How can I inference with multiple input network on TensorRT? - tensorrt

I would like to test GQ-CNN which is network in Dex-Net on tensorRT.
I successfully converted tflite file to uff file but when I tried to inference with that network, there is an error I couldn't figure out.
[TensorRT] ERROR: Parameter check failed at: ../builder/Network.cpp::addLRN::149, condition: lrnWindow & 0x1
python3: uff/orders.cpp:330: void UffParser::addTranspose(ParserLayer&, std::vector<int>): Assertion `outputs.size() == 1' failed.
The error is appeared when building model.
I tried to find clue from google but there are no codes and no references.
There's only different thing compare with example code that works well.
(I wrote captions which codes I added. If I remove that codes and replace model file to single input network, it works well.)
I registered input twice like below code because GQ-CNN has multiple input.
So I guess that registering multiple input using uffparser could be the main reason of that error.
class ModelData(object):
MODEL_FILE = "./gqcnn.uff"
INPUT_NAME_1 = "Placeholder"
INPUT_SHAPE_1 = (1, 32, 32)
INPUT_NAME_2 = "Placeholder_1"
INPUT_SHAPE_2 = (2,)
OUTPUT_NAME = "softmax/Softmax"
def build_engine(model_file):
# For more information on TRT basics, refer to the introductory samples.
with trt.Builder(TRT_LOGGER) as builder, builder.create_network() as network, trt.UffParser() as parser:
builder.max_workspace_size = common.GiB(1)
builder.fp16_mode = True
#builder.int8_mode = True
# Parse the Uff Network
parser.register_input(ModelData.INPUT_NAME_1, ModelData.INPUT_SHAPE_1)
parser.register_input(ModelData.INPUT_NAME_2, ModelData.INPUT_SHAPE_2) # added code
parser.register_output(ModelData.OUTPUT_NAME)
parser.parse(model_file, network)
# Build and return an engine.
return builder.build_cuda_engine(network)
# do inference
with build_engine(ModelData.MODEL_FILE) as engine:
# Build an engine, allocate buffers and create a stream.
# For more information on buffer allocation, refer to the introductory samples.
inputs, outputs, bindings, stream = common.allocate_buffers(engine)
with engine.create_execution_context() as context:
for idx in range(len(val_images)) :
start = time.time()
val_image = val_images[idx]
val_pose = val_poses[idx] # added code
np.copyto(inputs[0].host, val_image)
np.copyto(inputs[1].host, val_pose) # added code
[prediction] = common.do_inference(context, bindings=bindings, inputs=inputs, outputs=outputs, stream=stream)
Is there anyone who succeeded to inference with multiple input model?

Related

BertModel transformers outputs string instead of tensor

I'm following this tutorial that codes a sentiment analysis classifier using BERT with the huggingface library and I'm having a very odd behavior. When trying the BERT model with a sample text I get a string instead of the hidden state. This is the code I'm using:
import transformers
from transformers import BertModel, BertTokenizer
print(transformers.__version__)
PRE_TRAINED_MODEL_NAME = 'bert-base-cased'
PATH_OF_CACHE = "/home/mwon/data-mwon/paperChega/src_classificador/data/hugingface"
tokenizer = BertTokenizer.from_pretrained(PRE_TRAINED_MODEL_NAME,cache_dir = PATH_OF_CACHE)
sample_txt = 'When was I last outside? I am stuck at home for 2 weeks.'
encoding_sample = tokenizer.encode_plus(
sample_txt,
max_length=32,
add_special_tokens=True, # Add '[CLS]' and '[SEP]'
return_token_type_ids=False,
padding=True,
truncation = True,
return_attention_mask=True,
return_tensors='pt', # Return PyTorch tensors
)
bert_model = BertModel.from_pretrained(PRE_TRAINED_MODEL_NAME,cache_dir = PATH_OF_CACHE)
last_hidden_state, pooled_output = bert_model(
encoding_sample['input_ids'],
encoding_sample['attention_mask']
)
print([last_hidden_state,pooled_output])
that outputs:
4.0.0
['last_hidden_state', 'pooler_output']
While the answer from Aakash provides a solution to the problem, it does not explain the issue. Since one of the 3.X releases of the transformers library, the models do not return tuples anymore but specific output objects:
o = bert_model(
encoding_sample['input_ids'],
encoding_sample['attention_mask']
)
print(type(o))
print(o.keys())
Output:
transformers.modeling_outputs.BaseModelOutputWithPoolingAndCrossAttentions
odict_keys(['last_hidden_state', 'pooler_output'])
You can return to the previous behavior by adding return_dict=False to get a tuple:
o = bert_model(
encoding_sample['input_ids'],
encoding_sample['attention_mask'],
return_dict=False
)
print(type(o))
Output:
<class 'tuple'>
I do not recommend that, because it is now unambiguous to select a specific part of the output without turning to the documentation as shown in the example below:
o = bert_model(encoding_sample['input_ids'], encoding_sample['attention_mask'], return_dict=False, output_attentions=True, output_hidden_states=True)
print('I am a tuple with {} elements. You do not know what each element presents without checking the documentation'.format(len(o)))
o = bert_model(encoding_sample['input_ids'], encoding_sample['attention_mask'], output_attentions=True, output_hidden_states=True)
print('I am a cool object and you can acces my elements with o.last_hidden_state, o["last_hidden_state"] or even o[0]. My keys are; {} '.format(o.keys()))
Output:
I am a tuple with 4 elements. You do not know what each element presents without checking the documentation
I am a cool object and you can acces my elements with o.last_hidden_state, o["last_hidden_state"] or even o[0]. My keys are; odict_keys(['last_hidden_state', 'pooler_output', 'hidden_states', 'attentions'])
I faced the same issue while learning how to implement Bert. I noticed that using
last_hidden_state, pooled_output = bert_model(encoding_sample['input_ids'], encoding_sample['attention_mask'])
is the issue. Use:
outputs = bert_model(encoding_sample['input_ids'], encoding_sample['attention_mask'])
and extract the last_hidden state using
output[0]
You can refer to the documentation here which tells you what is returned by the BertModel

Google Earth Engine download problems, is this caused by immutable server side objects?

I have a function that will download an image collection as a TFrecord or a geotiff.
Heres the function -
def download_image_collection_to_drive(collection, aois, bands, limit, export_format):
if collection.size().lt(ee.Number(limit)):
bands = [band for band in bands if band not in ['SCL', 'QA60']]
for aoi in aois:
cluster = aoi.get('cluster').getInfo()
geom = aoi.bounds().getInfo()['geometry']['coordinates']
aoi_collection = collection.filterMetadata('cluster', 'equals', cluster)
for ts in range(1, 11):
print(ts)
ts_collection = aoi_collection.filterMetadata('interval', 'equals', ts)
if ts_collection.size().eq(ee.Number(1)):
image = ts_collection.first()
p_id = image.get("PRODUCT_ID").getInfo()
description = f'{cluster}_{ts}_{p_id}'
task_config = {
'fileFormat': export_format,
'image': image.select(bands),
'region': geom,
'description': description,
'scale': 10,
'folder': 'output'
}
if export_format == 'TFRecord':
task_config['formatOptions'] = {'patchDimensions': [256, 256], 'kernelSize': [3, 3]}
task = ee.batch.Export.image.toDrive(**task_config)
task.start()
else:
logger.warning(f'no image for interval {ts}')
else:
logger.warning(f'collection over {limit} aborting drive download')
It seems whenever it gets to the second aoi it fails, Im confused by this as if ts_collection.size().eq(ee.Number(1)) confirms there is an image there so it should manage to get product id from it.
line 24, in download_image_collection_to_drive
p_id = image.get("PRODUCT_ID").getInfo()
File "/lib/python3.7/site-packages/ee/computedobject.py", line 95, in getInfo
return data.computeValue(self)
File "/lib/python3.7/site-packages/ee/data.py", line 717, in computeValue
prettyPrint=False))['result']
File "/lib/python3.7/site-packages/ee/data.py", line 340, in _execute_cloud_call
raise _translate_cloud_exception(e)
ee.ee_exception.EEException: Element.get: Parameter 'object' is required.
am I falling foul of immutable server side objects somewhere?
This is a server-side value, problem, yes, but immutability doesn't have to do with it — your if statement isn't working as you intend.
ts_collection.size().eq(ee.Number(1)) is a server-side value — you've described a comparison that hasn't happened yet. That means that doing any local operation like a Python if statement cannot take the comparison outcome into account, and will just treat it as a true value.
Using getInfo would be a quick fix:
if ts_collection.size().eq(ee.Number(1)).getInfo():
but it would be more efficient to avoid using getInfo more than needed by fetching the entire collection's info just once, which includes the image info.
...
ts_collection_info = ts_collection.getInfo()
if ts_collection['features']: # Are there any images in the collection?
image = ts_collection.first()
image_info = ts_collection['features'][0] # client-side image info already downloaded
p_id = image_info['properties']['PRODUCT_ID'] # get ID from client-side info
...
This way, you only make two requests per ts: one to check for the match, and one to start the export.
Note that I haven't actually run this Python code, and there might be some small mistakes; if it gives you any trouble, print(ts_collection_info) and examine the structure you actually received to figure out how to interpret it.

How to create many Bokeh figures with multiprocessing?

I would like to speed up figure generation in Bokeh by multiprocessing:
jobs = []
for label in list(peakLabels):
args = {'data': rt_proj_data[label],
'label': label,
'tools': tools,
'colors': itertools.cycle(palette),
'files': files,
'highlight': highlight}
jobs.append(args)
pool = Pool(processes=cpu_count())
m = Manager()
q = m.Queue()
plots = pool.map_async(plot_peaks_parallel, jobs)
pool.close()
pool.join()
def plot_peaks_parallel(args):
data = args['data']
label = args['label']
colors = args['colors']
tools = args['tools']
files = args['files']
highlight = args['highlight']
p = figure(title=f'Peak: {label}',
x_axis_label='Retention Time',
y_axis_label='Intensity',
tools=tools)
...
return p
Though I ran into this error:
MaybeEncodingError: Error sending result: '[Figure(id='1078', ...)]'. Reason: 'PicklingError("Can't pickle at 0x7fc7df0c0ea0>: attribute lookup ColumnDataSource. on bokeh.models.sources failed")'
Can I do something to the object p, so that it becomes pickleable?
Individual Bokeh objects are not serializable in isolation, including with pickle. The smallest meaningful unit of serialization in Bokeh is the Document, which is a specific collection of Bokeh objects guaranteed to be complete with respect to following references. However, I would be surprised if pickle works with Document either (AFAIK you are the first person to ask about it since the project started, it's never been a priority, or even looked into that I know of). Instead, I would suggest if you want to do something like this, to use Bokeh's own JSON serialization functions, such as json_item:
# python code
p_serialized = json.dumps(json_item(p))
This will properly serialize p in the context of the Document it is a part of. Then you can pass this to your page templates to display with the Bokeh JS embed API:
# javascript code
p = JSON.parse(p_serialized);
Bokeh.embed.embed_item(p, "mydiv")

setup bosun snmp scollector to monitor CPU memory keep get error

i am trying to run scollector from bosun.
after I run the scolector, It cannot show me the memory information, but CPU information was right.
this CODE:
Host = "http://localhost:8070"
DisableSelf = true
Freq = 60
Filter = ["snmp-generic", "snmp-ifaces"]
[[SNMP]]
Community = "test"
Host = "name"
MIBs = [ "devicename"]
[Tags]
product = "fw"
[MIBs]
[MIBs.fw]
BaseOid = ".1.3.6.1.4.1.2620"
[[MIBs.fw.Metrics]]
Metric = "os.cpu"
Oid = ".1.6.7.2.4.0"
Unit = "percent"
RateType = "gauge"
[[MIBs.fw.Metrics]]
Metric = "os.mem.used"
Oid = ".1.6.7.4.5.0"
Unit = "bytes"
RateType = "gauge"
THIS IS LOG
**2016/11/07 17:24:42 error: interval.go:64: snmp-generic-name-fw: asn1: structure error: tags don't match (2 vs {class:0 tag:4 length:11 isCompound:false}) {optional:false explicit:false application:false defaultValue:<nil> tag:<nil> stringType:0 timeType:0 set:false omitEmpty:false} #2**
2016/11/07 17:24:43 info: queue.go:90: {"metric":"os.cpu","timestamp":1478539482,"value":2,"tags":{"host":"name","product":"fw"}}
It looks to me like this is an issue converting data types. The error is from deep in the bowels of the asn1 library we are using but I think it boils down to: cpu is represented as an integer, while memory is a string.
Our snmp collector attempts to parse all values into a big.Int, but apparently the string value is not able to be coerced into that by our asn1 library.
Unfortunately I don't see a good way to make this work, except perhaps look for an oid that returns an integer type. Without knowing what device you are using, that is as good as I can offer I'm afraid.

Sending vector data in the bus

I have a vector data (an array variable for example float32 mydata[5];). for transmitting a single primitve/basic data in a bus its pretty simple.
inside_data=Simulink.BusElement;
inside_data.Name='somename';
inside_data.SampleTime = -1;
inside_data.datatype='single';
this element can be put inside a using
Bus=Simulink.Bus;
Bus.Elements=inside_data;
But this works when the input is a primitive. But what if my data is a vector. like float32 a[5]; then how can i send this data element in a bus.
UPDATE
So I tried to use a constant block named a with datatype single in which the input part i changed it as [1 2 3] which is a vector input.
another element is b with uint8 datatype.
i used the s-function builder just to check the working of this model. i already set everything (bus_mode on , datatype to be bus type etc). in the output part i used something like:
y0[0]=u0->a[0];
y0[1]=u0->a[1];
y0[2]=u0->a[2];
y1[0]=u0->b;
But it throws error as
c:\program files (x86)\matlab_v7111_r10bsp1\extern\include\matrix.h(313) : error C2061: syntax error : identifier 'mxLogical'
c:\program files (x86)\matlab_v7111_r10bsp1\extern\include\matrix.h(313) : error C2059: syntax error : ';'
my final aim is to use it for s_function
so if i declare a variable in s_func as
real32_T *a_output[5]=(real32_T *)ssGetOutputPortRealSignal(S,0);
and then i have a strcuture(because am transmitting data with a bus so the bus header file has this structure) and how do i declare and assign the input to the output.
a_output[0]=my_struct->a_input[0];
a_output[1]=my_struct->a_input[1];
a_output[2]=my_struct->a_input[2];
a_output[3]=my_struct->a_input[3];
a_output[4]=my_struct->a_input[4];
but the problem is with the declaration. it gives me error cannot convert from real32_T to real32_T * .
The main idea is to create Bus of type you need.
I did it this way:
num = zeros(15,15,15);
move = zeros(15,15,15);
a = struct('number',num,'movement', move);
busInfo = Simulink.Bus.createObject(a);
You can see it's possible to create any data structure, array, vector anything you want and then create Bus Signal of the same type.
I use this in callbacks/preLoadFcn (Model Explorer) to define this type in workspace, it creates slBus1 variable (its Bus Signal of my type), so I need to define output (or input if necessary) of any block like slBus1 only. And then use Bus Selector to work array data.
Can it helps to you?
ADD NEW INFORMATION
It depends of what you want.
For example: I create s-function for feedback system. It use my structure like this:
function a = fcn(BusSignal)
%#codegen
num = zeros(15,15,15);
move = zeros(15,15,15);
%...some math actions with num and move...
a = struct('number',num,'movement', move);
%...and some action with a structure... for example:
if (c>b)
a.number(1,2,3) = 15;
a.movement(1,2,3) = 42;
else
a = BusSignal;
end
Look at this - I use Bus signal at entrance and at exit and use Bus Selector to work it's data with.
REMEMBER to define input and output data as Bus Signals!

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