I am trying to import a saved neural network in Tensorflow. I saved it after training with:
saver = tf.train.Saver()
saver.save(sess, filename)
and in the script I use for inference, I restore it with:
sess = tf.Session()
saver = tf.train.import_meta_graph(filename.meta)
saver.restore(sess, tf.train.latest_checkpoint('./'))
But during the import_meta_graph line, I get this error:
KeyError: "The name 'dropout1/cond/dropout/Shape/Switch:1' refers to a Tensor which does not exist. The operation, 'dropout1/cond/dropout/Shape/Switch', does not exist in the graph."
I looked at the names of the tensors and operations in the original notebook in which I trained the model, and the names mentionned in the error message do exist. Moreover, I used the same code for saving and importing other models and it works. The only difference is that I trained these on an AWS machine, with an older version of tensorflow, while I trained the problematic one on my computer.
Related
I want to use a pretrained tensorflow model provided by an unknown author. I do not know how he/she managed to save the tensorflow model (he/she used tensorflow version >= 1.2) to only one file with the extension '.model', as normally I get either three files '.meta', '.data', '.index' or one file with '.ckpt'.
How can I restore this pretrained model? How can I save a model to this format later?
Thanks.
I have also asked this question on a number of platforms with no assistance yet. So I decided to do some experimental work and this is what I found. This may be long but please bear with me.
To import a model in Tensor-flow we use
with tf.Session() as sess:
new_saver = tf.train.import_meta_graph('my_test_model-1000.meta')
new_saver.restore(sess, tf.train.latest_checkpoint('./'))
The .meta file contains all the variables, operations, collections, etc, of the trained model. What tf.train.latest_checkpoint('./') does is to use the checkpoint file (which simply keeps a record of latest checkpoint files saved) to import the xxxx_model.data-00000-of-00001. This .data-00000-of-00001 contains all the weights, biases, gradients, etc, that must be loaded into the variables contained in my_test_model-1000.meta.
Summary [Semi-complete code]
with tf.Session() as sess:
new_saver = tf.train.import_meta_graph('my_test_model-1000.meta')
#new_saver.restore(sess, tf.train.latest_checkpoint('./'))
tensor_variable = tf.trainable_variables()
for tensor_var in tensor_variable:
#print(sess.run(tensor_var))
print(tensor_var)
This initial code will print out all the variables from .meta that are trainable. If you try to run print(sess.run(tensor_var)) you will get an error. This is because, the variables have not been initialized. How ever, if you un-comment new_saver.restore(sess, tf.train.latest_checkpoint('./')) and run print(sess.run(tensor_var)), you will get all the variables alongside values loaded into the variables.
Now to “.model”
My best guess is that xxxxxx.model works a much like xxxx_model.data-00000-of-00001 from tensorflow. It does not contain variables and so if you try to do
with tf.Session() as sess:
new_saver = tf.train.import_meta_graph('xxx.model')
you will get an error. Remember, the reason is that, this .model file does not contain any variables nor operation graph of any form. If you also try to do
with tf.Session() as sess:
new_saver = tf.train.Saver()
new_saver.restore(sess, "xxxx.model")
you will similarly get an error. This is because, there are no corresponding variables to load values into. Therefore, if you ever obtain a xxx.model file, you will have to go through the pain of replicating all the variables and operations before trying to run new_saver.restore(sess, "xxxx.model"). If you are able to replicate the architecture, this will run smoothly with no issues, hopefully.
I am sorry this was long, but considering that there is almost no answer on the internet, I had to make a lecture out of it. :)
I have tried to save and restore the LSTM models according to the tutorial. Actually, it works in the normal models saving and restoring like CNN models. However when i tried to restore the LSTM models it throw the error
FailedPreconditionError (see above for traceback): Attempting to use uninitialized value RNN_model/RNN/multi_rnn_cell/cell_0/basic_lstm_cell/kernel
the key codes shows follow:
with tf.Session() as sess:
saver.restore(sess, saver_path)
with tf.variable_scope('RNN_model', reuse=None):
train_rnn = RNNmodel.LSTMmodel(True, RNNmodel.TRAIN_BATCH_SIZE, RNNmodel.NUM_STEP)
with tf.variable_scope('RNN_model', reuse=True):
test_rnn = RNNmodel.LSTMmodel(False, RNNmodel.EVAL_BATCH_SIZE, RNNmodel.NUM_STEP)
I wonder if there any difference between the normal models and LSTM models in the saving and restoring. Please help
EDIT:
i try to move the restore and it works, but when i run my models, it still throws the same error, my run_epoch code like:
def run_epoch(session, model, datas, train_op, is_log, epoch=3000):
state = session.run(model.initiate_state)
total_cost = 0
for i in range(epoch):
data, label = random_get_data(datas, model.batch_size, num_step=RNNmodel.NUM_STEP)
feed_dict = {
model.input_data: data,
model.target: label,
model.initiate_state: state
}
cost, state, argmax_logit, target, _ = session.run([model.loss, model.final_state, model.argmax_target, model.target, train_op], feed_dict)
the log located the error at the :
cost, state, argmax_logit, target, _ = session.run([model.loss, model.final_state, model.argmax_target, model.target, train_op], feed_dict)
and the log shows follow:
tensorflow.python.framework.errors_impl.FailedPreconditionError: Attempting to use uninitialized value RNN_model/RNN/multi_rnn_cell/cell_0/basic_lstm_cell/kernel
it seems that the restore does not restore the lstm kernel operation.should i do anything to initiate the lstm operation specially?
EDIT2:
I check out the checkpoint file at last and i am sure that save operation dose not save the variables about LSTM cells and i dont know why.It seems that i have to name the variables explicitly otherwise i cannot save it, and BasicLSTMCell class init() dose not have the name parameters.
There is no difference, RNNs use ordinary variables.
I think you have to move
saver.restore(sess, saver_path)
after you create the LSTMmodel. Otherwise it's variables are not in the graph when you call restore - so they won't be restored.
I finally figured it out. According to the Saving and Restoring a trained LSTM in Tensor Flow and the answer of Jeronimo Garcia-Loygorri, i move the creation of Saver after the LSTM model's definition, and then every problem gone!
I have run the distributed mnist example:
https://github.com/tensorflow/tensorflow/blob/r0.12/tensorflow/tools/dist_test/python/mnist_replica.py
Though I have set the
saver = tf.train.Saver(max_to_keep=0)
In previous release, like r11, I was able to run over each check point model and evaluate the precision of the model. This gave me a plot of the progress of the precision versus global steps (or iterations).
Prior to r12, tensorflow checkpoint models were saved in two files, model.ckpt-1234 and model-ckpt-1234.meta. One could restore a model by passing the model.ckpt-1234 filename like so saver.restore(sess,'model.ckpt-1234').
However, I've noticed that in r12, there are now three output files model.ckpt-1234.data-00000-of-000001, model.ckpt-1234.index, and model.ckpt-1234.meta.
I see that the the restore documentation says that a path such as /train/path/model.ckpt should be given to restore instead of a filename. Is there any way to load one checkpoint file at a time to evaluate it? I have tried passing the model.ckpt-1234.data-00000-of-000001, model.ckpt-1234.index, and model.ckpt-1234.meta files, but get errors like below:
W tensorflow/core/util/tensor_slice_reader.cc:95] Could not open logdir/2016-12-08-13-54/model.ckpt-0.data-00000-of-00001: Data loss: not an sstable (bad magic number): perhaps your file is in a different file format and you need to use a different restore operator?
NotFoundError (see above for traceback): Tensor name "hid_b" not found in checkpoint files logdir/2016-12-08-13-54/model.ckpt-0.index
[[Node: save/RestoreV2_1 = RestoreV2[dtypes=[DT_FLOAT], _device="/job:localhost/replica:0/task:0/cpu:0"](_recv_save/Const_0, save/RestoreV2_1/tensor_names, save/RestoreV2_1/shape_and_slices)]]
W tensorflow/core/util/tensor_slice_reader.cc:95] Could not open logdir/2016-12-08-13-54/model.ckpt-0.meta: Data loss: not an sstable (bad magic number): perhaps your file is in a different file format and you need to use a different restore operator?
I'm running on OSX Sierra with tensorflow r12 installed via pip.
Any guidance would be helpful.
Thank you.
I also used Tensorlfow r0.12 and I didn't think there is any issue for saving and restoring model. The following is a simple code that you can have a try:
import tensorflow as tf
# Create some variables.
v1 = tf.Variable(tf.random_normal([784, 200], stddev=0.35), name="v1")
v2 = tf.Variable(tf.random_normal([784, 200], stddev=0.35), name="v2")
# Add an op to initialize the variables.
init_op = tf.global_variables_initializer()
# Add ops to save and restore all the variables.
saver = tf.train.Saver()
# Later, launch the model, initialize the variables, do some work, save the
# variables to disk.
with tf.Session() as sess:
sess.run(init_op)
# Do some work with the model.
# Save the variables to disk.
save_path = saver.save(sess, "/tmp/model.ckpt")
print("Model saved in file: %s" % save_path)
# Later, launch the model, use the saver to restore variables from disk, and
# do some work with the model.
with tf.Session() as sess:
# Restore variables from disk.
saver.restore(sess, "/tmp/model.ckpt")
print("Model restored.")
# Do some work with the model
although in r0.12, the checkpoint is stored in multiple files, you can restore it by using the common prefix, which is 'model.ckpt' in your case.
The R12 has changed the checkpoint format. You should save the model in the old format.
import tensorflow as tf
from tensorflow.core.protobuf import saver_pb2
...
saver = tf.train.Saver(write_version = saver_pb2.SaverDef.V1)
saver.save(sess, './model.ckpt', global_step = step)
According to the TensorFlow v0.12.0 RC0’s release note:
New checkpoint format becomes the default in tf.train.Saver. Old V1
checkpoints continue to be readable; controlled by the write_version
argument, tf.train.Saver now by default writes out in the new V2
format. It significantly reduces the peak memory required and latency
incurred during restore.
see details in my blog.
You can restore the model like this:
saver = tf.train.import_meta_graph('./src/models/20170512-110547/model-20170512-110547.meta')
saver.restore(sess,'./src/models/20170512-110547/model-20170512-110547.ckpt-250000'))
Where the path '/src/models/20170512-110547/' contains three files:
model-20170512-110547.meta
model-20170512-110547.ckpt-250000.index
model-20170512-110547.ckpt-250000.data-00000-of-00001
And if in one directory there are more than one checkpoints,eg: there are checkpoint files in the path
./20170807-231648/:
checkpoint
model-20170807-231648-0.data-00000-of-00001
model-20170807-231648-0.index
model-20170807-231648-0.meta
model-20170807-231648-100000.data-00000-of-00001
model-20170807-231648-100000.index
model-20170807-231648-100000.meta
you can see that there are two checkpoints, so you can use this:
saver = tf.train.import_meta_graph('/home/tools/Tools/raoqiang/facenet/models/facenet/20170807-231648/model-20170807-231648-0.meta')
saver.restore(sess,tf.train.latest_checkpoint('/home/tools/Tools/raoqiang/facenet/models/facenet/20170807-231648/'))
OK, I can answer my own question. What I found was that my python script was adding an extra '/' to my path so I was executing:
saver.restore(sess,'/path/to/train//model.ckpt-1234')
somehow that was causing a problem with tensorflow.
When I removed it, calling:
saver.restore(sess,'/path/to/trian/model.ckpt-1234')
it worked as expected.
use only model.ckpt-1234
at least it works for me
I'm new to TF and met the same issue. After reading Yuan Ma's comments, I copied the '.index' to the same 'train\ckpt' folder together with '.data-00000-of-00001' file. Then it worked!
So, the .index file is sufficient when restoring the models.
I used TF on Win7, r12.
I am a bit of a beginner with tensorflow so please excuse if this is a stupid question and the answer is obvious.
I have created a Tensorflow graph where starting with placeholders for X and y I have optimized some tensors which represent my model. Part of the graph is something where a vector of predictions can be calculated, e.g. for linear regression something like
y_model = tf.add(tf.mul(X,w),d)
y_vals = sess.run(y_model,feed_dict={....})
After training has been completed I have acceptable values for w and d and now I want to save my model for later. Then, in a different python session I want to restore the model so that I can again run
## Starting brand new python session
import tensorflow as tf
## somehow restor the graph and the values here: how????
## so that I can run this:
y_vals = sess.run(y_model,feed_dict={....})
for some different data and get back the y-values.
I want this to work in a way where the graph for calculating the y-values from the placeholders is also stored and restored - as long as the placeholders get fed the correct data, this should work transparently without the user (the one who applies the model) needing to know what the graph looks like).
As far as I understand tf.train.Saver().save(..) only saves the variables but I also want to save the graph. I think that tf.train.export_meta_graph could be relevant here but I do not understand how to use it correctly, the documentation is a bit cryptic to me and the examples do not even use export_meta_graph anywhere.
From the docs, try this:
# Create some variables.
v1 = tf.Variable(..., name="v1")
v2 = tf.Variable(..., name="v2")
...
# Add an op to initialize the variables.
init_op = tf.global_variables_initializer()
# Add ops to save and restore all the variables.
saver = tf.train.Saver()
# Later, launch the model, initialize the variables, do some work, save the
# variables to disk.
with tf.Session() as sess:
sess.run(init_op)
# Do some work with the model.
..
# Save the variables to disk.
save_path = saver.save(sess, "/tmp/model.ckpt")
print("Model saved in file: %s" % save_path)
You can specify the path.
And if you want to restore the model, try:
with tf.Session() as sess:
saver = tf.train.import_meta_graph('/tmp/model.ckpt.meta')
saver.restore(sess, "/tmp/model.ckpt")
Saving Graph in Tensorflow:
import tensorflow as tf
# Create some placeholder variables
x_pl = tf.placeholder(..., name="x")
y_pl = tf.placeholder(..., name="y")
# Add some operation to the Graph
add_op = tf.add(x, y)
with tf.Session() as sess:
# Add variable initializer
init = tf.global_variables_initializer()
# Add ops to save variables to checkpoints
# Unless var_list is specified Saver will save ALL named variables
# in Graph
# Optionally set maximum of 3 latest models to be saved
saver = tf.train.Saver(max_to_keep=3)
# Run variable initializer
sess.run(init)
for i in range(no_steps):
# Feed placeholders with some data and run operation
sess.run(add_op, feed_dict={x_pl: i+1, y_pl: i+5})
saver.save(sess, "path/to/checkpoint/model.ckpt", global_step=i)
This will save the following files:
1) Meta Graph
.meta file:
MetaGraphDef protocol buffer representation of MetaGraph which saves the complete Tf Graph structure i.e. the GraphDef that describes the dataflow and all metadata associated with it e.g. all variables, operations, collections, etc.
importing the graph structure will recreate the Graph and all its variables, then the corresponding values for these variables can be restored from the checkpoint file
if you don't want to restore the Graph however you can reconstruct all of the information in the MetaGraphDef by re-executing the Python code that builds the model n.b. you must recreate the EXACT SAME variables first before restoring their values from the checkpoint
since Meta Graph file is not always needed, you can switch off writing the file in saver.save using write_meta_graph=False
2) Checkpoint files
.data file:
binary file containing VALUES of all saved variables outlined in tf.train.Saver() (default is all variables)
.index file:
immutable table describing all tensors and their metadata checkpoint file:
keeps a record of latest checkpoint files saved
Restoring Graph in Tensorflow:
import tensorflow as tf
latest_checkpoint = tf.train.latest_checkpoint("path/to/checkpoint")
# Load latest checkpoint Graph via import_meta_graph:
# - construct protocol buffer from file content
# - add all nodes to current graph and recreate collections
# - return Saver
saver = tf.train.import_meta_graph(latest_checkpoint + '.meta')
# Start session
with tf.Session() as sess:
# Restore previously trained variables from disk
print("Restoring Model: {}".format("path/to/checkpoint"))
saver.restore(sess, latest_checkpoint)
# Retrieve protobuf graph definition
graph = tf.get_default_graph()
print("Restored Operations from MetaGraph:")
for op in graph.get_operations():
print(op.name)
# Access restored placeholder variables
x_pl = graph.get_tensor_by_name("x_pl:0")
y_pl = graph.get_tensor_by_name("y_pl:0")
# Access restored operation to re run
accuracy_op = graph.get_tensor_by_name("accuracy_op:0")
This is just a quick example with the basics, for a working implementation see here.
In order to save the graph, you need to freeze the graph.
Here is the python script for freezing the graph : https://github.com/tensorflow/tensorflow/blob/master/tensorflow/python/tools/freeze_graph.py
Here is a code snippet for freezing graph:
from tensorflow.python.tools import freeze_graph
freeze_graph.freeze_graph(input_graph_path, input_saver_def_path,
input_binary, checkpoint_path, output_node
restore_op_name, filename_tensor_name,
output_frozen_graph_name, True, "")
where output node corresponds to output tensor variable.
output = tf.nn.softmax(outer_layer_name,name="output")
I'm attempting to export a model built and trained with Keras to a protobuffer that I can load in a C++ script (as in this example). I've generated a .pb file containing the model definition and a .ckpt file containing the checkpoint data. However, when I try to merge them into a single file using the freeze_graph script I get the error:
ValueError: Fetch argument 'save/restore_all' of 'save/restore_all' cannot be interpreted as a Tensor. ("The name 'save/restore_all' refers to an Operation not in the graph.")
I'm saving the model like this:
with tf.Session() as sess:
model = nndetector.architecture.models.vgg19((3, 50, 50))
model.load_weights('/srv/nn/weights/scratch-vgg19.h5')
init_op = tf.initialize_all_variables()
sess.run(init_op)
graph_def = sess.graph.as_graph_def()
tf.train.write_graph(graph_def=graph_def, logdir='.', name='model.pb', as_text=False)
saver = tf.train.Saver()
saver.save(sess, 'model.ckpt')
nndetector.architecture.models.vgg19((3, 50, 50)) is simply a vgg19-like model defined in Keras.
I'm calling the freeze_graph script like this:
bazel-bin/tensorflow/python/tools/freeze_graph --input_graph=[path-to-model.pb] --input_checkpoint=[path-to-model.ckpt] --output_graph=[output-path] --output_node_names=sigmoid --input_binary=True
If I run the freeze_graph_test script everything works fine.
Does anyone know what I'm doing wrong?
Thanks.
Best regards
Philip
EDIT
I've tried printing tf.train.Saver().as_saver_def().restore_op_name which returns save/restore_all.
Additionally, I've tried a simple pure tensorflow example and still get the same error:
a = tf.Variable(tf.constant(1), name='a')
b = tf.Variable(tf.constant(2), name='b')
add = tf.add(a, b, 'sum')
with tf.Session() as sess:
sess.run(tf.initialize_all_variables())
tf.train.write_graph(graph_def=sess.graph.as_graph_def(), logdir='.', name='simple_as_binary.pb', as_text=False)
tf.train.Saver().save(sess, 'simple.ckpt')
And I'm actually also unable to restore the graph in python. Using the following code throws ValueError: No variables to save if I execute it separately from saving the graph (that is, if I both save and restore the model in the same script, everything works fine).
with gfile.FastGFile('simple_as_binary.pb') as f:
graph_def = tf.GraphDef()
graph_def.ParseFromString(f.read())
with tf.Session() as sess:
tf.import_graph_def(graph_def)
saver = tf.train.Saver()
saver.restore(sess, 'simple.ckpt')
I'm not sure if the two problems are related, or if I'm simply not restoring the model correctly in python.
The problem is the order of these two lines in your original program:
tf.train.write_graph(graph_def=sess.graph.as_graph_def(), logdir='.', name='simple_as_binary.pb', as_text=False)
tf.train.Saver().save(sess, 'simple.ckpt')
Calling tf.train.Saver() adds a set of nodes to the graph, including one called "save/restore_all". However, this program calls it after writing out the graph, so the file you pass to freeze_graph.py doesn't contain those nodes, which are necessary for doing the rewriting.
Reversing the two lines should make the script work as intended:
tf.train.Saver().save(sess, 'simple.ckpt')
tf.train.write_graph(graph_def=sess.graph.as_graph_def(), logdir='.', name='simple_as_binary.pb', as_text=False)
So, I got it working. Sort of.
By using tensorflow.python.client.graph_util.convert_variables_to_constants directly instead of first saving GraphDef and a checkpoint to disk and then using the freeze_graph tool/script, I have been able to save a GraphDef containing both graph definition and variables converted to constants.
EDIT
mrry updated his answer, which solved my issue of freeze_graph not working, but I'll leave this answer as well, in case anyone else could find it useful.