Hi, I have a huge network of 240k+ nodes and I am using the following commands to try embedding it:
python3 ../GEMSEC/src/embedding_clustering.py --input in.csv --embeddi
ng-output out.csv --dimensions 3
100%|ββββββββββ| 228922/228922 [02:20<00:00, 1626.28it/s]
100%|ββββββββββ| 228922/228922 [02:06<00:00, 1803.60it/s]
100%|ββββββββββ| 228922/228922 [02:20<00:00, 1628.21it/s]
100%|ββββββββββ| 228922/228922 [02:33<00:00, 1493.90it/s]
100%|ββββββββββ| 228922/228922 [02:28<00:00, 1544.23it/s]
100%|ββββββββββ| 10921592/10921592 [06:13<00:00, 29266.91it/s]
WARNING:tensorflow:From /home/aznb/GEMSEC/src/model.py:118: The name tf.Session is deprecated. Please use tf.compat.v1.Session instead
.
2019-10-13 20:08:10.947046: I tensorflow/core/platform/cpu_feature_guard.cc:142] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 AVX
512F FMA
2019-10-13 20:08:10.981722: I tensorflow/core/platform/profile_utils/cpu_utils.cc:94] CPU Frequency: 3199290000 Hz
2019-10-13 20:08:10.984370: I tensorflow/compiler/xla/service/service.cc:168] XLA service 0x4b6c170 executing computations on platform Host. Devices:
2019-10-13 20:08:10.984438: I tensorflow/compiler/xla/service/service.cc:175] StreamExecutor device (0): <undefined>, <undefined>
2019-10-13 20:08:11.116679: 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_x
la_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.
0%| | 1/228922 [00:00<47:01:06, 1.35it/s]
Model initialization started.
Random walk series 1. initiated.
Random walk series 2. initiated.
Random walk series 3. initiated.
Random walk series 4. initiated.
Random walk series 5. initiated.
Weight calculation started.
Model Initialized.
Epoch 1. initiated.
Traceback (most recent call last):
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/client/session.py", line 1356, in _do_call
return fn(*args)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/client/session.py", line 1341, in _run_fn
options, feed_dict, fetch_list, target_list, run_metadata)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/client/session.py", line 1429, in _call_tf_sessionrun
run_metadata)
tensorflow.python.framework.errors_impl.InvalidArgumentError: indices[289] = 236440 is not in [0, 228922)
[[{{node sampled_softmax_loss/embedding_lookup_1}}]]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "../GEMSEC/src/embedding_clustering.py", line 22, in <module>
create_and_run_model(args)
File "../GEMSEC/src/embedding_clustering.py", line 18, in create_and_run_model
model.train()
File "/home/aznb/GEMSEC/src/model.py", line 134, in train
_, loss = session.run([self.train_op , self.loss], feed_dict=feed_dict)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/client/session.py", line 950, in run
run_metadata_ptr)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/client/session.py", line 1173, in _run
feed_dict_tensor, options, run_metadata)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/client/session.py", line 1350, in _do_run
run_metadata)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/client/session.py", line 1370, in _do_call
raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.InvalidArgumentError: indices[289] = 236440 is not in [0, 228922)
[[node sampled_softmax_loss/embedding_lookup_1 (defined at /home/aznb/GEMSEC/src/layers.py:55) ]]
Errors may have originated from an input operation.
Input Source operations connected to node sampled_softmax_loss/embedding_lookup_1:
Variable_2/read (defined at /home/aznb/GEMSEC/src/layers.py:28)
Original stack trace for 'sampled_softmax_loss/embedding_lookup_1':
File "../GEMSEC/src/embedding_clustering.py", line 22, in <module>
create_and_run_model(args)
File "../GEMSEC/src/embedding_clustering.py", line 11, in create_and_run_model
model = GEMSECWithRegularization(args, graph)
File "/home/aznb/GEMSEC/src/model.py", line 37, in __init__
self.build()
File "/home/aznb/GEMSEC/src/model.py", line 73, in build
self.loss = self.walker_layer()+self.gamma*self.cluster_layer(self.walker_layer)+self.regularizer_layer(self.walker_layer)
File "/home/aznb/GEMSEC/src/layers.py", line 55, in __call__
sampled_values = self.sampler)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/ops/nn_impl.py", line 2024, in sampled_softmax_loss
seed=seed)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/ops/nn_impl.py", line 1557, in _compute_sampled_logits
biases, all_ids, partition_strategy=partition_strategy)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/ops/embedding_ops.py", line 315, in embedding_lookup
transform_fn=None)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/ops/embedding_ops.py", line 133, in _embedding_lookup_and_transform
array_ops.gather(params[0], ids, name=name), ids, max_norm)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/util/dispatch.py", line 180, in wrapper
return target(*args, **kwargs)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/ops/array_ops.py", line 3475, in gather
return gen_array_ops.gather_v2(params, indices, axis, name=name)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/ops/gen_array_ops.py", line 4097, in gather_v2
batch_dims=batch_dims, name=name)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/framework/op_def_library.py", line 788, in _apply_op_helper
op_def=op_def)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/util/deprecation.py", line 507, in new_func
return func(*args, **kwargs)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/framework/ops.py", line 3616, in create_op
op_def=op_def)
File "/home/aznb/.linuxbrew/Cellar/python/3.7.4_1/lib/python3.7/site-packages/tensorflow/python/framework/ops.py", line 2005, in __init__
self._traceback = tf_stack.extract_stack()