NER script fails to run and gets killed

[Mahmedturk]

Hi, I am doing NER on a biomedical dataset and I get the follwing Warnings and then the process gets killed. Is there any workaround? usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) /usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) /usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) /usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) /usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) /usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) /usr/local/lib/python3.6/dist-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint8 = np.dtype([("qint8", np.int8, 1)]) /usr/local/lib/python3.6/dist-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint8 = np.dtype([("quint8", np.uint8, 1)]) /usr/local/lib/python3.6/dist-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint16 = np.dtype([("qint16", np.int16, 1)]) /usr/local/lib/python3.6/dist-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_quint16 = np.dtype([("quint16", np.uint16, 1)]) /usr/local/lib/python3.6/dist-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. _np_qint32 = np.dtype([("qint32", np.int32, 1)]) /usr/local/lib/python3.6/dist-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'. np_resource = np.dtype([("resource", np.ubyte, 1)]) Deprecated cache directory found (/home/zainab/.allennlp/datasets). Please remove this directory from your system to free up space. WARNING:tensorflow:From Train_NER.py:12: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.

WARNING:tensorflow:From Train_NER.py:16: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead.

2020-01-06 13:07:57.220411: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA 2020-01-06 13:07:58.074543: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 2904000000 Hz 2020-01-06 13:07:58.075286: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x6ce4b40 executing computations on platform Host. Devices: 2020-01-06 13:07:58.075360: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): , WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:524: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:4377: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:74: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.

WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:3183: add_dispatch_support..wrapper (from tensorflow.python.ops.array_ops) is deprecated and will be removed in a future version. Instructions for updating: Use tf.where in 2.0, which has the same broadcast rule as np.where WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:3678: calling dropout (from tensorflow.python.ops.nn_ops) with keep_prob is deprecated and will be removed in a future version. Instructions for updating: Please use rate instead of keep_prob. Rate should be set to rate = 1 - keep_prob. WARNING:tensorflow:From /usr/local/lib/python3.6/dist-packages/keras/optimizers.py:790: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.

Training: 0 Batch [00:00, ? Batch/s]2020-01-06 13:17:56.245974: W tensorflow/compiler/jit/mark_for_compilation_pass.cc:1412] (One-time warning): Not using XLA:CPU for cluster because envvar TF_XLA_FLAGS=--tf_xla_cpu_global_jit was not set. If you want XLA:CPU, either set that envvar, or use experimental_jit_scope to enable XLA:CPU. To confirm that XLA is active, pass --vmodule=xla_compilation_cache=1 (as a proper command-line flag, not via TF_XLA_FLAGS) or set the envvar XLA_FLAGS=--xla_hlo_profile. Training: 18885 Batch [4:43:43, 1.56 Batch/s]Killed

[nreimers]

Try to use exactly the versions of keras and tensorflow defined in this file: https://github.com/UKPLab/elmo-bilstm-cnn-crf/blob/master/docker/requirements.txt

With newer versions of tensorflow, I don't expect that the code runs smoothly.

[Mahmedturk]

Hi,

I have changed the tf version as per requirements. However i still get the below error. What is surprising is that I was able to run this code with the same dataset last week and it is casuing memory issues. RuntimeError: [enforce fail at CPUAllocator.cpp:64] . DefaultCPUAllocator: can't allocate memory: you tried to allocate 31088768 bytes. Error code 12 (Cannot allocate memory)

[nreimers]

Seems like you run out of memory: https://discuss.pytorch.org/t/got-error-cannot-allocate-memory/20736/5