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Zhihan1996 avatar Zhihan1996 commented on May 31, 2024

Hey,

Can you try to run the model in the distributed mode with torchrun --nproc-per-node=8 xxx.py instead of using python xxx.py?

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anihab avatar anihab commented on May 31, 2024

Hello! Apologies for the late response, I've been travelling. I tried running in distributed mode but ran into this output error instead (file linked below).

torchrun-output.txt

Do you think this could possibly be an issue with my environment? I'm using the conda environment that I built using the requirements file from your github and some additional packages (like pandas, since the output indicated it was missing on my first couple runs). I have following installed:

# packages in environment:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                        main  
_openmp_mutex             5.1                       1_gnu  
accelerate                0.20.3                   pypi_0    pypi
aiohttp                   3.8.4                    pypi_0    pypi
aiosignal                 1.3.1                    pypi_0    pypi
antlr4-python3-runtime    4.9.3                    pypi_0    pypi
async-timeout             4.0.2                    pypi_0    pypi
attrs                     23.1.0                   pypi_0    pypi
biopython                 1.78             py38h7f8727e_0  
blas                      1.0                         mkl  
bottleneck                1.3.5            py38h7deecbd_0  
ca-certificates           2023.05.30           h06a4308_0  
certifi                   2023.5.7                 pypi_0    pypi
charset-normalizer        3.2.0                    pypi_0    pypi
cmake                     3.26.4                   pypi_0    pypi
datasets                  2.13.1                   pypi_0    pypi
dill                      0.3.6                    pypi_0    pypi
einops                    0.6.1                    pypi_0    pypi
evaluate                  0.4.0                    pypi_0    pypi
filelock                  3.12.2                   pypi_0    pypi
frozenlist                1.3.3                    pypi_0    pypi
fsspec                    2023.6.0                 pypi_0    pypi
huggingface-hub           0.16.4                   pypi_0    pypi
idna                      3.4                      pypi_0    pypi
intel-openmp              2023.1.0         hdb19cb5_46305  
jinja2                    3.1.2                    pypi_0    pypi
joblib                    1.2.0            py38h06a4308_0  
ld_impl_linux-64          2.38                 h1181459_1  
libffi                    3.4.4                h6a678d5_0  
libgcc-ng                 11.2.0               h1234567_1  
libgfortran-ng            11.2.0               h00389a5_1  
libgfortran5              11.2.0               h1234567_1  
libgomp                   11.2.0               h1234567_1  
libstdcxx-ng              11.2.0               h1234567_1  
lit                       16.0.6                   pypi_0    pypi
markupsafe                2.1.3                    pypi_0    pypi
mkl                       2023.1.0         h6d00ec8_46342  
mkl-service               2.4.0            py38h5eee18b_1  
mkl_fft                   1.3.6            py38h417a72b_1  
mkl_random                1.2.2            py38h417a72b_1  
mpmath                    1.3.0                    pypi_0    pypi
multidict                 6.0.4                    pypi_0    pypi
multiprocess              0.70.14                  pypi_0    pypi
ncurses                   6.4                  h6a678d5_0  
networkx                  3.1                      pypi_0    pypi
numexpr                   2.8.4            py38hc78ab66_1  
numpy                     1.24.4                   pypi_0    pypi
numpy-base                1.24.3           py38h060ed82_1  
nvidia-cublas-cu11        11.10.3.66               pypi_0    pypi
nvidia-cuda-cupti-cu11    11.7.101                 pypi_0    pypi
nvidia-cuda-nvrtc-cu11    11.7.99                  pypi_0    pypi
nvidia-cuda-runtime-cu11  11.7.99                  pypi_0    pypi
nvidia-cudnn-cu11         8.5.0.96                 pypi_0    pypi
nvidia-cufft-cu11         10.9.0.58                pypi_0    pypi
nvidia-curand-cu11        10.2.10.91               pypi_0    pypi
nvidia-cusolver-cu11      11.4.0.1                 pypi_0    pypi
nvidia-cusparse-cu11      11.7.4.91                pypi_0    pypi
nvidia-nccl-cu11          2.14.3                   pypi_0    pypi
nvidia-nvtx-cu11          11.7.91                  pypi_0    pypi
omegaconf                 2.3.0                    pypi_0    pypi
openssl                   3.0.9                h7f8727e_0  
packaging                 23.1                     pypi_0    pypi
pandas                    2.0.3                    pypi_0    pypi
peft                      0.3.0                    pypi_0    pypi
pip                       23.1.2           py38h06a4308_0  
psutil                    5.9.5                    pypi_0    pypi
pyarrow                   12.0.1                   pypi_0    pypi
python                    3.8.17               h955ad1f_0  
python-dateutil           2.8.2              pyhd3eb1b0_0  
pytz                      2023.3                   pypi_0    pypi
pyyaml                    6.0                      pypi_0    pypi
readline                  8.2                  h5eee18b_0  
regex                     2023.6.3                 pypi_0    pypi
requests                  2.31.0                   pypi_0    pypi
responses                 0.18.0                   pypi_0    pypi
safetensors               0.3.1                    pypi_0    pypi
scikit-learn              1.2.2            py38h6a678d5_1  
scipy                     1.9.3            py38hf6e8229_2  
setuptools                67.8.0           py38h06a4308_0  
six                       1.16.0             pyhd3eb1b0_1  
sqlite                    3.41.2               h5eee18b_0  
sympy                     1.12                     pypi_0    pypi
tbb                       2021.8.0             hdb19cb5_0  
threadpoolctl             2.2.0              pyh0d69192_0  
tk                        8.6.12               h1ccaba5_0  
tokenizers                0.13.3                   pypi_0    pypi
torch                     2.0.1                    pypi_0    pypi
tqdm                      4.65.0                   pypi_0    pypi
transformers              4.30.2                   pypi_0    pypi
triton                    2.0.0                    pypi_0    pypi
typing-extensions         4.7.1                    pypi_0    pypi
tzdata                    2023.3                   pypi_0    pypi
urllib3                   2.0.3                    pypi_0    pypi
wheel                     0.38.4           py38h06a4308_0  
xxhash                    3.2.0                    pypi_0    pypi
xz                        5.4.2                h5eee18b_0  
yarl                      1.9.2                    pypi_0    pypi
zlib                      1.2.13               h5eee18b_0  

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lucaskbobadilla avatar lucaskbobadilla commented on May 31, 2024

Any ideas here? getting the same error

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