How read data from csv file in locust performance test scripts? - locust

I am trying to read the data from csv file that contails 1 row and 5 column using the following code
def __init__(self):
super(data, self).__init__()
global data
if (data == None):
with open('var.csv', 'r') as l:
reader = csv.reader(l)
data = list(reader)
def on_start(self):
if len(data) > 0:
self.my_value = data.pop()
My output is ('sample') and I want it to be sample


Change the last line from self.my_value = data.pop() to self.my_value = data.pop()[0].
But you could also use locust plugins csv reader: https://github.com/SvenskaSpel/locust-plugins/blob/master/examples/csvreader_ex.py

Related

Is there a tool that shows a distribution of lines of code per file of a folder?

I want to know how big files are within my repository in terms of lines of code, to see the 'health' of a repository.
In order to answer this, I would like to see a distribution (visualised or not) of the number of files for a specific range (can be 1):
#lines of code #files
1-10 1
11-20 23
etc...
(A histogram of this would be nice)
Is there quick why to get this, with for example cloc or any other (command line) tool?

A combination of cloc and Pandas can handle this. First, capture the line counts with cloc to a csv file using --by-file and --csv switches, for example
cloc --by-file --csv --out data.csv curl-7.80.0.tar.bz2
then use the Python program below to aggregate and bin the data by folders:
./aggregate_by_folder.py data.csv
The code for aggregate_by_folder.py is
#!/usr/bin/env python
import sys
import os.path
import pandas as pd
def add_folder(df):
"""
Return a Pandas dataframe with an additional 'folder' column
containing each file's parent directory
"""
header = 'github.com/AlDanial/cloc'
df = df.drop(df.columns[df.columns.str.contains(header)], axis=1)
df['folder'] = df['filename'].dropna().apply(os.path.dirname)
return df
def bin_by_folder(df):
bins = list(range(0,1000,50))
return df.groupby('folder')['code'].value_counts(bins=bins).sort_index()
def file_count_by_folder(df):
df_files = pd.pivot_table(df, index=['folder'], aggfunc='count')
file_counts = df_files.rename(columns={'blank':'file count'})
return file_counts[['file count']]
def main():
if len(sys.argv) != 2:
print(f"Usage: {sys.argv[0]} data.csv")
print(" where the .csv file is created with")
print(" cloc --by-file --csv --out data.csv my_code_base")
raise SystemExit
pd.set_option('display.max_rows', None)
pd.set_option('display.width', None)
pd.set_option('display.max_colwidth', -1)
df = add_folder(pd.read_csv(sys.argv[1]))
print(pd.pivot_table(df, index=['folder'], aggfunc='sum'))
print('-' * 50)
print(file_count_by_folder(df))
print('-' * 50)
print(bin_by_folder(df))
if __name__ == "__main__": main()

Trying to install a corpus for countVectorizer in sklearn package

I am trying to load a corpus from my local drive into python at one time with a for loop and then read each text file and save it for analysis with countVectorizer. But, I am only getting the last file. How do I get the results from all of the files to be stored for analysis with countVectorizer?
This code brings out the text from last file in folder.
folder_path = "folder"
#import and read all files in animal_corpus
for filename in glob.glob(os.path.join(folder_path, '*.txt')):
with open(filename, 'r') as f:
txt = f.read()
print(txt)
MyList= [txt]
## Create a CountVectorizer object that you can use
MyCV1 = CountVectorizer()
## Call your MyCV1 on the data
DTM1 = MyCV1.fit_transform(MyList)
## get col names
ColNames=MyCV1.get_feature_names()
print(ColNames)
## convert DTM to DF
MyDF1 = pd.DataFrame(DTM1.toarray(), columns=ColNames)
print(MyDF1)
This code works, but would not work for a huge corpus that I am preparing it for.
#import and read text files
f1 = open("folder/animal_1.txt",'r')
f1r = f1.read()
f2 = open("/folder/animal_2.txt",'r')
f2r = f2.read()
f3 = open("/folder/animal_3.txt",'r')
f3r = f3.read()
#reassemble corpus in python
MyCorpus=[f1r, f2r, f3r]
## Create a CountVectorizer object that you can use
MyCV1 = CountVectorizer()
## Call your MyCV1 on the data
DTM1 = MyCV1.fit_transform(MyCorpus)
## get col names
ColNames=MyCV1.get_feature_names()
print(ColNames)
## convert DTM to DF
MyDF2 = pd.DataFrame(DTM1.toarray(), columns=ColNames)
print(MyDF2)

I figured it out. Just gotta keep grinding.
MyCorpus=[]
#import and read all files in animal_corpus
for filename in glob.glob(os.path.join(folder_path, '*.txt')):
with open(filename, 'r') as f:
txt = f.read()
MyCorpus.append(txt)

Storage values using os.stat(filename)

I'm trying to create an EDUCATIONAL PURPOSES ONLY virus. I do not plan on spreading it. It's purpose is to grow a file to the point your storage is full and slow your computer down. It prints the size of the file every 0.001 seconds. With that, I also want to know how fast it is growing the file. The following code doesn't seem to let it run:
class Vstatus():
def _init_(Status):
Status.countspeed == True
Status.active == True
Status.growingspeed == 0
import time
import os
#Your storage is at risk of over-expansion. Please do not let this file run forever, as your storage will fill continuously.
#This is for educational purposes only.
while Vstatus.Status.countspeed == True:
f = open('file.txt', 'a')
f.write('W')
fsize = os.stat('file.txt')
Key1 = fsize
time.sleep(1)
Key2 = fsize
Vstatus.Status.growingspeed = (Key2 - Key1)
Vstatus.Status.countspeed = False
while Vstatus.Status.active == True:
time.sleep(0.001)
f = open('file.txt', 'a')
f.write('W')
fsize = os.stat('file.txt')
print('size:' + fsize.st_size.__str__() + ' at a speed of ' + Vstatus.Status.growingspeed + 'bytes per second.')
This is for Educational Purposes ONLY
The main error I keep getting when running the file is here:
TypeError: unsupported operand type(s) for -: 'os.stat_result' and 'os.stat_result'
What does this mean? I thought os.stat returned an integer Can I get a fix on this?

Vstatus.Status.growingspeed = (Key2 - Key1)
You can't subtract os.stat objects. Your code also has some other problems. Your loops will run sequentially, meaning that your first loop will try to estimate how quickly the file is being written to without writing anything to the file.
import time # Imports at the top
import os
class VStatus:
def __init__(self): # double underscores around __init__
self.countspeed = True # Assignment, not equality test
self.active = True
self.growingspeed = 0
status = VStatus() # Make a VStatus instance
# You need to do the speed estimation and file appending in the same loop
with open('file.txt', 'a+') as f: # Only open the file once
start = time.time() # Get the current time
starting_size = os.fstat(f.fileno()).st_size
while status.active: # Access the attribute of the VStatus instance
size = os.fstat(f.fileno()).st_size # Send file desciptor to stat
f.write('W') # Writing more than one character at a time will be your biggest speed up
f.flush() # make sure the byte is written
if status.countspeed:
diff = time.time() - start
if diff >= 1: # More than a second has gone by
status.countspeed = False
status.growingspeed = (os.fstat(f.fileno()).st_size - starting_size)/diff # get rate of growth
else:
print(f"size: {size} at a speed of {status.growingspeed}")

Using pytorch cuda for RNNs on google colaboratory

I have a code (a code we saw in a class) of a recurrent neural network that reads a given text and tries to produce its own text similar to the example. The code is written in python and uses the pytorch library. I wanted to modify to see whether I could increase its speed by using GPU instead of CPU and I made some tests on google collaboratory. The GPU version of the code runs fine but is about three times slower than the CPU version. I do not know the details of GPU architecture so I can not really understand why it is slower. I know that GPUs can do more arithmetic operations per cycle but have more limited memory so I am curious if I am having a memory issue. I also tried using CUDA with a generative adversarial network and in this case it was almost ten times faster. Any tips on this would be welcome.
The code (CUDA version) is below. I am new at this stuff so sorry if some of the terminology is not correct.
The architecture is input->encoder->recursive network->decoder->output.
import torch
import time
import numpy as np
from torch.autograd import Variable
import matplotlib.pyplot as plt
from google.colab import files
#uploding text on google collab
uploaded = files.upload()
for fn in uploaded.keys():
print('User uploaded file "{name}" with length {length} bytes'.format(
name=fn, length=len(uploaded[fn])))
#data preprocessing
with open('text.txt','r') as file:
#with open closes the file after we are done with it
rawtxt=file.read()
rawtxt = rawtxt.lower()
#a function that assigns a number to each unique character in the text
def create_map(rawtxt):
letters = list(set(rawtxt))
lettermap = dict(enumerate(letters)) #gives each letter in the list a number
return lettermap
num_to_let = create_map(rawtxt)
#inverse to num_to_let
let_to_num =dict(zip(num_to_let.values(), num_to_let.keys()))
print(num_to_let)
#turns a text of characters into text of numbers using the mapping
#given by the input mapdict
def maparray(txt, mapdict):
txt = list(txt)
for k, letter in enumerate(txt):
txt[k]=mapdict[letter]
txt=np.array(txt)
return txt
X=maparray(rawtxt, let_to_num) #the data text in numeric format
Y= np.roll(X, -1, axis=0) #shifted data text in numeric format
X=torch.LongTensor(X)
Y=torch.LongTensor(Y)
#up to here we are done with data preprocessing
#return a random batch for training
#this reads a random piece inside data text
#with the size chunk_size
def random_chunk(chunk_size):
k=np.random.randint(0,len(X)-chunk_size)
return X[k:k+chunk_size], Y[k:k+chunk_size]
nchars = len(num_to_let)
#define the recursive neural network class
class rnn(torch.nn.Module):
def __init__(self,input_size,hidden_size,output_size, n_layers=1):
super().__init__()
self.input_size = input_size
self.hidden_size = hidden_size
self.output_size = output_size
self.n_layers= n_layers
self.encoder = torch.nn.Embedding (input_size, hidden_size)
self.rnn = torch.nn.RNN(hidden_size, hidden_size, n_layers, batch_first=True)
self.decoder = torch.nn.Linear (hidden_size, output_size)
def forward (self,x,hidden):
x=self.encoder(x.view(1,-1))
output, hidden = self.rnn(x.view(1,1,-1), hidden)
output = self.decoder(output.view(1,-1))
return output, hidden
def init_hidden(self):
return Variable(torch.zeros(self.n_layers , 1 , self.hidden_size)).cuda()
#hyper-params
lr = 0.009
no_epochs = 50
chunk_size = 150
myrnn = rnn(nchars, 150, nchars,1)
myrnn.cuda()
criterion = torch.nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(myrnn.parameters(), lr=lr)
t0 = time.time()
for epoch in range(no_epochs):
totcost=0
generated = ''
for _ in range(len(X)//chunk_size):
h=myrnn.init_hidden()
cost = 0
x, y=random_chunk(chunk_size)
x, y= Variable(x).cuda(), Variable(y).cuda()
for i in range(chunk_size):
out, h = myrnn.forward(x[i],h)
_, outl = out.data.max(1)
letter = num_to_let[outl[0]]
generated+=letter
cost += criterion(out, y[i])
optimizer.zero_grad()
cost.backward()
optimizer.step()
totcost+=cost
totcost/=len(X)//chunk_size
print('Epoch', epoch, 'Avg cost/chunk: ', totcost)
print(generated[0:750],'\n\n\n')
t1 = time.time()
total = t1-t0
print('total',total)
#we encode each word into a vector of fixed size

Callbackfunction modelcheckpoint causes error in keras

I seem to get this error when I am using the callback function modelcheckpoint..
I read from a github issue that the solution would be make use of model.get_weight, but I am implicitly only storing that since i am only storing the one with best weight.
Keras only seem to save weights using h5, which make me question is there any other way to do store them using the eras API, if so how? If not, how do i store it?
Made an example to recreate the problem:
#!/usr/bin/python
import glob, os
import sys
from os import listdir
from os.path import isfile, join
import numpy as np
import warnings
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from keras.utils import np_utils
from keras import metrics
import keras
from keras import backend as K
from keras.models import Sequential
from keras.optimizers import SGD, Adam
from keras.layers.core import Dense, Activation, Lambda, Reshape,Flatten
from keras.layers import Conv1D,Conv2D,MaxPooling2D, MaxPooling1D, Reshape
#from keras.utils.visualize_util import plot
from keras.models import Model
from keras.layers import Input, Dense
from keras.layers.merge import Concatenate, Add
import h5py
import random
import tensorflow as tf
import math
from keras.callbacks import CSVLogger
from keras.callbacks import ModelCheckpoint
if len(sys.argv) < 5:
print "Missing Arguments!"
print "python keras_convolutional_feature_extraction.py <workspace> <totale_frames> <fbank-dim> <window-height> <batch_size>"
print "Example:"
print "python keras_convolutional_feature_extraction.py deltas 15 40 5 100"
sys.exit()
total_frames = int(sys.argv[2])
total_frames_with_deltas = total_frames*3
dim = int(sys.argv[3])
window_height = int(sys.argv[4])
inserted_batch_size = int(sys.argv[5])
stride = 1
splits = ((dim - window_height)+1)/stride
#input_train_data = "/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_train_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(inserted_batch_size)+"_fws_input"
#output_train_data ="/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_train_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(inserted_batch_size)+"_fws_output"
#input_test_data = "/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_test_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(1)+"_fws_input"
#output_test_data = "/media/carl/E2302E68302E443F/"+str(sys.argv[1])+"/fbank/org_test_total_frames_"+str(total_frames)+"_dim_"+str(dim)+"_winheig_"+str(window_height)+"_batch_"+str(1)+"_fws_output"
#train_files =[f for f in listdir(input_train_data) if isfile(join(input_train_data, f))]
#test_files =[f for f in listdir(input_test_data) if isfile(join(input_test_data, f))]
#print len(train_files)
np.random.seed(100)
print "hallo"
def train_generator():
while True:
# input = random.choice(train_files)
# h5f = h5py.File(input_train_data+'/'+input, 'r')
# train_input = h5f['train_input'][:]
# train_output = h5f['train_output'][:]
# h5f.close()
train_input = np.random.randint(100,size=((inserted_batch_size,splits*total_frames_with_deltas,window_height,3)))
train_list_list = []
train_input = train_input.reshape((inserted_batch_size,splits*total_frames_with_deltas,window_height,3))
train_input_list = np.split(train_input,splits*total_frames_with_deltas,axis=1)
for i in range(len(train_input_list)):
train_input_list[i] = train_input_list[i].reshape(inserted_batch_size,window_height,3)
#for i in range(len(train_input_list)):
# train_input_list[i] = train_input_list[i].reshape(inserted_batch_size,33,window_height,1,3)
train_output = np.random.randint(5, size = (1,total_frames,5))
middle = int(math.ceil(total_frames/2))
train_output = train_output[:,middle:middle+1,:].reshape((inserted_batch_size,1,5))
#print train_output.shape
#print len(train_input_list)
#print train_input_list[0].shape
yield (train_input_list, train_output)
print "hallo"
def test_generator():
while True:
# input = random.choice(test_files)
# h5f = h5py.File(input_test_data+'/'+input, 'r')
# test_input = h5f['test_input'][:]
# test_output = h5f['test_output'][:]
# h5f.close()
test_input = np.random.randint(100,size=((inserted_batch_size,splits*total_frames_with_deltas,window_height,3)))
test_input = test_input.reshape((inserted_batch_size,splits*total_frames_with_deltas,window_height,3))
test_input_list = np.split(test_input,splits*total_frames_with_deltas,axis=1)
#test_input_list = np.split(test_input,45,axis=3)
for i in range(len(test_input_list)):
test_input_list[i] = test_input_list[i].reshape(inserted_batch_size,window_height,3)
#for i in range(len(test_input_list)):
# test_input_list[i] = test_input_list[i].reshape(inserted_batch_size,33,window_height,1,3)
test_output = np.random.randint(5, size = (1,total_frames,5))
middle = int(math.ceil(total_frames/2))
test_output = test_output[:,middle:middle+1,:].reshape((inserted_batch_size,1,5))
yield (test_input_list, test_output)
print "hallo"
def fws():
#print "Inside"
# Params:
# batch , lr, decay , momentum, epochs
#
#Input shape: (batch_size,40,45,3)
#output shape: (1,15,50)
# number of unit in conv_feature_map = splitd
next(train_generator())
model_output = []
list_of_input = [Input(shape=(8,3)) for i in range(splits*total_frames_with_deltas)]
output = []
#Conv
skip = total_frames_with_deltas
for steps in range(total_frames_with_deltas):
conv = Conv1D(filters = 100, kernel_size = 8)
column = 0
for _ in range(splits):
#print "column " + str(column) + "steps: " + str(steps)
output.append(conv(list_of_input[(column*skip)+steps]))
column = column + 1
#print len(output)
#print splits*total_frames_with_deltas
conv = []
for section in range(splits):
column = 0
skip = splits
temp = []
for _ in range(total_frames_with_deltas):
temp.append(output[((column*skip)+section)])
column = column + 1
conv.append(Add()(temp))
#print len(conv)
output_conc = Concatenate()(conv)
#print output_conc.get_shape
output_conv = Reshape((splits, -1))(output_conc)
#print output_conv.get_shape
#Pool
pooled = MaxPooling1D(pool_size = 6, strides = 2)(output_conv)
reshape = Reshape((1,-1))(pooled)
#Fc
dense1 = Dense(units = 1024, activation = 'relu', name = "dense_1")(reshape)
#dense2 = Dense(units = 1024, activation = 'relu', name = "dense_2")(dense1)
dense3 = Dense(units = 1024, activation = 'relu', name = "dense_3")(dense1)
final = Dense(units = 5, activation = 'relu', name = "final")(dense3)
model = Model(inputs = list_of_input , outputs = final)
sgd = SGD(lr=0.1, decay=1e-1, momentum=0.9, nesterov=True)
model.compile(loss="categorical_crossentropy", optimizer=sgd , metrics = ['accuracy'])
print "compiled"
model_yaml = model.to_yaml()
with open("model.yaml", "w") as yaml_file:
yaml_file.write(model_yaml)
print "Model saved!"
log= CSVLogger('/home/carl/kaldi-trunk/dnn/experimental/yesno_cnn_50_training_total_frames_'+str(total_frames)+"_dim_"+str(dim)+"_window_height_"+str(window_height)+".csv")
filepath='yesno_cnn_50_training_total_frames_'+str(total_frames)+"_dim_"+str(dim)+"_window_height_"+str(window_height)+"weights-improvement-{epoch:02d}-{val_acc:.2f}.hdf5"
checkpoint = ModelCheckpoint(filepath, monitor='val_acc', verbose=1, save_weights_only=True, mode='max')
print "log"
#plot_model(model, to_file='model.png')
print "Fit"
hist_current = model.fit_generator(train_generator(),
steps_per_epoch=444,#len(train_files),
epochs = 10000,
verbose = 1,
validation_data = test_generator(),
validation_steps=44,#len(test_files),
pickle_safe = True,
workers = 4,
callbacks = [log,checkpoint])
fws()
Execute the script by: python name_of_script.py yens 50 40 8 1
which give me a full traceback:
full traceback
Error:
carl#ca-ThinkPad-T420s:~/Dropbox$ python mini.py yesno 50 40 8 1
Using TensorFlow backend.
Couldn't import dot_parser, loading of dot files will not be possible.
hallo
hallo
hallo
compiled
Model saved!
log
Fit
/usr/local/lib/python2.7/dist-packages/keras/backend/tensorflow_backend.py:2252: UserWarning: Expected no kwargs, you passed 1
kwargs passed to function are ignored with Tensorflow backend
warnings.warn('\n'.join(msg))
Epoch 1/10000
2017-05-26 13:01:45.851125: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.1 instructions, but these are available on your machine and could speed up CPU computations.
2017-05-26 13:01:45.851345: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use SSE4.2 instructions, but these are available on your machine and could speed up CPU computations.
2017-05-26 13:01:45.851392: W tensorflow/core/platform/cpu_feature_guard.cc:45] The TensorFlow library wasn't compiled to use AVX instructions, but these are available on your machine and could speed up CPU computations.
443/444 [============================>.] - ETA: 4s - loss: 100.1266 - acc: 0.3138Epoch 00000: saving model to yesno_cnn_50_training_total_frames_50_dim_40_window_height_8weights-improvement-00-0.48.hdf5
Traceback (most recent call last):
File "mini.py", line 205, in <module>
File "mini.py", line 203, in fws
File "/usr/local/lib/python2.7/dist-packages/keras/legacy/interfaces.py", line 88, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/keras/engine/training.py", line 1933, in fit_generator
callbacks.on_epoch_end(epoch, epoch_logs)
File "/usr/local/lib/python2.7/dist-packages/keras/callbacks.py", line 77, in on_epoch_end
callback.on_epoch_end(epoch, logs)
File "/usr/local/lib/python2.7/dist-packages/keras/callbacks.py", line 411, in on_epoch_end
self.model.save_weights(filepath, overwrite=True)
File "/usr/local/lib/python2.7/dist-packages/keras/engine/topology.py", line 2503, in save_weights
save_weights_to_hdf5_group(f, self.layers)
File "/usr/local/lib/python2.7/dist-packages/keras/engine/topology.py", line 2746, in save_weights_to_hdf5_group
f.attrs['layer_names'] = [layer.name.encode('utf8') for layer in layers]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2684)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2642)
File "/usr/local/lib/python2.7/dist-packages/h5py/_hl/attrs.py", line 93, in __setitem__
self.create(name, data=value, dtype=base.guess_dtype(value))
File "/usr/local/lib/python2.7/dist-packages/h5py/_hl/attrs.py", line 183, in create
attr = h5a.create(self._id, self._e(tempname), htype, space)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2684)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/tmp/pip-4rPeHA-build/h5py/_objects.c:2642)
File "h5py/h5a.pyx", line 47, in h5py.h5a.create (/tmp/pip-4rPeHA-build/h5py/h5a.c:1904)
RuntimeError: Unable to create attribute (Object header message is too large)

If you look at the amount of data Keras is trying to save under layer_names attribute (inside the output HDF5 file being create), you will find that it takes more than 64kB.
np.asarray([layer.name.encode('utf8') for layer in model.layers]).nbytes
>> 77100
I quote from https://support.hdfgroup.org/HDF5/faq/limits.html:
Is there an object header limit and how does that affect HDF5 ?
There is a limit (in HDF5-1.8) of the object header, which is 64 KB.
The datatype for a dataset is stored in the object header, so there is
therefore a limit on the size of the datatype that you can have. (See
HDFFV-1089)
The code above was (almost entirely) copied from the traceback:
File "/usr/local/lib/python2.7/dist-packages/keras/engine/topology.py", line 2746, in save_weights_to_hdf5_group
f.attrs['layer_names'] = [layer.name.encode('utf8') for layer in layers]
I am using numpy asarray method to get the figure fast but h5py gets similar figure (I guess), see https://github.com/h5py/h5py/blob/master/h5py/_hl/attrs.py#L102 if you want to find exact figure.
Anyway, either you will need to implement your own methods for saving/loading of the weights (or use existing workarounds), or you need to give a really short name to ALL the layers inside your model :), something like this:
list_of_input = [Input(shape=(8,3), name=('i%x' % i)) for i in range(splits*total_frames_with_deltas)]
conv = Conv1D(filters = 100, kernel_size = 8, name='cv%x' % steps)
conv.append(Add(name='add%x' % section)(temp))
output_conc = Concatenate(name='ct')(conv)
output_conv = Reshape((splits, -1), name='rs1')(output_conc)
pooled = MaxPooling1D(pool_size = 6, strides = 2, name='pl')(output_conv)
reshape = Reshape((1,-1), name='rs2')(pooled)
dense1 = Dense(units = 1024, activation = 'relu', name = "d1")(reshape)
dense2 = Dense(units
= 1024, activation = 'relu', name = "d2")(dense1)
dense3 = Dense(units = 1024, activation = 'relu', name = "d3")(dense1)
final = Dense(units = 5, activation = 'relu', name = "fl")(dense3)
You mustn't forget to name all the layers because the (numpy) string array into which the layer names are converted is using the size of the longest string for each individual string in it when it is saved!
After renaming the layers as proposed above (which takes almost 26kB) the model is saved successfully. Hope this elaborate answer helps someone.
Update: I have just made a PR to Keras which should fix the issue without implementing any custom loading/saving methods, see 7508

A simple solution, albeit possibly not the most elegant, could be to run a while loop with epochs = 1.
Get the weights at the end of every epoch together with the accuracy and the loss
Save the weights to file 1 with model.get_weight
if accuracy is greater than at the previous epoch (i.e. loop), store the weights to a different file (file 2)
Run the loop again loading the weights from file 1
Break the loops setting a manual early stopping so that it breaks if the loss does not improve for a certain number of loops

You can use get_weights() together with numpy.save.
It's not the best solution, because it will save several files, but it actually works.
The problem is that you won't have the "optimizer" saved with the current states. But you can perhaps work around that by using smaller learning rates after loading.
Custom callback using numpy.save:
def myCallback(epoch,logs):
global storedLoss
#do your comparisons here using the "logs" var.
print(logs)
if (logs['loss'] < storedLoss):
storedLoss = logs['loss']
for i in range(len(model.layers)):
WandB = model.layers[i].get_weights()
if len (WandB) > 0: #necessary because some layers have no weights
np.save("W" + "-" + str(i), WandB[0],False)
np.save("B" + "-" + str(i), WandB[1],False)
#remember that get and set weights use a list: [weights,biases]
#it may happen (not sure) that there is no bias, and thus you may have to check it (len(WandB)==1).
The logs var brings a dictionary with named metrics, such as "loss", and "accuracy", if you used it.
You can store the losses within the callback in a global var, and compare if each loss is better or worse than the last.
When fitting, use the lambda callback:
from keras.callbacks import LambdaCallback
model.fit(...,callbacks=[LambdaCallback(on_epoch_end=myCallback)])
In the example above, I used the LambdaCallback, which has more possibilities than just on_epoch_end.
For loading, do a similar loop:
#you have to create the model first and then set the layers
def loadModel(model):
for i in range(len(model.layers)):
WandBForCheck = model.layers[i].get_weights()
if len (WandBForCheck) > 0: #necessary because some layers have no weights
W = np.load(Wfile + str(i))
B = np.load(Bfile + str(i))
model.layers[i].set_weights([W,B])

See follow-up at https://github.com/fchollet/keras/issues/6766 and https://github.com/farizrahman4u/keras-contrib/pull/90.
I saw the YAML and the root cause is probably that you have so many Inputs. A few Inputs with many dimensions is preferred to many Inputs, especially if you can use scanning and batch operations to do everything efficiently.
Now, ignoring that entirely, here is how you can save and load your model if it has too much stuff to save as JSON efficiently:
You can pass save_weights_only=True. That won't save optimizer weights, so isn't a great solution.
Just put together a PR for saving model weights and optimizer weights but not configuration. When you want to load, first instantiate and compile the model as you did when you were going to train it, then use load_all_weights to load the model and optimizer weights into that model. I'll try to merge it soon so you can use it from the master branch.
You could use it something like this:
from keras.callbacks import LambdaCallback
from keras_contrib.utils.save_load_utils import save_all_weights, load_all_weights
# do some stuff to create and compile model
# use `save_all_weights` as a callback to checkpoint your model and optimizer weights
model.fit(..., callbacks=[LambdaCallback(on_epoch_end=lambda epoch, logs: save_all_weights(model, "checkpoint-{:05d}.h5".format(epoch))])
# use `load_all_weights` to load model and optimizer weights into an existing model
# if not compiled (no `model.optimizer`), this will just load model weights
load_all_weights(model, 'checkpoint-1337.h5')
So I don't endorse the model, but if you want to get it to save and load anyways this should probably work for you.
As a side note, if you want to save weights in a different format, something like this would work.
pickle.dump([K.get_value(w) for w in model.weights], open( "save.p", "wb" ) )
Cheers

Your model architecture must be too large to be saved.
USE get_weights AND set_weights TO SAVE AND LOAD MODEL, RESPECTIVELY.
Do not use callback model checkpoint. just once the training ends, save its weights with pickle.
Have a look at this link: Unable to save DataFrame to HDF5 ("object header message is too large")