Comments (5)
Note that the master branch is updated now. The server should not have the issues as described above anymore.
from prosit.
@gessulat thank you,
the new version works great, no hiccups!
from prosit.
Try this branch:
https://github.com/kusterlab/prosit/tree/fix/server_issue
I don't quite understand why this happens for some environments and not for others.
from prosit.
@gessulat
Tnx
from prosit.
@gessulat
I tried the fixed server branch https://github.com/kusterlab/prosit/tree/fix/server_issue
It runs and gives results, however submitting a second file will break the server.
~/prosit$ curl -F "peptides=@examples/peptidelist.csv" http://127.0.0.1:5000/predict/
Intensities Masses Matches Modified Sequence Charge
1.0;0.41259626;0.73062277;0.30424523;0.11640168;0.093716405;0.08098759;0.1923069;0.08597337;0.15234001;0.08258821;0.012585764;0.034173176;0.013465268;0.0030653037;0.0014310256;0.008246724;0.004191969;0.00061403663;0.0013039891;0.0022206986;0.0005943045 175.118952167;322.15434716699997;435.238411167;548.322475167;619.359589167;690.3967031669999;761.4338171669999;263.088246467;360.141010467;431.178124467;502.21523846699995;573.2523524669999;218.122843817;429.74692881699997;132.047761467;180.574143467;216.092700467;251.61125746699997;207.12471403366666;230.80375203366665;254.48279003366665;229.45032313366664 y1;y2;y3;y4;y5;y6;y7;b2;b3;b4;b5;b6;y3(2+);y8(2+);b2(2+);b3(2+);b4(2+);b5(2+);y5(3+);y6(3+);y7(3+);b7(3+) MMPAAALIM(ox)R 3
0.031838626;0.05340379;0.0008666609;0.16591543;0.6199195;1.0;0.3755796;0.006878452;0.8553704;0.18602312;0.009526462;0.1253908;0.6669085;0.056322724;0.00025479423;0.0041989647 147.112804167;294.148199167;407.232263167;504.285027167;601.3377911670001;698.3905551670001;769.4276691670001;882.5117331670001;245.131825467;316.168939467;413.221703467;301.17253381700004;349.69891581700006;385.21747281700004;158.58810796699998;207.114489967 y1;y2;y3;y4;y5;y6;y7;y8;b2;b3;b4;y5(2+);y6(2+);y7(2+);b3(2+);b4(2+) MLAPPPIM(ox)K 2
0.6478142;0.7623719;1.0;0.78580517;0.24467614;0.037683975;0.98502636;0.46840557;0.30539873;0.5721372;0.27308717;0.025923852;0.31577614;0.6946651;0.4260823;0.0029871135;0.016204849;0.0243927;0.0019134118;0.027638009;0.008317641;0.0010335244 175.118952167;419.20711116699994;516.259875167;613.312639167;710.3654031670001;132.047761467;288.148872467;359.185986467;472.27005046700003;585.354114467;698.4381784670001;811.5222424670001;258.633575817;307.159957817;355.68633981700003;180.096631467;236.63866346700001;293.180695467;349.722727467;59.044501700333335;237.45998536700003;44.68743813366666 y1;y3;y4;y5;y6;b1;b2;b3;b4;b5;b6;b7;y4(2+);y5(2+);y6(2+);b3(2+);b4(2+);b5(2+);b6(2+);y1(3+);y6(3+);b1(3+) MRALLLIPPPPM(ox)R 6
The second time to curl the same CSV file will break the server.
* Running on http://0.0.0.0:5000/ (Press CTRL+C to quit)
172.17.0.1 - - [24/Jun/2019 22:59:26] "POST /predict/ HTTP/1.1" 200 -
[2019-06-24 23:03:20,541] ERROR in app: Exception on /predict/ [POST]
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 2311, in wsgi_app
response = self.full_dispatch_request()
File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1834, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1737, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/usr/local/lib/python3.5/dist-packages/flask/_compat.py", line 36, in reraise
raise value
File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1832, in full_dispatch_request
rv = self.dispatch_request()
File "/usr/local/lib/python3.5/dist-packages/flask/app.py", line 1818, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/root/prosit/server.py", line 29, in predict
result = prediction.predict(tensor, model, model_config, graph)
File "/root/prosit/prediction.py", line 17, in predict
x, verbose=verbose, batch_size=constants.PRED_BATCH_SIZE
File "/usr/local/lib/python3.5/dist-packages/keras/engine/training.py", line 1167, in predict
steps=steps)
File "/usr/local/lib/python3.5/dist-packages/keras/engine/training_arrays.py", line 294, in predict_loop
batch_outs = f(ins_batch)
File "/usr/local/lib/python3.5/dist-packages/keras/backend/tensorflow_backend.py", line 2666, in __call__
return self._call(inputs)
File "/usr/local/lib/python3.5/dist-packages/keras/backend/tensorflow_backend.py", line 2636, in _call
fetched = self._callable_fn(*array_vals)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/client/session.py", line 1382, in __call__
run_metadata_ptr)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/framework/errors_impl.py", line 519, in __exit__
c_api.TF_GetCode(self.status.status))
tensorflow.python.framework.errors_impl.FailedPreconditionError: Attempting to use uninitialized value dense_1/kernel
[[Node: dense_1/kernel/read = Identity[T=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:GPU:0"](dense_1/kernel)]]
[[Node: out/Reshape/_23 = _Recv[client_terminated=false, recv_device="/job:localhost/replica:0/task:0/device:CPU:0", send_device="/job:localhost/replica:0/task:0/device:GPU:0", send_device_incarnation=1, tensor_name="edge_606_out/Reshape", tensor_type=DT_FLOAT, _device="/job:localhost/replica:0/task:0/device:CPU:0"]()]]
172.17.0.1 - - [24/Jun/2019 23:03:20] "POST /predict/ HTTP/1.1" 500 -
basically after one process the GPU memory is not freed. nvidia-smi shows
full memory allocation, even when the GPU is not used anymore.
See also keras-team/keras#12625
| 1 GeForce GTX 108... Off | 00000000:03:00.0 Off | N/A |
| 30% 49C P8 17W / 250W | 10787MiB / 11178MiB | 0% Default |
from prosit.
Related Issues (20)
- Prosit prediction is not deterministic on RTX3070 HOT 3
- Error occured. Status code: 2 HOT 6
- An error occurred. Status code 2 HOT 1
- intensities_raw in .hdf5 file is different from msms.txt in .zip file HOT 1
- Expected time for job completion on server, and related feature request HOT 5
- MSP files "Num peaks" always reporting 174 peaks HOT 4
- Missing predictions for some peptides under length 30
- Error code gotten in one of 20 parts HOT 1
- Please make sure that your uploaded "msms.txt" is also named "msms.txt" HOT 8
- How to run prosit locally in high performance computing environment? HOT 1
- Missing config.yml from Prosit-TMT model files HOT 6
- Error log which non-ncbi database
- Percolator subset-max-train Flag
- Error when running TMT models HOT 2
- Unable to download spectral library HOT 1
- Is there a way to run Prosit on Jupyter Notebook (Google Collab)?
- "Can't get the response from the server" HOT 1
- Prosit Download showing server issues HOT 3
- Prosit rescoring on own server HOT 1
- Error with spectral prediction HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from prosit.