Akanksha2511
commented
3 years ago Hi Daniel,
Thanks for giving ReorientExpress a go and sorry about the issue. It seems like the library path issue. Please have a look at the below post to resolve it and see it if helps. https://stackoverflow.com/questions/41890549/tensorflow-cannot-open-libcuda-so-1
Thanks, Akanksha
Dear ReorientExpress Developers,
Thank you for making this tool. I've had some issues getting it to run, but have now managed to call the script for the first time. The output only produces the following error;
2021-01-10 19:04:26.534986: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set 2021-01-10 19:04:26.537813: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/slurm/20.02.1/lib64 2021-01-10 19:04:26.538716: W tensorflow/stream_executor/cuda/cuda_driver.cc:326] failed call to cuInit: UNKNOWN ERROR (303) 2021-01-10 19:04:26.539313: I tensorflow/stream_executor/cuda/cuda_diagnostics.cc:156] kernel driver does not appear to be running on this host (n19-28-384-nicknack.hpc.hutton.ac.uk): /proc/driver/nvidia/version does not exist 2021-01-10 19:04:26.544915: I tensorflow/core/platform/cpu_feature_guard.cc:142] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX512F To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags. 2021-01-10 19:04:26.545745: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set [dphillip@gruffalo reorientexpress]$ cat slurm-507501.out 2021-01-10 19:04:18.579510: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/slurm/20.02.1/lib64 2021-01-10 19:04:18.581020: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
I'm a beginner, so I'm really not sure what this means. I was hoping you could help. My code was;
python reorientexpress.py -predict -data My_ONT_RNAseq.fastq -model ./saved_models/Hs_transcriptome_mlp.model -source experimental -output ./Results/test_predictions
[Quick Edit - I forgot to mention, the script is still running. The error just makes me nervous and want to cancel it.] Any ideas?
Best wishes, Daniel