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License: MIT License
This package contains deep learning models and related scripts for RoseTTAFold
License: MIT License
Hi, Could you please tell if its possible to extract embeddings from the pre-final layers similar to Facebook's ESM1v / ESM1b models?
Thank you
Hi, first of all thank you for open sourcing this amazing tool!
The paper mentions that
The final layer of the end-to-end version of our 3-track network generates 3D structure
models by combining features from discontinuous crops of the protein sequence (two segments
of the protein with a chain break between them). Because the network can seamlessly handle
chain breaks, it can be readily utilized to predict the structure of protein-protein complexes
directly from sequence information.
Looking at the code in Refine_module.py
and predict_e2e.py
, it looks like there are quite a lot of details to get right and many ways to screw up how the information from two disjoint chains should be merged. According to the supplementary material there's also changes in the positional encoding
needed for this to work (the +200 offset).
Is there an example script or some guidelines that you could share that shows how to properly do a structure prediction for a Protein-Protein complex?
Finally, I was wondering if any experiments were done trying to estimate binding affinity scores from the hidden layer activations of the Refine_Module? This would be a very useful extension for doing protein design...
I encountered this error with the e2e script, with my protein of 255AA in length. The error happens at the last step when building the 3D models. Any idea why this is happening and what can I do to fix it? I am using a GTX1660, a better setup is not possible in the near future.
Thanks,
Wenzhe
RuntimeError: CUDA out of memory. Tried to allocate 456.00 MiB (GPU 0; 5.80 GiB
total capacity; 3.24 GiB already allocated; 420.88 MiB free; 3.66 GiB reserved i
n total by PyTorch)
Thank you so much for your great repo.
You only showed the size of zip files. Could you please tell us how many TBs of data files are after unzipping?
Hi,
I'm reading your code, and find one place might be typo:
input_t2d = t2d[:,:,sel][:,:,:,sel].to(self.device)
RoseTTAFold/network/predict_e2e.py
Line 174 in d0de739
I think it should be input_t2d = t2d[:,:,sel][:,sel].to(self.device)
or else? Sorry for my poor skill of using index...
Hi, RoseTTAFold team~
Since i need to predict thousands of proteins, but the scripts (run_e2e_ver.sh and run_pyrosetta_ver.sh) seem to only input one protein at the same time. What should i do to speedup my analysis?
Currently, i use the for
loop to run pyrosetta for each protein, any suggustion?
Thanks!
Rusfell
Multiple users having issues using the PDB100 database with HHblits (v3.3) (see soedinglab/hh-suite#275). I noticed that PDB100 does not contain the the _a3m
database. This causes the per-merge to crash.
Is there any reason to not include the a3m file?
Hello!
I run the example use the command ../run_pyrosetta_ver.sh input.fa
but error: realpath: missing operand Try 'realpath --help' for more information.
how to do?
When I try to run 'run_pyrosetta_ver.sh input.fa .', the error will be reported in 'network.stderr' file. Why is this?
Thanks.
Using backend: pytorch
Traceback (most recent call last):
File "/home/ganjh/RoseTTAFold/network/predict_pyRosetta.py", line 199, in <module>
pred = Predictor(model_dir=args.model_dir, use_cpu=args.use_cpu)
File "/home/ganjh/RoseTTAFold/network/predict_pyRosetta.py", line 67, in __init__
self.model = RoseTTAFoldModule(**MODEL_PARAM).to(self.device)
File "/home/ganjh/.conda/envs/RoseTTAFold/lib/python3.8/site-packages/torch/nn/modules/module.py", line 852, in to
return self._apply(convert)
File "/home/ganjh/.conda/envs/RoseTTAFold/lib/python3.8/site-packages/torch/nn/modules/module.py", line 530, in _apply
module._apply(fn)
File "/home/ganjh/.conda/envs/RoseTTAFold/lib/python3.8/site-packages/torch/nn/modules/module.py", line 530, in _apply
module._apply(fn)
File "/home/ganjh/.conda/envs/RoseTTAFold/lib/python3.8/site-packages/torch/nn/modules/module.py", line 552, in _apply
param_applied = fn(param)
File "/home/ganjh/.conda/envs/RoseTTAFold/lib/python3.8/site-packages/torch/nn/modules/module.py", line 850, in convert
return t.to(device, dtype if t.is_floating_point() or t.is_complex() else None, non_blocking)
RuntimeError: CUDA error: the provided PTX was compiled with an unsupported toolchain.
CUDA kernel errors might be asynchronously reported at some other API call,so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.
Is it possible to get side chain information from e2e script? Thx!
In the step 1.clone the package , '.git' is missed when running git clone.
Hi there;
Thanks for sharing your great job;
Do you plan to share your training dataset (+22000 target) publicly as well?
Thanks
Hi,
I am trying to install the RoseTTAfold on a Linux based cluster, and I am at the last step of the installation
6. Obtain a PyRosetta licence and install the package in the newly created folding conda environment (link).
I am a little confused which package to use and how would I configure the install at this step. Do you mind giving a little more clarification on this please?
Thanks,
Albert
Phosphorylation could change the structure of the protein. I wonder if the current program can include such variations?
Hi,
I want to use RoseTTAFold, but our Linux server has no GPU and only CPUs. Is it OK? Thank you!
Rusfell
Hello,
I am just wondering if the md5 hash is available for those large database files and those decompressed files to compare. It took long to download and decompress, just want to make sure the files are intact.
I found that for the 272G bfd database file, wondering if it's available for the other two database files.
Thank you!
Hi,
When I run ’run_pyrosetta_ver.sh input.fa .’, the result gets two folders hhblits and log. I don't get five final models. Why is this ?
Thank you
it looks the model only predicts backbone: N, C, C-alpha; no C-beta and O; no sidechain?
Hello:
When I run commad'conda env create -f RoseTTAFold-linux-cu101.yml' or 'conda env create -f RoseTTAFold-linux.yml', I'm both getting the following error:
Collecting package metadata (repodata.json): done
Solving environment: failed
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Is this my problem with my running environment. How to solve this problem?
Thany you!
runs normal, however, there is no pdb file out in the result folder
$ run_pyrosetta_ver.sh XXX.fasta .
Running HHblits
Running PSIPRED
Running hhsearch
Predicting distance and orientations
Running parallel RosettaTR.py
$ ls
hhblits log parallel.fold.list pdb-3track t000_.3track.npz t000_.atab t000_.hhr t000_.msa0.a3m t000_.msa0.ss2.a3m t000_.ss2
$ ls pdb-3track
any suggestion? run e2e version normal, thanks
Hi,
Any plan to address these would be appreciated:
Make proper release versions
This would help install and distribute software, generally, and especially on HPC systems.
I only have a Windows laptop. Will this work on Windows system?
I have an older version of the NVIDIA driver (450.36), which does not support CUDA toolkit >= 11.1 (CUDA compatibility)
In such cases, network/predict_*.py scripts failed to run smoothly using GPUs because of the compatibility issue.
Do the script really necessary to be run with the CUDA toolkit=11.1? When I created another RoseTTAFold conda environment with
, the scripts seem to work fine.
Someone who struggles with the same issue may use this YAML file for the RoseTTAFold conda environment creation.
Hi. Can you add miracles or torrents for sequence and structure databases?
Download speed is very slow now.
Thanks.
I'm not sure if there's a way to tell from the output of the prediction if 2 or more proteins can't "merge".
This would be a nice feature to use for online predictions when testing combinations of proteins
Hi,
I followed the installation using conda and installed the pyrosetta into the folding environment. However, I found that in the provided run_e2e script, it asks to conda activate RosettaFold rather than folding. I am wondering which one of the anaconda environments I should use to run.
Best,
Albert
Hi RoseTTAFold team,
Much appreciated for the great work and provides the insight for protein science!
If I am going to study viral protein complex rather than bacterium enzyme, should I still use/download the BFD?
In addition, could I use NCBI blast database instead of using Unipro? If so, should I download “UniRef30_2020_06”?
Thanks!
David
I tried these installation-packages or compiled version, all of them are segmentation fault.
#hh-suite
#wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-SSE2-Linux.tar.gz
#tar xvfz hhsuite-3.3.0-SSE2-Linux.tar.gz
#wget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz
#tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz
#wget https://mmseqs.com/hhsuite/hhsuite-linux-avx2.tar.gz --no-check-certificate
#tar xvfz hhsuite-linux-avx2.tar.gz
wget https://github.com/soedinglab/hh-suite/archive/refs/heads/master.zip --no-check-certificate
unzip hh-suite-master.zip
mv hh-suite-master hhsuite
cd hhsuite
mkdir -p ./build && cd ./build
apt install cmake
cmake -DCMAKE_INSTALL_PREFIX=.. ..
make -j 12
make install
I realized that paths for the database are hard-coded in the bash scripts. For example, in the "run_pyrosetta_ver.sh", the PDB100 database is referred as
DB="$PIPEDIR/pdb100_2021Mar03/pdb100_2021Mar03"
I am suggesting that it would be better to have a configuration file for the database paths for further updates on the databases.
The example provided for complex estimation and the make_joint_MSA_bacterial.py
script refer to just 2 proteins. In the cases where more than 2 proteins must be docked (the paper talks about two or more sequences), how does the pipeline work?
Should we run make_joint_MSA_bacterial.py
iteratively adding one protein at a time (after the first 2 have been docked)?
I'm working through getting RoseTTAFold operational using the example sequence.
HHblits and PSIPRED run to completion, however I encounter an error during hhsearch. In the hhsearch.stderr logfile, it says that the sequence ss_pred contains no residues. I checked t000_.msa0.ss2.a3m and the fastas for >ss_pred and >ss_conf are indeed empty, however the other alignment sequences are still present.
I tried to fix by recompiling hhsuite using the source binaries as suggested in your FAQ, however that doesn't seem to fix the issue. Does anyone have suggestions on how to move forward?
Hello:
Can you please let me know what the conditions are to use this software in a commercial setting, i.e. for a drug discovery project?
Thank you,
Markus
Hi RoseTTAFold,
I met a problem after installing the software in my University's server and start running a single model job.
I see four print info as below:
Running HHblits
Running PSIPRED
Running hhsearch
Predicting distance and orientations
Then I thought it was finished, but I cannot find any pdb result. Then I open your log folder try to figure out what happened. I see something strange in the network.stderr, as below:
RuntimeError: The following operation failed in the TorchScript interpreter.
Traceback of TorchScript (most recent call last):
File "/mnt/home/lipai/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_geometric/utils/softmax.py", line 41, in softmax
elif index is not None:
N = maybe_num_nodes(index, num_nodes)
src_max = scatter(src, index, dim, dim_size=N, reduce='max')
~~~~~~~ <--- HERE
src_max = src_max.index_select(dim, index)
out = (src - src_max).exp()
File "/mnt/home/lipai/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_scatter/scatter.py", line 161, in scatter
return scatter_min(src, index, dim, out, dim_size)[0]
elif reduce == 'max':
return scatter_max(src, index, dim, out, dim_size)[0]
~~~~~~~~~~~ <--- HERE
else:
raise ValueError
File "/mnt/home/lipai/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_scatter/scatter.py", line 73, in scatter_max
out: Optional[torch.Tensor] = None,
dim_size: Optional[int] = None) -> Tuple[torch.Tensor, torch.Tensor]:
return torch.ops.torch_scatter.scatter_max(src, index, dim, out, dim_size)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <--- HERE
RuntimeError: CUDA error: a PTX JIT compilation failed
CUDA kernel errors might be asynchronously reported at some other API call,so the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1.
According to the last recommendation. I first ran CUDA_LAUNCH_BLOCKING=1 in the shell input and then run the code, but the same error happens.
Here is what I did to get the failure:
I also give you a link of all my half-way failure result, as below:
https://github.com/phylars/shared_files_for_bugs/raw/main/RosettaFold_error/to_be_folded.zip
Could you please help with it?
Hi,
I am trying to download the weights dataset using the command :
wget https://files.ipd.uw.edu/pub/RoseTTAFold/weights.tar.gz as suggested in readme.
but I get the following error:
--2021-08-05 21:50:01-- https://files.ipd.uw.edu/pub/RoseTTAFold/weights.tar.gz
Resolving files.ipd.uw.edu (files.ipd.uw.edu)... 2607:4000:406::160:134, 2607:4000:406::160:135, 128.95.160.135, ...
Connecting to files.ipd.uw.edu (files.ipd.uw.edu)|2607:4000:406::160:134|:443... connected.
OpenSSL: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Unable to establish SSL connection.
Hi all. Excited to try this library. Right now I'm getting the following error:
21:20:37.467 ERROR: In hh-suite/src/hhdatabase.cpp:446: getTemplateHMM:
21:20:37.467 ERROR: Unrecognized HMM file format in '2703739471'.
21:20:37.467 ERROR: Context:
'EPEEEYMLAKRWVDHEDTEAAHRLVTSHLRLAAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTSAQKKLFFNLRKAKSKLGALEEgDlrpeNVKKIAHDLSVTEAEVIEMNRRLAGSDASLNAQLGgSEGEGGsEWM--EWLEDEDADQAGDYAERDEMDSRRALLAQALDVLNERERDILTERKLRDEPVTLEDLSTRYGVSRERIRQIEVRAFEKIQKRMKALARERGLLPAA--------------------------------------------------------------
21:20:37.467 ERROR: >UniRef100_A0A2N3CLL8 RNA polymerase factor sigma-32 n=1 Tax=Alphaproteobacteria bacterium HGW-Alphaproteobacteria-2 TaxID=2013665 RepID=A0A2N3CLL8_9PROT
21:20:37.467 ERROR: ---------------------------------------------------------------------------------------------------------------------MTKHLD--PERAFYRHAMAQELLDAETEADLARAWRDRRDEAALHRLITAYGRLALSIAQRYRRYQLPLEDIVQQAHLGLMRAADKFDPERGVRFSTYSAWWIKAAIQDYVMRNWSIVRGGATAAQKSLFFNLRRIHAEVERraqarGAVmTgeeIAEEIAGTLGVPLEQVRGMLGRVAGADLSLNATQRTEDGSREWQ--DLLEDDAPQAEEIVIEAAHRRRVTGALQAALRDLPARERHIVIERRLREEPRTLTDLGIELGVSKERVRQLEERALGRLRTAMAGLAEAGA-------------------------------------------------------------------'
Does anyone have any idea what I'm doing wrong?
Thank you.
when running ../run_pyrosetta_ver.sh input.fa .
encouter error !
more make_ss.stderr
/training/nong/protein/RoseTTAFold/input_prep/make_ss.sh: line 11: /training/nong/protein/RoseTTAFold/csblast-2.2.3/bi
n/csbuild: No such file or directory
[makemat] FATAL ERROR: Unable to open file t000_.msa0.tmp.chk
Bad psipred pass1 file format!
rm: cannot remove '/training/nong/protein/RoseTTAFold/example2/t000_.msa0.a3m.csb.hhblits.ss2': No such file or direct
ory
It seems csblast was not in the install folder
I am running some experiment with RoseTTAFold on CASP14 targets, but are uncertain about a few detailed settings:
run_e2e_ver.sh
and/or run_pyrosetta_ver.sh
(or any other scripts), so as to reproduce results as reported in the paper?Could you clarify above questions? Many thanks in advance.
Hi,
I am using pyrosetta4 and line 86 in folding/utils.py :
spline = rosetta.core.scoring.func.SplineFunc("", 1.0, 0.0, step, x,y)
throws the following error:
TypeError: __init__(): incompatible constructor arguments. The following argument types are supported:
1. pyrosetta.rosetta.core.scoring.func.SplineFunc()
2. pyrosetta.rosetta.core.scoring.func.SplineFunc(arg0: pyrosetta.rosetta.core.scoring.func.SplineFunc)
3. pyrosetta.rosetta.core.scoring.func.SplineFunc(arg0: pyrosetta.rosetta.core.scoring.func.SplineFunc)
Is there a PyRosetta4 version issue here?
First of all, great work folks.
And now the issue / my suggestion:
Can you get rid of the symlinks in the example file (under model) or make them relative paths ? They are making Git flip out.
Looking forward to seeing this project grow!
This is a wonderful job. But I have two questions.
RuntimeError: Error(s) in loading state_dict for RoseTTAFoldModule_e2e:
Missing key(s) in state_dict: "templ_emb.encoder_L.layers.0.attn_L.to_q.weight", "templ_emb.encoder_L.layers.0.attn_L.to_k.weight",
Could you provided the code for amd drivers compatible with ROCm?
Hi, RoseTTAFold team.
There was no pdb outcome in the model folder when running pyrosetta version.
$ cat pick.stderr
Traceback (most recent call last):
File "/data/Rusfell/03.RoseTTAFold/RoseTTAFold/DAN-msa/pick_final_models.div.py", line 113, in
pool = mp.Pool(n_core_pool)
File "/home/Rusfell/anaconda3/envs/folding/lib/python3.7/multiprocessing/context.py", line 119, in Pool
context=self.get_context())
File "/home/Rusfell/anaconda3/envs/folding/lib/python3.7/multiprocessing/pool.py", line 169, in init
raise ValueError("Number of processes must be at least 1")
ValueError: Number of processes must be at least 1
Rusfell
Hi, thank you very much for this awesome work!
I tried to do complex modeling, but I encountered the following error.
$ python network/predict_complex.py -i example/complex_modeling/filtered2.a3m -o complex -Ls 218 310
Using backend: pytorch
Traceback (most recent call last):
File "network/predict_complex.py", line 8, in <module>
from RoseTTAFoldModel import RoseTTAFoldModule_e2e
File "/home/shengfa/RoseTTAFold/network/RoseTTAFoldModel.py", line 4, in <module>
from Attention_module_w_str import IterativeFeatureExtractor
File "/home/shengfa/RoseTTAFold/network/Attention_module_w_str.py", line 9, in <module>
from InitStrGenerator import InitStr_Network
File "/home/shengfa/RoseTTAFold/network/InitStrGenerator.py", line 6, in <module>
import torch_geometric
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_geometric/__init__.py", line 5, in <module>
import torch_geometric.data
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_geometric/data/__init__.py", line 1, in <module>
from .data import Data
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_geometric/data/data.py", line 8, in <module>
from torch_sparse import coalesce, SparseTensor
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/site-packages/torch_sparse/__init__.py", line 14, in <module>
torch.ops.load_library(importlib.machinery.PathFinder().find_spec(
File "/home/shengfa/.local/lib/python3.8/site-packages/torch/_ops.py", line 105, in load_library
ctypes.CDLL(path)
File "/home/shengfa/anaconda3/envs/RoseTTAFold/lib/python3.8/ctypes/__init__.py", line 381, in __init__
self._handle = _dlopen(self._name, mode)
OSError: libtorch_cuda_cu.so: cannot open shared object file: No such file or directory
I have installed the environment using the below script:
# If your NVIDIA driver compatible with cuda11
conda env create -f RoseTTAFold-linux.yml
And the drivers are as follows:
$ nvidia-smi
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 455.23.05 Driver Version: 455.23.05 CUDA Version: 11.1 |
|-------------------------------+----------------------+----------------------+
$ conda list
# packages in environment at /home/shengfa/anaconda3/envs/RoseTTAFold:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main conda-forge
_openmp_mutex 4.5 1_gnu
biopython 1.78 py38h497a2fe_2 conda-forge
blas 1.0 mkl conda-forge
blast-legacy 2.2.26 2 biocore
brotlipy 0.7.0 py38h497a2fe_1001 conda-forge
bzip2 1.0.8 h7b6447c_0
ca-certificates 2021.5.25 h06a4308_1
certifi 2021.5.30 py38h06a4308_0
cffi 1.14.5 py38ha65f79e_0 conda-forge
chardet 3.0.4 pypi_0 pypi
cryptography 3.4.7 py38ha5dfef3_0 conda-forge
cudatoolkit 11.1.74 h6bb024c_0 nvidia
decorator 4.4.2 pypi_0 pypi
dgl-cu110 0.6.1 pypi_0 pypi
ffmpeg 4.3 hf484d3e_0 pytorch
freetype 2.10.4 h5ab3b9f_0
gmp 6.2.1 h2531618_2
gnutls 3.6.15 he1e5248_0
googledrivedownloader 0.4 pyhd3deb0d_1 conda-forge
hhsuite 3.3.0 py38pl5262hc37a69a_2 bioconda
idna 2.10 pyh9f0ad1d_0 conda-forge
intel-openmp 2021.2.0 h06a4308_610
jinja2 3.0.1 pyhd8ed1ab_0 conda-forge
joblib 1.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9b h024ee3a_2
lame 3.100 h7b6447c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.35.1 h7274673_9
libblas 3.9.0 9_mkl conda-forge
libcblas 3.9.0 9_mkl conda-forge
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgfortran-ng 7.5.0 h14aa051_19 conda-forge
libgfortran4 7.5.0 h14aa051_19 conda-forge
libgomp 9.3.0 h5101ec6_17
libiconv 1.15 h63c8f33_5
libidn2 2.3.1 h27cfd23_0
liblapack 3.9.0 9_mkl conda-forge
libpng 1.6.37 hbc83047_0
libstdcxx-ng 9.3.0 hd4cf53a_17
libtasn1 4.16.0 h27cfd23_0
libtiff 4.2.0 h85742a9_0
libunistring 0.9.10 h27cfd23_0
libuv 1.40.0 h7b6447c_0
libwebp-base 1.2.0 h27cfd23_0
lie-learn 0.0.1.post1 pypi_0 pypi
lz4-c 1.9.3 h2531618_0
markupsafe 2.0.1 py38h497a2fe_0 conda-forge
mkl 2021.2.0 h06a4308_296
mkl-service 2.3.0 py38h27cfd23_1
mkl_fft 1.3.0 py38h42c9631_2
mkl_random 1.2.1 py38ha9443f7_2
ncurses 6.2 he6710b0_1
nettle 3.7.3 hbbd107a_1
networkx 2.5 py_0 conda-forge
ninja 1.10.2 hff7bd54_1
numpy 1.20.2 py38h2d18471_0
numpy-base 1.20.2 py38hfae3a4d_0
olefile 0.46 py_0 conda-forge
openh264 2.1.0 hd408876_0
openssl 1.1.1k h27cfd23_0
packaging 20.9 pyhd3eb1b0_0
pandas 1.2.5 py38h1abd341_0 conda-forge
perl 5.26.2 h36c2ea0_1008 conda-forge
pillow 8.2.0 py38he98fc37_0
pip 21.1.3 py38h06a4308_0
psipred 4.01 1 biocore
pycparser 2.20 pyh9f0ad1d_2 conda-forge
pyopenssl 20.0.1 pyhd8ed1ab_0 conda-forge
pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge
pyrosetta 2021.29+release.d8f55669792 pypi_0 pypi
pysocks 1.7.1 py38h578d9bd_3 conda-forge
python 3.8.10 h12debd9_8
python-dateutil 2.8.1 py_0 conda-forge
python-louvain 0.15 pyhd3deb0d_0 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytorch 1.9.0 py3.8_cuda11.1_cudnn8.0.5_0 pytorch
pytorch-cluster 1.5.9 py38_torch_1.9.0_cu111 rusty1s
pytorch-geometric 1.7.2 py38_torch_1.9.0_cu111 rusty1s
pytorch-scatter 2.0.7 py38_torch_1.9.0_cu111 rusty1s
pytorch-sparse 0.6.10 py38_torch_1.9.0_cu111 rusty1s
pytorch-spline-conv 1.2.1 py38_torch_1.9.0_cu111 rusty1s
pytz 2021.1 pyhd8ed1ab_0 conda-forge
readline 8.1 h27cfd23_0
requests 2.25.1 pyhd3deb0d_0 conda-forge
scikit-learn 0.24.2 py38ha9443f7_0
scipy 1.7.0 pypi_0 pypi
setuptools 52.0.0 py38h06a4308_0
six 1.16.0 pyhd3eb1b0_0
sqlite 3.36.0 hc218d9a_0
threadpoolctl 2.1.0 pyh5ca1d4c_0 conda-forge
tk 8.6.10 hbc83047_0
torchaudio 0.9.0 py38 pytorch
torchvision 0.10.0 py38_cu111 pytorch
tqdm 4.61.1 pyhd8ed1ab_0 conda-forge
typing_extensions 3.10.0.0 pyh06a4308_0
urllib3 1.25.11 pypi_0 pypi
wheel 0.36.2 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.9 haebb681_0
How can I fix this error?
Thank you for any help you can offer.
here is the error:
./input_prep/make_ss.sh: line 18: 11775 Aborted (core dumped) psipred $ID.mtx $DATADIR/weights.dat $DATADIR/weights.dat2 $DATADIR/weights.dat3 > $ID.ss
I am running the fasta file in example/input.fa, I think this might be the gcc version error. Can you help me? and which version of gcc do you use?
Hello RoseTTAFold team,
Thank you for sharing the code and supporting the community.
I test the code on our HPC cluster, refer to README documentation, and hit a CUDA out of memory error.
$ python network/predict_complex.py -i example/complex_modeling/filtered.a3m -o complex -Ls 218 31
RuntimeError: CUDA out of memory. Tried to allocate 9.14 GiB (GPU 0; 15.78 GiB total capacity; 7.04 GiB already allocated; 6.08 GiB free; 8.36 GiB reserved in total by PyTorch)
From google search, find an article https://stackoverflow.com/questions/59129812/how-to-avoid-cuda-out-of-memory-in-pytorch;
I tried the following, it does not help.
import torch
torch.cuda.empty_cache()
Attempt to try the following, but I don't understand what are the 'variables' ? Should I try this on command line or embed it in the python code?
import gc
del variables
gc.collect()
If you have any suggestion, I much appreciate!
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