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run_multimer_jobs issue #342
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Hi @J-Held, the first part of your errors says that can't use GPU cause you have a problem with your TensorRT. But the script don't crash cause of that, but probably cause of yours command. Take care of your backslash and personally I prefer write the command in line with one space to avoid writing errors. Like this : Quentin |
Yes, that was it. Thank you @Qrouger and @dingquanyu! Regarding the GPU, it looks like I'm getting many of the error messages brought up in #339, but the job appears to still be running. Is it just going to time out? Output log below: I0521 10:54:40.655257 22582644975424 run_multimer_jobs.py:389] Modeling new interaction for /storage/home/jbh249/scratch/output/models/HrpN_and_WAK3 |
No, he just run slowly on CPU. Quentin. |
Hi @J-Held Glad it worked. These messages are not actually errors but some logs that reflect the status of you modelling job. Since you have this Yours |
I am trying to run the run_multimer_jobs script on GPU using this command:
run_multimer_jobs.py
--mode=all_vs_all
--num_cycle=3
--num_predictions_per_model=1
--output_path=/storage/home/jbh249/scratch/output/models/
--data_dir=/storage/home/jbh249/scratch/alphaDatabase/ \
--protein_lists=/storage/home/jbh249/scratch/candidates.txt
--monomer_objects_dir=/storage/home/jbh249/scratch/output/features
The job terminates almost immediately with this error:
/storage/home/jbh249/micromamba/envs/AlphaPulldown/lib/python3.10/site-packages/Bio/Data/SCOPData.py:18: BiopythonDeprecationWarning: The 'Bio.Data.SCOPData' module will be deprecated in a future release of Biopython in favor of 'Bio.Data.PDBData.
warnings.warn(
2024-05-20 16:09:31.137214: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
2024-05-20 16:09:35.260966: W tensorflow/core/common_runtime/gpu/gpu_device.cc:2251] Cannot dlopen some GPU libraries. Please make sure the missing libraries mentioned above are installed properly if you would like to use GPU. Follow the guide at https://www.tensorflow.org/install/gpu for how to download and setup the required libraries for your platform.
Skipping registering GPU devices...
I0520 16:09:35.261087 23134891243328 utils.py:271] checking if output_dir exists /storage/home/jbh249/scratch/output/models/
Traceback (most recent call last):
File "/storage/home/jbh249/micromamba/envs/AlphaPulldown/bin/run_multimer_jobs.py", line 462, in
app.run(main)
File "/storage/home/jbh249/micromamba/envs/AlphaPulldown/lib/python3.10/site-packages/absl/app.py", line 308, in run
_run_main(main, args)
File "/storage/home/jbh249/micromamba/envs/AlphaPulldown/lib/python3.10/site-packages/absl/app.py", line 254, in _run_main
sys.exit(main(argv))
File "/storage/home/jbh249/micromamba/envs/AlphaPulldown/bin/run_multimer_jobs.py", line 437, in main
all_proteins = read_all_proteins(FLAGS.protein_lists[0])
TypeError: 'NoneType' object is not subscriptable
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