I have used the vlfeat toolbox and the vl_sift, lot of times with no problem. I decided to use it in Matlab R2009a, with ubuntu 14.04. This is the error I get while running vl_setup()
??? XML-file failed validation against schema located in:
/home/tonystark/Matlab_prg/sys/namespace/info/v1/info.xsd
XML-file name:
/home/tonystark/freelancing/Content_based_image_retrieval/code/new_code/vlfeat-0.9.18/toolbox/info.xml
To retest the XML-file against the schema, call the following java method:
com.mathworks.xml.XMLValidator.validate(...
'/home/tonystark/freelancing/Content_based_image_retrieval/code/new_code/vlfeat-0.9.18/toolbox/info.xml',...
'/home/tonystark/Matlab_prg/sys/namespace/info/v1/info.xsd', true)
Errors:
org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found
starting with element 'help_contents_icon'. One of '{product_name_ends_with_type,
help_addon, preference_panel, dialogpref_registrar, project_plugin, state_item, list}'
is expected.
But when I run the same code again, the error doesn't come and the code vl_setup compiles, but no output displayed
And when I run this sample code
clc;
close all;
clear all;
I1 = imread('/home/tonystark/freelancing/Content_based_image_retrieval/Dataset/all_souls_000140.jpg');
I2 = imread('/home/tonystark/freelancing/Content_based_image_retrieval/Dataset/all_souls_000146.jpg');
[f1 d1] = vl_sift(single(rgb2gray(I1)));
[f2 d2] = vl_sift(single(rgb2gray(I2)));
matlab crashes with the following error on the terminal
*** invalid %N$ use detected ***
Aborted (core dumped)
I am stuck here for quite some time without any specific direction. If somebody can point me in the right direction or solve this, it would be of great help! Your help is much appreciated.
UPDATE 1
The readme file of vlfeat says it requires matlab 2009b min, for the toolbox to work. could that be a reason?
Related
this is my first topic if anything wrong please advise me.
I am not a great matlab user but I need to use matlab with sensoray 826 to capture the data.
However, once I install the driver and try to run 826 Matlab demo I got the error code below.
Warning: Warnings messages were produced while parsing. Check the functions you intend to use for correctness. Warning text can be viewed using:
[notfound,warnings]=loadlibrary(...)
I try to find the root cause of this problem and get new error.
[notfound, warnings] = loadlibrary('C:\Program Files (x86)\Sensoray\826\API\x64\s826.dll')
Error using loadlibrary
There was an error loading the library "C:\Program Files (x86)\Sensoray\826\API\x64\s826.dll"
Unrecognized function or variable 's826_proto'.
Caused by:
Error using feval
Unrecognized function or variable 's826_proto'.
At this point I believe that the error is cause from incorrect DLL file from the sensoray.
I try to contact the Sensoray but they rarely answer back to me.
If anyone know how to solve this issue please kindly reply back to me.
The code I use to run in Matlab:
% Load the 826 API and open a connection to the 826 board
dllPath = 'C:\Program Files (x86)\Sensoray\826\API\x64\s826.dll'; % Replace with the correct path to the DLL file
hdrPath = 'C:\Program Files (x86)\Sensoray\826\API\826api.h'; % Replace with the correct path to the header file
[errcode, boardflags] = s826.SystemOpen(dllPath, hdrPath);
if errcode ~= 0
error('Error opening connection to 826 board: %d', errcode);
end
% Configure the rotary sensor
counter = 0; % Choose the counter that the rotary sensor is connected to (0-3)
s826.CounterModeWrite(counter, s826.CNTR_QUADX4); % Configure the counter for quadrature input
s826.CounterPreloadWrite(counter, 0, 0); % Reset the counter
% Read the counter value
count = s826.CounterRead(counter);
% Close the connection to the 826 board
s826.SystemClose();
I would like to go step by step since I never use this 826 cards before.
So first just correctly call the DLL and H file is enough for me.
I am running the following MATLAB code on a system with one GTX 1080 and a K80 (with 2 GPUs)
delete(gcp('nocreate'));
parpool('local',2);
spmd
gpuDevice(labindex+1)
end
reset(gpuDevice(2))
reset(gpuDevice(3))
parfor i=1:100
SingleGPUMatlabCode(i);
end
The code runs for around a second. When I rerun the code after few seconds. I get the message:
Error using parallel.gpu.CUDADevice/reset
An unexpected error occurred during CUDA execution. The
CUDA error was:
unknown error
Error in CreateDictionary
reset(gpuDevice(2))
I tried increasing TdrDelay, but it did not help.
Something in your GPU code is causing an error on the device. Because the code is running asynchronously, this error is not picked up until the next synchronisation point, which is when you run the code again. I would need to see the contents of SingleGPUMatlabCode to know what that error might be. Perhaps there's an allocation failure or an out of bounds access. Errors that aren't correctly handled will get converted to 'unknown error' at the next CUDA operation.
Try adding wait(gpuDevice) inside the loop to identify when the error is occurring.
If either device 2 or 3 are the GTX1080, you may have discovered an issue with MATLAB's restricted support for the Pascal architecture. See https://www.mathworks.com/matlabcentral/answers/309235-can-i-use-my-nvidia-pascal-architecture-gpu-with-matlab-for-gpu-computing
If this is caused by the Windows timeout, you would see a several second screen blackout.
I asked today a question about Parallel Computing with Matlab-Simulink. Since my earlier question is a bit messy and there are a lot of things in the code which doesnt really belong to the problem.
My problem is
I want to simulate something in a parfor-Loop, while my Simulink-Simulation uses the "From Workspace" block to integrate the needed Data from the workspace into the simulation. For some reason it doesnt work.
My code looks as follows:
load DemoData
path = pwd;
apool = gcp('nocreate');
if isempty(apool)
apool = parpool('local');
end
parfor k = 1 : 2
load_system(strcat(path,'\DemoMDL'))
set_param('DemoMDL/Mask', 'DataInput', 'DemoData')
SimOut(k) = sim('DemoMDL')
end
delete(apool);
My simulation looks as follows
The DemoData-File is just a zeros(100,20)-Matrix. It's an example for Data.
Now if I simulate the Script following error message occures:
Errors
Error using DemoScript (line 9)
Error evaluating parameter 'DataInput' in 'DemoMDL/Mask'
Caused by:
Error using parallel_function>make_general_channel/channel_general (line 907)
Error evaluating parameter 'DataInput' in 'DemoMDL/Mask'
Error using parallel_function>make_general_channel/channel_general (line 907)
Undefined function or variable 'DemoData'.
Now do you have an idea why this happens??
The strange thing is, that if I try to acces the 'DemoData' inside the parfor-Loop it works. For excample with that code:
load DemoData
path = pwd;
apool = gcp('nocreate');
if isempty(apool)
apool = parpool('local');
end
parfor k = 1 : 2
load_system(strcat(path,'\DemoMDL'))
set_param('DemoMDL/Mask', 'DataInput', 'DemoData')
fprintf(num2str(DemoData))
end
delete(apool);
Thats my output without simulating and displaying the Data
'>>'DemoScript
00000000000000000 .....
Thanks a lot. That's the original question with a lot more (unnecessary) details:
EarlierQuestion
I suspect the issue is that when MATLAB is pre-processing the parfor loop to determine what variables need to be passed to the workers it does not know what DemoData is. In your first example it's just a string, so no data gets sent over. In your second example it explicitly knows about the variable and hence does pass it over.
You could try either using the Model Workspace, or perhaps just inserting the line
DemoData = DemoData;
in the parfor loop code.
Your error is because workers did not have access to DemoData in the client workspace.
When running parallel simulations with Simulink it would be easier to manage data from workspace if you move them to model workspace. Then each worker can access this data from its model workspace. You can load a MAT file or write MATLAB code to initialize data in model workspace. You can access model workspace using the Simulink model menu View->Model Explorer->Model Workspace.
Also see documentation at http://www.mathworks.com/help/simulink/ug/running-parallel-simulations.html that talks about "Resolving workspace access issues".
You can also move the line
load DemoData
to within the parfor loop. Doing this, you assure that the data will be available in each worker base workspace, wich is accessible to the model, instead of the client workspace.
I am running Matlab from a Fortran function and am having a persistent problem that I am getting the error
*** glibc detected *** /matlab/8.5/bin/glnxa64/MATLAB: double free or corruption (out): 0x00002b11a9a86f20 ***
I am not sure which line the error is occuring on but I have quite a few that follow this pattern
MLVar = engGetVariable(ep, 'un')
call mxCopyPtrToReal8(mxGetPr(MLVar), SurfaceField, BoundaryCells)
call mxDestroyArray(MLVar)
and I go through this function between 1 and 100s of times before this error occurs.
It looks like here they said to use mxDestroyArray which I'm already using.
Any advise?
The problem ended up being completely unrelated. I am submitting this to a remote cluster using a submission script, and I used a "V" option and then when I closed my terminal connection with Matlab forced close.
I'm trying to parallelize my code, and I finally got the parfor loops set up such that Matlab doesn't crash every time. However, I've now got an error that I can't seem to figure out.
I have a driver script (Driver12.m) that calls the script that I'm trying to parallelize (Worker12.m). If I run Worker12.m directly, it usually finishes with no problem. However, every time I try to run it from Driver12.m, it either 1) causes Matlab to crash, or 2) throws a strange error at me. Here's some of my code:
%Driver script
run('(path name)/Worker12.m');
%Relevant worker script snippet
parfor q=1:number_of_ranges
timenumber = squeeze(new_TS(q,:,:));
timenumber_shift = circshift(timenumber, [0 1]);
for m = 1:total_working_channels
timenumberm = timenumber(m,:);
for n = 1:total_working_channels
R_P(m,n,q) = mean(timenumberm.*conj(timenumber(n,:)),2);
R_V(m,n,q) = mean(timenumberm.*conj(timenumber_shift(n,:)),2);
end
end
end
Outcome #1: "Matlab has encountered an unexpected error and needs to close."
Outcome #2: "An UndefinedFunction error was thrown on the workers for ''. This might be because the file containing '' is not accessible on the workers. Use addAttachedFiles(pool, files) to specify the required files to be attached. See the documentation for 'parallel.Pool/addAttachedFiles' for more details. Caused by: Undefined function or variable ""."
However, if I run Worker12.m directly, it works fine. It's only when I run it from the driver script that I get issues. Obviously, this error message from Outcome #2 isn't all that useful. Any suggestions?
Edit: So I created a toy example that reproduces an error, but now both my toy example and the original code are giving me a new, 3rd error. Here's the toy example:
%Driver script
run('parpoolexample.m')
%parpoolexample.m
clear all
new_TS = rand([1000,32,400]);
[number_of_ranges,total_working_channels,~] = size(new_TS);
R_P = zeros(total_working_channels,total_working_channels,number_of_ranges);
R_V = zeros(total_working_channels,total_working_channels,number_of_ranges);
parfor q=1:number_of_ranges
timenumber = squeeze(new_TS(q,:,:));
timenumber_shift = circshift(timenumber, [0 1]);
for m = 1:total_working_channels
timenumberm = timenumber(m,:);
for n = 1:total_working_channels
R_P(m,n,q) = mean(timenumberm.*conj(timenumber(n,:)),2);
R_V(m,n,q) = mean(timenumberm.*conj(timenumber_shift(n,:)),2);
end
end
end
Outcome #3: "Index exceeds matrix dimensions (line 7)."
So, at the 'parfor' line, it's saying that I'm exceeding the matrix dimensions, even though I believe that should not be the case. Now I can't even get my original script to recreate Outcomes #1 or #2.
Don't use run with parallel language constructs like parfor and spmd. Unfortunately it doesn't work very well. Instead, use cd or addpath to let MATLAB see your script.