab18f5_6 conda-forge
zstandard 0.23.0 py39h623c9ba_0 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
@johnny-rodriguez
Copy link
Author

In addition can someone share the conda environment package list? I want to see if the package versions themselves are causing the problem.

@bjing2016
Copy link
Owner

Hi Johnny,
It looks like there was an issue with the most recent PR. I have unmerged the PR --- could you pull and see if it's working now?

@lcscs12345
Copy link

Hi,

Sorry about the recent PR. I have been running it (ESMFlow) without an issue using Apptainer.
https://hub.docker.com/repository/docker/lcscs12345/alphaflow/general

Here are the dependencies. biopandas is an additional dependency in the PR. Can you spot any issues @bjing2016 ?

# packages in environment at /opt/conda/envs/alphaflow:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
absl-py                   2.1.0                    pypi_0    pypi
aiohttp                   3.9.3                    pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
astunparse                1.6.3                    pypi_0    pypi
async-timeout             4.0.3                    pypi_0    pypi
attrs                     23.2.0                   pypi_0    pypi
biopandas                 0.4.1              pyhd8ed1ab_1    conda-forge
biopython                 1.79                     pypi_0    pypi
bzip2                     1.0.8                h7b6447c_0  
c-ares                    1.19.1               h5eee18b_0  
ca-certificates           2024.2.2             hbcca054_0    conda-forge
certifi                   2024.2.2                 pypi_0    pypi
charset-normalizer        3.3.2                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
contextlib2               21.6.0                   pypi_0    pypi
curl                      8.5.0                hdbd6064_0  
dm-tree                   0.1.6                    pypi_0    pypi
docker-pycreds            0.4.0                    pypi_0    pypi
einops                    0.7.0                    pypi_0    pypi
expat                     2.5.0                h6a678d5_0  
fair-esm                  2.0.0                    pypi_0    pypi
frozenlist                1.4.1                    pypi_0    pypi
fsspec                    2024.2.0                 pypi_0    pypi
gdbm                      1.18                 hd4cb3f1_4  
gettext                   0.21.0               h39681ba_1  
git                       2.40.1          pl5340h36fbf9e_1  
gitdb                     4.0.11                   pypi_0    pypi
gitpython                 3.1.42                   pypi_0    pypi
icu                       73.1                 h6a678d5_0  
idna                      3.6                      pypi_0    pypi
ihm                       1.0                      pypi_0    pypi
krb5                      1.20.1               h143b758_1  
ld_impl_linux-64          2.38                 h1181459_1  
libblas                   3.9.0           22_linux64_openblas    conda-forge
libcblas                  3.9.0           22_linux64_openblas    conda-forge
libcurl                   8.5.0                h251f7ec_0  
libedit                   3.1.20230828         h5eee18b_0  
libev                     4.33                 h7f8727e_1  
libffi                    3.4.4                h6a678d5_0  
libgcc-ng                 13.2.0               h77fa898_7    conda-forge
libgfortran-ng            13.2.0               h69a702a_7    conda-forge
libgfortran5              13.2.0               hca663fb_7    conda-forge
libgomp                   13.2.0               h77fa898_7    conda-forge
liblapack                 3.9.0           22_linux64_openblas    conda-forge
libnghttp2                1.57.0               h2d74bed_0  
libopenblas               0.3.27          pthreads_h413a1c8_0    conda-forge
libssh2                   1.10.0               hdbd6064_2  
libstdcxx-ng              11.2.0               h1234567_1  
libxml2                   2.10.4               hf1b16e4_1  
lightning-utilities       0.10.1                   pypi_0    pypi
mdtraj                    1.9.9                    pypi_0    pypi
ml-collections            0.1.0                    pypi_0    pypi
modelcif                  0.7                      pypi_0    pypi
msgpack                   1.0.7                    pypi_0    pypi
multidict                 6.0.5                    pypi_0    pypi
ncurses                   6.4                  h6a678d5_0  
numpy                     1.21.2                   pypi_0    pypi
openfold                  1.0.1                    pypi_0    pypi
openssl                   3.3.0                h4ab18f5_2    conda-forge
packaging                 23.2                     pypi_0    pypi
pandas                    1.5.3                    pypi_0    pypi
pcre2                     10.42                hebb0a14_0  
perl                      5.34.0               h5eee18b_2  
pip                       23.3.1           py39h06a4308_0  
protobuf                  4.25.3                   pypi_0    pypi
psutil                    5.9.8                    pypi_0    pypi
pyparsing                 3.1.1                    pypi_0    pypi
python                    3.9.18               h955ad1f_0  
python-dateutil           2.8.2                    pypi_0    pypi
python_abi                3.9                      2_cp39    conda-forge
pytorch-lightning         2.0.4                    pypi_0    pypi
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pyyaml                    6.0.1                    pypi_0    pypi
readline                  8.2                  h5eee18b_0  
requests                  2.31.0                   pypi_0    pypi
scipy                     1.7.1                    pypi_0    pypi
sentry-sdk                1.40.5                   pypi_0    pypi
setproctitle              1.3.3                    pypi_0    pypi
setuptools                68.2.2           py39h06a4308_0  
six                       1.16.0             pyh6c4a22f_0    conda-forge
smmap                     5.0.1                    pypi_0    pypi
sqlite                    3.41.2               h5eee18b_0  
tk                        8.6.12               h1ccaba5_0  
torch                     1.12.1+cu113             pypi_0    pypi
torchmetrics              1.3.1                    pypi_0    pypi
tqdm                      4.66.2                   pypi_0    pypi
typing-extensions         4.9.0                    pypi_0    pypi
tzdata                    2024a                h04d1e81_0  
urllib3                   2.2.1                    pypi_0    pypi
wandb                     0.16.3                   pypi_0    pypi
wheel                     0.41.2           py39h06a4308_0  
xz                        5.4.5                h5eee18b_0  
yarl                      1.9.4                    pypi_0    pypi
zlib                      1.2.13               h5eee18b_0

@johnny-rodriguez
Copy link
Author

Using the environment I originally built (running Cuda 11.3), I was able to run your new code successfully! However, I saw you removed a lot of the analysis from the predict.py file. Do you plan to add that back? I want to get an idea of how confident the pdb file generated is.

@johnny-rodriguez
Copy link
Author

johnny-rodriguez commented Sep 3, 2024 •
edited
Loading

@lcscs12345 I could not figure out how to download the image from your link. I tried docker and apptainer.

@lcscs12345
Copy link

@johnny-rodriguez Could you try this?

apptainer pull alphaflow.sif oras://docker.io/lcscs12345/alphaflow:a1cd789

@johnny-rodriguez
Copy link
Author

I was able to pull the apptainer. How do you run it?

@lcscs12345
Copy link

The image has no alphaflow installed.

First, check the GPU availability.
apptainer exec --nv alphaflow.sif python -c "import torch; print(torch.cuda.device_count())"

Then run
apptainer shell --nv alphaflow.sif

and run alphaflow from a local directory as usual, or

apptainer exec --nv alphaflow.sif \
    python alphaflow/predict.py \
    --mode esmfold \
    --input_csv input.csv \
    --weights alphaflow/weights/esmflow_md_base_202402.pt \
    --outpdb output/ \
    --samples 250

Make sure the paths are correct.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@lcscs12345 @bjing2016 @johnny-rodriguez