Error while running linkage function

5 次查看（过去 30 天）
Arnab Roy
Arnab Roy 2017-9-26
回答： Yussif M. Awelisah 2019-4-22
I want to create dendrogram from a large distance matrix (2583x2583). So, I'm using linkage function to create a tree of hierarchical clusters. My distance matrix is not symmetric. So, I'll be doing this with lower and upper diagonal. Since I already have the distance matrix in a square form, I needed to get it in the 'pdist' output format. For that, I used 'squareform' function. Following is the code I am using.
load correl; %A correlation coefficient matrix
correlDist = 1 - correl;
lhd = tril(correlDist,-1) + (tril(correlDist,-1))'; %get lower half-diagonal
%Get the distance matrix in the pdist output format
lhdPdist = squareform(lhd);
lZ = linkage(lhdPdist,'average');
I am getting the following error:
------------------------------------------------------------------------
Access violation detected at Tue Sep 26 16:41:49 2017
------------------------------------------------------------------------
Configuration:
Crash Decoding : Disabled
Default Encoding : windows-1252
Graphics card 1 : Intel Corporation ( 0x8086 ) Intel(R) HD Graphics Version
0.0.0.0
MATLAB Architecture: win64
MATLAB Root : C:\Program Files\MATLAB\R2014b
MATLAB Version : 8.4.0.150421 (R2014b)
Operating System : Microsoft Windows 7 Professional
Processor ID : x86 Family 6 Model 58 Stepping 9, GenuineIntel
Software OpenGL : 1
Virtual Machine : Java 1.7.0_11-b21 with Oracle Corporation Java HotSpot(TM)
64-Bit Server VM mixed mode
Window System : Version 6.1 (Build 7601: Service Pack 1)
Fault Count: 1
Abnormal termination:
Access violation
Register State (from fault):
RAX = 000000000032e229 RBX = 0000000023cf0060
RCX = 000000000032e446 RDX = 0000000000000222
RSP = 0000000004025040 RBP = 0000000000000227
RSI = 00000000000009c6 RDI = 000000000032d501
R8 = 0000000025659a18 R9 = 0000000000000052
R10 = 0000000000000a16 R11 = 00000000000009c5
R12 = 000000000000012e R13 = 0000000000000002
R14 = 0000000000000130 R15 = 000000000000004f
RIP = 000000000ed93c7a EFL = 00010213
CS = 0033 FS = 0053 GS = 002b
Stack Trace (from fault):
[ 0] 0x000000000ed93c7a C:\Program
Files\MATLAB\R2014b\toolbox\stats\stats\private\linkagemex.mexw64+00015482
[ 1] 0x000000000ed9a4c8 C:\Program
Files\MATLAB\R2014b\toolbox\stats\stats\private\linkagemex.mexw64+00042184
[ 2] 0x000000000eda0baf C:\Program
Files\MATLAB\R2014b\toolbox\stats\stats\private\linkagemex.mexw64+00068527
mexFunction+00000143
[ 3] 0x00000000fc5f3701 C:\Program
Files\MATLAB\R2014b\bin\win64\libmex.dll+00079617 mexRunMexFile+00000129
[ 4] 0x00000000fc5f2762 C:\Program
Files\MATLAB\R2014b\bin\win64\libmex.dll+00075618 inSwapMexfileReader+00000690
[ 5] 0x00000000fc5f2248 C:\Program
Files\MATLAB\R2014b\bin\win64\libmex.dll+00074312 mexUnlock+00006008
[ 6] 0x00000000052605e3 C:\Program
Files\MATLAB\R2014b\bin\win64\m_dispatcher.dll+00067043
Mfh_file::dispatch_fh+00000659
[ 7] 0x0000000005260aee C:\Program
Files\MATLAB\R2014b\bin\win64\m_dispatcher.dll+00068334
Mfunction_handle::dispatch+00000766
[ 8] 0x000000000534b606 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00112134
MathWorks::MException::IMExceptionData::IMExceptionData+00037094
[ 9] 0x000000000534aa20 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00109088
MathWorks::MException::IMExceptionData::IMExceptionData+00034048
[ 10] 0x0000000005349219 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00102937
MathWorks::MException::IMExceptionData::IMExceptionData+00027897
[ 11] 0x0000000005348de5 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00101861
MathWorks::MException::IMExceptionData::IMExceptionData+00026821
[ 12] 0x000000000539b708 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00440072
inPathNotification::function_delete_notification+00128952
[ 13] 0x0000000005373ea5 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00278181
inGetNameInSymbolTable+00022053
[ 14] 0x0000000005371b4f C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00269135
inGetNameInSymbolTable+00013007
[ 15] 0x0000000005371ab1 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00268977
inGetNameInSymbolTable+00012849
[ 16] 0x000000000539406f C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00409711
inPathNotification::function_delete_notification+00098591
[ 17] 0x00000000053927af C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00403375
inPathNotification::function_delete_notification+00092255
[ 18] 0x0000000005391359 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00398169
inPathNotification::function_delete_notification+00087049
[ 19] 0x00000000052605e3 C:\Program
Files\MATLAB\R2014b\bin\win64\m_dispatcher.dll+00067043
Mfh_file::dispatch_fh+00000659
[ 20] 0x0000000005260aee C:\Program
Files\MATLAB\R2014b\bin\win64\m_dispatcher.dll+00068334
Mfunction_handle::dispatch+00000766
[ 21] 0x000000000534b606 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00112134
MathWorks::MException::IMExceptionData::IMExceptionData+00037094
[ 22] 0x000000000534aa20 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00109088
MathWorks::MException::IMExceptionData::IMExceptionData+00034048
[ 23] 0x0000000005349219 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00102937
MathWorks::MException::IMExceptionData::IMExceptionData+00027897
[ 24] 0x0000000005348de5 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00101861
MathWorks::MException::IMExceptionData::IMExceptionData+00026821
[ 25] 0x000000000539b708 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00440072
inPathNotification::function_delete_notification+00128952
[ 26] 0x0000000005393fa8 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00409512
inPathNotification::function_delete_notification+00098392
[ 27] 0x00000000053927af C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00403375
inPathNotification::function_delete_notification+00092255
[ 28] 0x0000000005391359 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00398169
inPathNotification::function_delete_notification+00087049
[ 29] 0x00000000052607a4 C:\Program
Files\MATLAB\R2014b\bin\win64\m_dispatcher.dll+00067492
Mfh_file::dispatch_fh+00001108
[ 30] 0x0000000005260aee C:\Program
Files\MATLAB\R2014b\bin\win64\m_dispatcher.dll+00068334
Mfunction_handle::dispatch+00000766
[ 31] 0x00000000053c4a88 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00608904
inPathNotification::function_delete_notification+00297784
[ 32] 0x00000000053c4a04 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00608772
inPathNotification::function_delete_notification+00297652
[ 33] 0x00000000053c49c5 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00608709
inPathNotification::function_delete_notification+00297589
[ 34] 0x00000000053c4992 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00608658
inPathNotification::function_delete_notification+00297538
[ 35] 0x00000000053c4947 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00608583
inPathNotification::function_delete_notification+00297463
[ 36] 0x000000000533d69d C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+00054941 inEvalExp+00001309
[ 37] 0x000000000546525d C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+01266269
inEvalCmdWithLocalReturn+00000285
[ 38] 0x0000000005465181 C:\Program
Files\MATLAB\R2014b\bin\win64\m_interpreter.dll+01266049
inEvalCmdWithLocalReturn+00000065
[ 39] 0x000000000688e31d C:\Program
Files\MATLAB\R2014b\bin\win64\libmwbridge.dll+00058141 mnGetPrompt+00001517
[ 40] 0x000000000688ed09 C:\Program
Files\MATLAB\R2014b\bin\win64\libmwbridge.dll+00060681 mnParser+00000745
[ 41] 0x00000000fd0dd834 C:\Program
Files\MATLAB\R2014b\bin\win64\mcr.dll+00383028
mcrInstance::mnParser_on_interpreter_thread+00000036
[ 42] 0x00000000fd0a68e7 C:\Program
Files\MATLAB\R2014b\bin\win64\mcr.dll+00157927
mcr::runtime::setInterpreterThreadToCurrent+00019751
[ 43] 0x00000000fd0a6923 C:\Program
Files\MATLAB\R2014b\bin\win64\mcr.dll+00157987
mcr::runtime::setInterpreterThreadToCurrent+00019811
[ 44] 0x00000000fd0a7121 C:\Program
Files\MATLAB\R2014b\bin\win64\mcr.dll+00160033
mcr::runtime::setInterpreterThreadToCurrent+00021857
[ 45] 0x00000000fab5d3a6 C:\Program
Files\MATLAB\R2014b\bin\win64\uiw.dll+00512934 UIW_AttachThreadInput+00001270
[ 46] 0x00000000fab5cc35 C:\Program
Files\MATLAB\R2014b\bin\win64\uiw.dll+00511029 wsd_to_MSW+00004373
[ 47] 0x00000000fab5ccb9 C:\Program
Files\MATLAB\R2014b\bin\win64\uiw.dll+00511161 wsd_to_MSW+00004505
[ 48] 0x00000000773887b2
C:\Windows\system32\USER32.dll+00165810 GetMenuBarInfo+00000626
[ 49] 0x000000007736f587
C:\Windows\system32\USER32.dll+00062855 SystemParametersInfoW+00000247
[ 50] 0x0000000077374815
C:\Windows\system32\USER32.dll+00083989 IsProcessDPIAware+00000453
[ 51] 0x00000000775cbc65
C:\Windows\SYSTEM32\ntdll.dll+00310373 KiUserCallbackDispatcher+00000031
[ 52] 0x000000007737908a
C:\Windows\system32\USER32.dll+00102538 PeekMessageW+00000182
[ 53] 0x000000007737506e
C:\Windows\system32\USER32.dll+00086126 GetKeyState+00000238
[ 54] 0x0000000077373a07
C:\Windows\system32\USER32.dll+00080391 PeekMessageA+00000087
[ 55] 0x000007fef1750a83 C:\Program Files\Bitdefender Antivirus
Free\atcuf\262824135760000000\atcuf64.dll+00133763
[ 56] 0x000007fef173479a C:\Program Files\Bitdefender Antivirus
Free\atcuf\262824135760000000\atcuf64.dll+00018330
[ 57] 0x00000000000200c6 <unknown-
module>+00000000
[ 58] 0x0000000000000001 <unknown-
module>+00000000
[ 59] 0x000036556a35ef26 <unknown-
module>+00000000
[ 60] 0x000000000402f430 <unknown-
module>+00000000
[ 61] 0x00000000ffffffff C:\Program
Files\MATLAB\R2014b\bin\win64\libmwservices.dll+00065535
svSetDisplayQueryFunctions+00018159
[ 62] 0x000000000402f4a9 <unknown-
module>+00000000
[ 63] 0x00000000ffffffff C:\Program
Files\MATLAB\R2014b\bin\win64\libmwservices.dll+00065535
svSetDisplayQueryFunctions+00018159
[ 64] 0x00000000ffffffff C:\Program
Files\MATLAB\R2014b\bin\win64\libmwservices.dll+00065535
svSetDisplayQueryFunctions+00018159
[ 65] 0x000000000e03fbc0 <unknown-
module>+00000000
This error was detected while a MEX-file was running. If the MEX-file
is not an official MathWorks function, please examine its source code
for errors. Please consult the External Interfaces Guide for information
on debugging MEX-files.
If this problem is reproducible, please submit a Service Request via:
http://www.mathworks.com/support/contact_us/
A technical support engineer might contact you with further information.
Thank you for your help.** This crash report has been saved to disk as
C:\Users\DEEPA\AppData\Local\Temp\matlab_crash_dump.2328-1 **
Caught MathWorks::System::FatalException
[Please exit and restart MATLAB]>>
When I run lZ = linkage(lhdPdist); then no errors are given. Only when I give 'average' option as method I get the above erro. I went through some posts here. It seems like MATLAB is expecting another input. But while I am using distance matrix, I don't think I need any other option. Please suggest.

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回答（2 个）

Vladimir Calderón
Vladimir Calderón 2019-1-30
I tried making a copy custom of linkage script to ignore using the linkagemex, which is where the bug is, and use the linkageold function within linkage.m script, i,e commenting th if sentence and always use the else sentence of these lines:
if exist('linkagemex','file')==3
% call mex file
if passX
if (memEff)
%call the memory efficient algorithm
Z = linkagemex(Y',method,{'euc'},memEff); %note that Y is transposed here
else
Z = linkagemex(Y,method,pdistArg, memEff);
end
else
Z = linkagemex(Y,method);
end
if any(strcmp(method,{'av' 'wa' 'co' 'we'}))
% if 'ave','ward', 'com' or 'weighted average' is used, we need to
% re-arrange the rows in Z matrix by sorting the third rows of Z matrix.
Z = rearrange(Z);
end
else
warning(message('stats:linkage:NoMexFilePresent'));
if passX
Y = pdist(Y,pdistArg{:});
end
% optional old linkage function (use if mex file is not present)
Z = linkageold(Y,method);
end
However it became horribly slow, so I'm just ignoring some kinds of linkage.
The best solution would be debugging linkagemex.
Yussif M. Awelisah
Yussif M. Awelisah 2019-4-22
Please Prof. Arnab Roy, I have tried using the Windowed raise cosine empirical mode decomposition but i hvave been struggling a bit with matab code for the algorithm.
Please I will be grateful if you can help me with the matlab code.
Email: ymawelisah@gmail.com

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