luhong88
commented
1 month ago Hi, can you provide more context on this error message, such as the (python) traceback, how you are submitting/running the script, and your local compute environment/setup?
Closed jxzly closed 1 month ago
luhong88
commented
1 month ago Hi, can you provide more context on this error message, such as the (python) traceback, how you are submitting/running the script, and your local compute environment/setup?
jxzly
commented
1 month ago I run python run_ga.py 1 in int_seq_des/benchmarks/RfaH_benchmark.
My python env:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_kmp_llvm conda-forge
about-time 4.2.1 pypi_0 pypi
accelerate 0.33.0 pypi_0 pypi
aiohappyeyeballs 2.3.4 pypi_0 pypi
aiohttp 3.10.0 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
alive-progress 3.1.5 pypi_0 pypi
anarci 1.3 pypi_0 pypi
aria2 1.37.0 h347180d_1 conda-forge
asttokens 2.0.5 pyhd3eb1b0_0
async-timeout 4.0.3 pypi_0 pypi
attrs 23.2.0 pypi_0 pypi
autograd 1.6.2 pypi_0 pypi
backcall 0.2.0 pyhd3eb1b0_0
billiard 4.2.0 pypi_0 pypi
bio 1.6.2 pypi_0 pypi
biopython 1.83 pypi_0 pypi
biothings-client 0.3.1 pypi_0 pypi
biotite 0.40.0 pypi_0 pypi
bzip2 1.0.8 h4bc722e_7 conda-forge
c-ares 1.32.3 h4bc722e_0 conda-forge
ca-certificates 2024.7.2 h06a4308_0
certifi 2024.7.4 pypi_0 pypi
charset-normalizer 3.3.2 pypi_0 pypi
click 8.1.7 pypi_0 pypi
cma 3.2.2 pypi_0 pypi
comm 0.2.1 py38h06a4308_0
cudatoolkit 11.7.0 hd8887f6_10 conda-forge
cycler 0.12.1 pypi_0 pypi
datasets 2.14.4 pypi_0 pypi
debugpy 1.6.7 py38h6a678d5_0
decorator 5.1.1 pyhd3eb1b0_0
deprecated 1.2.14 pypi_0 pypi
dill 0.3.7 pypi_0 pypi
et-xmlfile 1.1.0 pypi_0 pypi
executing 0.8.3 pyhd3eb1b0_0
fair-esm 2.0.1 pypi_0 pypi
filelock 3.15.4 pypi_0 pypi
foldseek 8.ef4e960 pl5321hb365157_1 bioconda
frozenlist 1.4.1 pypi_0 pypi
fsspec 2024.6.1 pypi_0 pypi
future 1.0.0 pypi_0 pypi
gawk 5.3.0 ha916aea_0 conda-forge
gettext 0.22.5 h59595ed_2 conda-forge
gettext-tools 0.22.5 h59595ed_2 conda-forge
gmp 6.3.0 hac33072_2 conda-forge
gprofiler-official 1.0.0 pypi_0 pypi
grapheme 0.6.0 pypi_0 pypi
hmmer 3.3.2 hdbdd923_4 bioconda
huggingface-hub 0.24.5 pypi_0 pypi
icu 73.2 h59595ed_0 conda-forge
idna 3.7 pypi_0 pypi
importlib-metadata 8.2.0 pypi_0 pypi
importlib_metadata 7.0.1 hd3eb1b0_0
int-seq-des 0.0.0 pypi_0 pypi
ipykernel 6.28.0 py38h06a4308_0
ipython 8.12.2 py38h06a4308_0
jedi 0.19.1 py38h06a4308_0
jinja2 3.1.4 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
jupyter_client 8.6.0 py38h06a4308_0
jupyter_core 5.7.2 py38h06a4308_0
kiwisolver 1.4.5 pypi_0 pypi
ld_impl_linux-64 2.38 h1181459_1
libasprintf 0.22.5 h661eb56_2 conda-forge
libasprintf-devel 0.22.5 h661eb56_2 conda-forge
libffi 3.4.4 h6a678d5_1
libgcc-ng 14.1.0 h77fa898_0 conda-forge
libgettextpo 0.22.5 h59595ed_2 conda-forge
libgettextpo-devel 0.22.5 h59595ed_2 conda-forge
libiconv 1.17 hd590300_2 conda-forge
libidn2 2.3.7 hd590300_0 conda-forge
libsodium 1.0.18 h7b6447c_0
libsqlite 3.46.0 hde9e2c9_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 14.1.0 hc0a3c3a_0 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libxml2 2.12.7 hc051c1a_1 conda-forge
libzlib 1.2.13 h4ab18f5_6 conda-forge
llvm-openmp 18.1.7 ha31de31_0 conda-forge
llvmlite 0.41.1 pypi_0 pypi
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.4.3 pypi_0 pypi
matplotlib-inline 0.1.6 py38h06a4308_0
mpfr 4.2.1 h38ae2d0_2 conda-forge
msgpack 1.0.8 pypi_0 pypi
multidict 6.0.5 pypi_0 pypi
multiprocess 0.70.15 pypi_0 pypi
mygene 3.2.2 pypi_0 pypi
ncurses 6.4 h6a678d5_0
nest-asyncio 1.6.0 py38h06a4308_0
networkx 3.1 pypi_0 pypi
numba 0.58.1 pypi_0 pypi
numba-progress 1.1.0 pypi_0 pypi
numpy 1.24.4 pypi_0 pypi
openpyxl 3.1.5 pypi_0 pypi
openssl 3.3.1 h4bc722e_2 conda-forge
packaging 24.1 py38h06a4308_0
pandas 2.0.3 pypi_0 pypi
parso 0.8.3 pyhd3eb1b0_0
peft 0.12.0 pypi_0 pypi
perl 5.32.1 7_hd590300_perl5 conda-forge
pexpect 4.8.0 pyhd3eb1b0_3
pickleshare 0.7.5 pyhd3eb1b0_1003
pillow 10.4.0 pypi_0 pypi
pip 24.0 py38h06a4308_0
platformdirs 4.2.2 pypi_0 pypi
pooch 1.8.2 pypi_0 pypi
prompt-toolkit 3.0.43 py38h06a4308_0
psutil 6.0.0 pypi_0 pypi
ptyprocess 0.7.0 pyhd3eb1b0_2
pure_eval 0.2.2 pyhd3eb1b0_0
pyarrow 17.0.0 pypi_0 pypi
pygments 2.15.1 py38h06a4308_1
pymoo 0.6.1.2 pypi_0 pypi
pyparsing 3.1.2 pypi_0 pypi
python 3.8.19 h955ad1f_0
python-dateutil 2.9.0post0 py38h06a4308_2
pytz 2024.1 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
pyzmq 25.1.2 py38h6a678d5_0
readline 8.2 h5eee18b_0
regex 2024.7.24 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
ruamel-yaml 0.18.6 pypi_0 pypi
ruamel-yaml-clib 0.2.8 pypi_0 pypi
safetensors 0.4.3 pypi_0 pypi
scikit-learn 1.3.2 pypi_0 pypi
scipy 1.10.1 pypi_0 pypi
seaborn 0.13.2 pypi_0 pypi
setuptools 69.5.1 py38h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.45.3 h5eee18b_0
stack_data 0.2.0 pyhd3eb1b0_0
threadpoolctl 3.5.0 pypi_0 pypi
tk 8.6.14 h39e8969_0
tokenizers 0.19.1 pypi_0 pypi
torch 1.13.1+cu117 pypi_0 pypi
torch-cluster 1.6.0+pt113cu117 pypi_0 pypi
torch-geometric 2.2.0 pypi_0 pypi
torch-scatter 2.1.0+pt113cu117 pypi_0 pypi
torch-sparse 0.6.16+pt113cu117 pypi_0 pypi
torch-spline-conv 1.2.1+pt113cu117 pypi_0 pypi
torchaudio 0.13.1+cu117 pypi_0 pypi
torchvision 0.14.1+cu117 pypi_0 pypi
tornado 6.4.1 py38h5eee18b_0
tqdm 4.66.4 pypi_0 pypi
traitlets 5.14.3 py38h06a4308_0
transformers 4.43.3 pypi_0 pypi
typing-extensions 4.12.2 pypi_0 pypi
typing_extensions 4.11.0 py38h06a4308_0
tzdata 2024.1 pypi_0 pypi
urllib3 2.2.2 pypi_0 pypi
wcwidth 0.2.5 pyhd3eb1b0_0
wget 1.21.4 hda4d442_0 conda-forge
wheel 0.43.0 py38h06a4308_0
wrapt 1.16.0 pypi_0 pypi
xxhash 3.4.1 pypi_0 pypi
xz 5.4.6 h5eee18b_1
yarl 1.9.4 pypi_0 pypi
zeromq 4.3.5 h6a678d5_0
zipp 3.19.2 pypi_0 pypi
zlib 1.2.13 h4ab18f5_6 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forgeIt seems that you are encountering the error on this line. The script is attempting to parallelize calculations using an SGE cluster that is not available in your local compute environment. If you have access to a GPU, I would suggest running the calculation on the GPU without invoking an SGE cluster. You can take a look at the PapD and CaM benchmark code, which is setup to do just that. Let me know if this helps.
jxzly
commented
1 month ago It's work when I set cluster_parallelization= False. I think the default setting is not user-friendly. Maybe you can change it.
And I get a new error:
from pgen.esm_sampler import ESM_sampler
ModuleNotFoundError: No module named 'pgen.esm_sampler'I didn't find the package pgen in project/int_seq_des/setup.cfg.
luhong88
commented
1 month ago Please see the pgen repo for instructions on how to setup that package.
The default value for cluster_parallelization is False in the run_ngsa() function.
jxzly
commented
1 month ago Thanks. The cluster_parallelization is True in int_seq_des/benchmarks/RfaH_benchmark/run_ga.py.
Thanks for sharing nice code. I get a warning when run
int_seq_des/benchmarks/RfaH_benchmark/run_ga.py. How to fix it?