ERROR: benchmark.py script terminated with non-zero exit-code, execution log:
Running Singularity container...
Command line: singularity exec --contain --cleanenv --no-home --bind /scratch/benchmark/nobu-5/w/.singularity.home:/home/benchmark --bind /home/benchmark/release:/home/benchmark/release_root --bind /home/benchmark/prefix/fragment_picking_database/2019.05.19:/home/benchmark/fragment_picking_database --bind /scratch/benchmark/nobu-5/w/T/commits-24.827843.ubuntu-20.04.clang.python39.rfd.0:/home/benchmark/working_dir --bind /scratch/benchmark/nobu-5/w/rosetta/commits/RFdiffusion:/home/benchmark/rosetta --bind /scratch/benchmark/nobu-5/w/prefix/ubuntu-20.04:/home/benchmark/prefix --hostname nobu-5 --workdir /scratch/benchmark/nobu-5/w/.singularity.tmpfs --pwd /home/benchmark/rosetta/.rosetta-ci /scratch/benchmark/nobu-5/b3/back/../../w/.singularity.images/ubuntu-20.04.simg python3 ./benchmark.py --setup /home/benchmark/working_dir/.execution.setup.json <<<''
Loading test from: tests/rfd.py, suite+test: 'rfd', test: ''
Getting python configuration info...
unset __PYVENV_LAUNCHER__ && cd /home/benchmark/prefix/nobu-5/ubuntu-20.04/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin && PATH=.:$PATH && /home/benchmark/prefix/nobu-5/ubuntu-20.04/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/bin/python3.9-config --prefix --includes
/home/benchmark/prefix/nobu-5/ubuntu-20.04/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd
-I/home/benchmark/prefix/nobu-5/ubuntu-20.04/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/include/python3.9 -I/home/benchmark/prefix/nobu-5/ubuntu-20.04/python-3.9.gcc/99a1a29fd465f86265a7c5b92d75dbcd/include/python3.9
unpacking ppi scaffolds...
cd /home/benchmark/rosetta && tar -xvf examples/ppi_scaffolds_subset.tar.gz -C examples
ppi_scaffolds/
ppi_scaffolds/HEEHE_2518_ss.pt
ppi_scaffolds/HHH_b1_00611_ss.pt
ppi_scaffolds/HHH_b1_00312_ss.pt
ppi_scaffolds/01d461f506ab04f7d0ebca3e58138a95_0001_ss.pt
ppi_scaffolds/HHH_b2_00055_adj.pt
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ppi_scaffolds/HHH_b2_03550_adj.pt
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ppi_scaffolds/HHH_b2_02422_ss.pt
ppi_scaffolds/HHH_b2_02121_ss.pt
ppi_scaffolds/HHH_b2_04798_adj.pt
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ppi_scaffolds/915c467777ae14ad0cbad57e3ac0e165_0001_adj.pt
ppi_scaffolds/HHH_b2_07193_adj.pt
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Building wheels for collected packages: antlr4-python3-runtime
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[?25h Created wheel for antlr4-python3-runtime: filename=antlr4_python3_runtime-4.9.3-py3-none-any.whl size=144554 sha256=db923967b331cbdad509b90172e9113276fa08d181f5f5e15404932b27d1ef44
Stored in directory: /home/benchmark/.cache/pip/wheels/23/cf/80/f3efa822e6ab23277902ee9165fe772eeb1dfb8014f359020a
Successfully built antlr4-python3-runtime
Installing collected packages: mpmath, antlr4-python3-runtime, urllib3, typing-extensions, tqdm, sympy, smmap, six, setproctitle, PyYAML, pyrsistent, pynvml, pygments, psutil, protobuf, platformdirs, parso, packaging, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, numpy, networkx, MarkupSafe, idna, fsspec, filelock, executing, decorator, colorama, click, charset-normalizer, certifi, triton, sentry-sdk, scipy, requests, opt_einsum, omegaconf, nvidia-cusparse-cu12, nvidia-cudnn-cu12, jinja2, jedi, gitdb, docker-pycreds, asttokens, nvidia-cusolver-cu12, icecream, hydra-core, gitpython, wandb, torch, torchdata, opt-einsum-fx, e3nn, dgl
Successfully installed MarkupSafe-2.1.5 PyYAML-6.0.1 antlr4-python3-runtime-4.9.3 asttokens-2.4.1 certifi-2024.2.2 charset-normalizer-3.3.2 click-8.1.7 colorama-0.4.6 decorator-5.1.1 dgl-2.1.0 docker-pycreds-0.4.0 e3nn-0.5.1 executing-2.0.1 filelock-3.14.0 fsspec-2024.3.1 gitdb-4.0.11 gitpython-3.1.43 hydra-core-1.3.2 icecream-2.1.3 idna-3.7 jedi-0.19.1 jinja2-3.1.4 mpmath-1.3.0 networkx-3.2.1 numpy-1.26.4 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-8.9.2.26 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.20.5 nvidia-nvjitlink-cu12-12.4.127 nvidia-nvtx-cu12-12.1.105 omegaconf-2.3.0 opt-einsum-fx-0.1.4 opt_einsum-3.3.0 packaging-24.0 parso-0.8.4 platformdirs-4.2.1 protobuf-4.25.3 psutil-5.9.8 pygments-2.18.0 pynvml-11.5.0 pyrsistent-0.20.0 requests-2.31.0 scipy-1.13.0 sentry-sdk-2.1.1 setproctitle-1.3.3 six-1.16.0 smmap-5.0.1 sympy-1.12 torch-2.3.0 torchdata-0.7.1 tqdm-4.66.4 triton-2.3.0 typing-extensions-4.11.0 urllib3-2.2.1 wandb-0.17.0
Installing local se3-transformer package...
cd /home/benchmark/rosetta/env/SE3Transformer && /home/benchmark/working_dir/tmppfqnj7uq/bin/pip3 install --editable .
Obtaining file:///home/benchmark/rosetta/env/SE3Transformer
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[?25h Created wheel for se3-transformer: filename=se3_transformer-1.0.0-0.editable-py3-none-any.whl size=3887 sha256=d179b621db539ef6073c00a992b178077b0e45649b069c6ca9fd8351a24d6f37
Stored in directory: /tmp/pip-ephem-wheel-cache-60xg876h/wheels/d3/61/06/8e79422440d27b9c1baa85d4bc82527dfcce8663dc9be8dd82
Successfully built se3-transformer
Installing collected packages: se3-transformer
Successfully installed se3-transformer-1.0.0
Installing RFdiffusion package...
cd /home/benchmark/rosetta && /home/benchmark/working_dir/tmppfqnj7uq/bin/pip3 install --editable .
Obtaining file:///home/benchmark/rosetta
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[?25hRequirement already satisfied: torch in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from rfdiffusion==1.1.0) (2.3.0)
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Requirement already satisfied: filelock in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (3.14.0)
Requirement already satisfied: typing-extensions>=4.8.0 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (4.11.0)
Requirement already satisfied: sympy in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (1.12)
Requirement already satisfied: networkx in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (3.2.1)
Requirement already satisfied: jinja2 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (3.1.4)
Requirement already satisfied: fsspec in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (2024.3.1)
Requirement already satisfied: nvidia-cuda-nvrtc-cu12==12.1.105 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (12.1.105)
Requirement already satisfied: nvidia-cuda-runtime-cu12==12.1.105 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (12.1.105)
Requirement already satisfied: nvidia-cuda-cupti-cu12==12.1.105 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (12.1.105)
Requirement already satisfied: nvidia-cudnn-cu12==8.9.2.26 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (8.9.2.26)
Requirement already satisfied: nvidia-cublas-cu12==12.1.3.1 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (12.1.3.1)
Requirement already satisfied: nvidia-cufft-cu12==11.0.2.54 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (11.0.2.54)
Requirement already satisfied: nvidia-curand-cu12==10.3.2.106 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (10.3.2.106)
Requirement already satisfied: nvidia-cusolver-cu12==11.4.5.107 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (11.4.5.107)
Requirement already satisfied: nvidia-cusparse-cu12==12.1.0.106 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (12.1.0.106)
Requirement already satisfied: nvidia-nccl-cu12==2.20.5 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (2.20.5)
Requirement already satisfied: nvidia-nvtx-cu12==12.1.105 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (12.1.105)
Requirement already satisfied: triton==2.3.0 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from torch->rfdiffusion==1.1.0) (2.3.0)
Requirement already satisfied: nvidia-nvjitlink-cu12 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from nvidia-cusolver-cu12==11.4.5.107->torch->rfdiffusion==1.1.0) (12.4.127)
Requirement already satisfied: MarkupSafe>=2.0 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from jinja2->torch->rfdiffusion==1.1.0) (2.1.5)
Requirement already satisfied: mpmath>=0.19 in /home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages (from sympy->torch->rfdiffusion==1.1.0) (1.3.0)
Building wheels for collected packages: rfdiffusion
Building editable for rfdiffusion (pyproject.toml) ... [?25l- \ | / done
[?25h Created wheel for rfdiffusion: filename=rfdiffusion-1.1.0-0.editable-py3-none-any.whl size=6098 sha256=5d1303796db86ee684031ddeaedc1903a8d7cb3913f93f4d66c68fea32e1a598
Stored in directory: /tmp/pip-ephem-wheel-cache-frjiy5iv/wheels/55/b1/5d/99d5f27fce1e7e58cb6468ce75c5d8bbb7b81dbebb3a094895
Successfully built rfdiffusion
Installing collected packages: rfdiffusion
Successfully installed rfdiffusion-1.1.0
running RFdiffusion tests...
unset __PYVENV_LAUNCHER__ && . /home/benchmark/working_dir/tmppfqnj7uq/bin/activate && cd /home/benchmark/rosetta/tests && python test_diffusion.py
/home/benchmark/rosetta/rfdiffusion/util.py:253: UserWarning: Using torch.cross without specifying the dim arg is deprecated.
Please either pass the dim explicitly or simply use torch.linalg.cross.
The default value of dim will change to agree with that of linalg.cross in a future release. (Triggered internally at ../aten/src/ATen/native/Cross.cpp:62.)
Z = torch.cross(Xn, Yn)
DGL backend not selected or invalid. Assuming PyTorch for now.
Setting the default backend to "pytorch". You can change it in the ~/.dgl/config.json file or export the DGLBACKEND environment variable. Valid options are: pytorch, mxnet, tensorflow (all lowercase)
Traceback (most recent call last):
File "/home/benchmark/rosetta/tests/test_diffusion.py", line 8, in <module>
from rfdiffusion.inference import utils as iu
File "/home/benchmark/rosetta/rfdiffusion/inference/utils.py", line 6, in <module>
from rfdiffusion.diffusion import get_beta_schedule
File "/home/benchmark/rosetta/rfdiffusion/diffusion.py", line 12, in <module>
from rfdiffusion.util_module import ComputeAllAtomCoords
File "/home/benchmark/rosetta/rfdiffusion/util_module.py", line 7, in <module>
import dgl
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/dgl/__init__.py", line 16, in <module>
from . import (
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/dgl/dataloading/__init__.py", line 13, in <module>
from .dataloader import *
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/dgl/dataloading/dataloader.py", line 27, in <module>
from ..distributed import DistGraph
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/dgl/distributed/__init__.py", line 5, in <module>
from .dist_graph import DistGraph, DistGraphServer, edge_split, node_split
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/dgl/distributed/dist_graph.py", line 11, in <module>
from .. import backend as F, graphbolt as gb, heterograph_index
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/dgl/graphbolt/__init__.py", line 8, in <module>
from .base import *
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/dgl/graphbolt/base.py", line 8, in <module>
from torchdata.datapipes.iter import IterDataPipe
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/torchdata/__init__.py", line 9, in <module>
from . import datapipes
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/torchdata/datapipes/__init__.py", line 9, in <module>
from . import iter, map, utils
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/torchdata/datapipes/iter/__init__.py", line 79, in <module>
from torchdata.datapipes.iter.util.cacheholder import (
File "/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/torchdata/datapipes/iter/util/cacheholder.py", line 24, in <module>
from torch.utils.data.datapipes.utils.common import _check_unpickable_fn, DILL_AVAILABLE
ImportError: cannot import name 'DILL_AVAILABLE' from 'torch.utils.data.datapipes.utils.common' (/home/benchmark/working_dir/tmppfqnj7uq/lib/python3.9/site-packages/torch/utils/data/datapipes/utils/common.py)
Traceback (most recent call last):
File "/usr/lib/python3.8/shutil.py", line 791, in move
os.rename(src, real_dst)
OSError: [Errno 18] Invalid cross-device link: '/home/benchmark/rosetta/tests/outputs' -> '/home/benchmark/working_dir/outputs'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "./benchmark.py", line 410, in <module>
if __name__ == "__main__": main(sys.argv)
File "./benchmark.py", line 407, in main
run_test(setup)
File "./benchmark.py", line 324, in run_test
if api_version == '1.0': res = test_suite.run(test=test_name, repository_root=os.path.abspath('./..'), working_dir=working_dir, platform=dict(setup.platform), config=setup.config, hpc_driver=hpc_driver, verbose=True, debug=setup.debug)
File "tests/rfd.py", line 110, in run
if test == '': return run_main_test_suite(repository_root=repository_root, working_dir=working_dir, platform=platform, config=config, debug=debug)
File "tests/rfd.py", line 91, in run_main_test_suite
shutil.move(f'{repository_root}/tests/outputs', f'{working_dir}/outputs')
File "/usr/lib/python3.8/shutil.py", line 811, in move
copy_function(src, real_dst)
File "/usr/lib/python3.8/shutil.py", line 435, in copy2
copyfile(src, dst, follow_symlinks=follow_symlinks)
File "/usr/lib/python3.8/shutil.py", line 264, in copyfile
with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst:
FileNotFoundError: [Errno 2] No such file or directory: '/home/benchmark/rosetta/tests/outputs'
ERROR: Benchmark back-end script terminates abnormally, marking test state as 'script failed'!