SGenheden
commented
3 years ago Hello @pkrezel
This all looks like Tensorflow/CUDA warnings about that you have a Tensorflow GPU version installed that cannot use your GPUs because of missing drivers. There is plenty of information about this on the Internet. If you don't have a GPU you can ignore it. For predicting synthesis routes, there is very little advantage to running the models on a GPU compared to a CPU.
In the latest version on the master branch I suppress all of these messages because you can typically ignore them. This is also gonna be the behavior in the next minor release. It shouldn't have any affect on either the CLI or the Jupyter notebook interface.
Hi,
Thank you for having shared AiZynthFinder. I am working on Linux Centos 7. I tested the GUI application, it works. However, if I launch the batch mode from a console (see below), many errors appears but finally it works. Certainly because of that it is not possible to launch it from a Jupyter notebook.
Do you have the same phenomena? If not, how to avoid that ?
Sincerely.
Pascal KREZEL
(aizynth-env) [krezel@localhost Notebooks]$ aizynthcli --config config.yml --smiles smiles.txt 2021-05-10 11:39:52.415791: 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: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:52.415836: 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. Loading expansion policy model from /home/pkrezel/Documents/Projets/001_CEA_retrosynthesis/Notebooks/uspto_model.hdf5 to uspto 2021-05-10 11:39:54.125856: I tensorflow/compiler/jit/xla_cpu_device.cc:41] Not creating XLA devices, tf_xla_enable_xla_devices not set 2021-05-10 11:39:54.126600: I tensorflow/stream_executor/platform/default/dso_loader.cc:49] Successfully opened dynamic library libcuda.so.1 2021-05-10 11:39:54.130630: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1720] Found device 0 with properties: pciBusID: 0000:02:00.0 name: Quadro K4000 computeCapability: 3.0 coreClock: 0.8105GHz coreCount: 4 deviceMemorySize: 2.95GiB deviceMemoryBandwidth: 125.53GiB/s 2021-05-10 11:39:54.130798: 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: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.130910: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcublas.so.11'; dlerror: libcublas.so.11: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.131013: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcublasLt.so.11'; dlerror: libcublasLt.so.11: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.131118: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcufft.so.10'; dlerror: libcufft.so.10: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.131233: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcurand.so.10'; dlerror: libcurand.so.10: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.131338: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcusolver.so.10'; dlerror: libcusolver.so.10: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.131442: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcusparse.so.11'; dlerror: libcusparse.so.11: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.131543: W tensorflow/stream_executor/platform/default/dso_loader.cc:60] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /home/yourusername/VTK:/home/yourusername/VTK/jni::/home/pkrezel/Programmes/rDock_2013.1_src/lib 2021-05-10 11:39:54.131574: W tensorflow/core/common_runtime/gpu/gpu_device.cc:1757] 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... 2021-05-10 11:39:54.132495: I tensorflow/compiler/jit/xla_gpu_device.cc:99] Not creating XLA devices, tf_xla_enable_xla_devices not set 2021-05-10 11:39:54.132536: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1261] Device interconnect StreamExecutor with strength 1 edge matrix: 2021-05-10 11:39:54.132560: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1267] Loading templates from /home/pkrezel/Documents/Projets/001_CEA_retrosynthesis/Notebooks/uspto_templates.hdf5 to uspto Loading filter policy model from /home/pkrezel/Documents/Projets/001_CEA_retrosynthesis/Notebooks/uspto_filter_model.hdf5 to uspto Loading stock from /home/pkrezel/Documents/Projets/001_CEA_retrosynthesis/Notebooks/zinc_stock.hdf5 to zinc Selected as stock: zinc Compounds in stock: 17422831 Selected as expansion policy: uspto 2021-05-10 11:40:01.245333: I tensorflow/compiler/mlir/mlir_graph_optimization_pass.cc:116] None of the MLIR optimization passes are enabled (registered 2) 2021-05-10 11:40:01.245759: I tensorflow/core/platform/profile_utils/cpu_utils.cc:112] CPU Frequency: 3691235000 Hz