I am trying to load a 3rd-party library (.so file) into MATLAB under RHEL.
I am getting an error: undefined:symbol: _intel_fast_memmove.
From Symbol lookup error: _FileName_: undefined symbol: _intel_fast_memmove it seems like I need to add a sub-directory of /opt/intel to my LD_LIBRARY_PATH environment variable, but I don't have an /opt/intel directory.
UPDATE:
MATLAB said that the problem came when trying to load libifcoremt.so.5. I have since installed Intel's Redistributable Libraries and all that did was call Intel's version of libifcoremt.so.5 but still looked for _intel_fast_memmove (but still didn't find it). So now I'm thinking that there must be some other "definitions" file somewhere that I'm missing.
It took me a few days, but I was able to figure out what was going on.
In the end, there were two problems:
I was missing some libraries -- not the ones that I mention in my question, but Intel's Redistributable Libraries.
Even with all of the libraries on my computer, MATLAB was still using an older version of the some of the .os files.
I failed to mention in my question that while the 3rd-party library is fairly recent, I was calling it from MATLAB 2012B because I needed to integrate it with a software package that doesn't work correctly with later MATLAB versions. My apologies for that omission -- it turns out to be a critical piece of the puzzle.
While diagnosing this issue, I learned that MATLAB has it's own copy of the Intel libraries in the <MATLAB>/sys/os/glnxa64 sub-directory and that it creates an internal version of LD_LIBRARY_PATH that points to its internal version before the LD_LIBRARY_PATH that it imports from the Linux OS. Since the version of MATLAB I'm using is 6 years old, so is it's Intel library, which doesn't contain some symbols defined in the new library, such as intel_fast_memmove.
To get the integrated system up and running, I instituted a workaround to rename the sys/os/glnxa64 before calling the 3rd-party library so that MATLAB found the newer Intel library instead of the MATLAB 2012B version. And then named it back when done (without that directory, MATLAB won't start).
Note: I first tried editing the value of LD_LIBRARY_PATH inside MATLAB 2012B to prefer the new Intel library, but found that even though the external variable value changed, loadlibrary still used the original value that placed MATLAB's library first on the path.
Related
My m file was compiled by MATLAB R2008b. When I distributed it to others, their PC seem to lack certain DLL (mclmcrrt79.dll). Thus, I was looking for MCR7.9 but couldn't find any official copy. I did find some on the web: MCR7.9 download but am not sure whether it is safe to be installed. Is it OK to use this copy or is there any official MCR7.9 available?
Since R2012a, the MCR for each version of MATLAB has been available as a download from MathWorks.
Versions of the MCR prior to R2012a are not distributed in the same way by MathWorks, and should be distributed by the developer of the application along with the compiled component directly to end users. If you are the developer, you should distribute it along with the component - specifically, you should send them the MCR installer (you have this - it's in \toolbox\compiler\deploy\<ARCH>, where <ARCH> is your platform).
In fact, in R2012a there was a license-related change: for versions prior to that, you're not actually allowed to make the MCR (or the installer) available as public download (so the people who are making it available at the SourceForge site you link to are, strictly speaking, in breach of the license).
One other confusion may be causing you difficulty: R2008b is MATLAB version 7.7. MATLAB version 7.9 is R2009b. You need to make sure that you use the right version of the MCR for the version of MATLAB you used to compile.
For reference, I solved the problem related to "My Own Exception: Fatal error finding symbol mxCalcSingleSubscript_700 in D:\XYZ\libmx.dll Error:" It was done by sending libmx.dll to the user. The file is stored at \MATLAB\bin\win32\
I want to use the export_fig package for Matlab. At one point this worked, but now it's broken. The error occurs here:
>> system('pdftops -h')
dyld: Library not loaded: /opt/local/lib/libtiff.5.dylib
Referenced from: /opt/local/bin/pdftops
Reason: Incompatible library version: pdftops requires version 8.0.0 or later, but libtiff.5.dylib provides version 6.0.0
pdftops -h: Trace/breakpoint trap
But when I call pdftops from my own bash terminal everything works fine. I suppose it must be because Matlab has some bad library paths or something, but I don't know where to go from here?
Some relevant environmental vars used by matlab:
>> system('env')
SHELL=/bin/bash
OSG_LD_LIBRARY_PATH=/Applications/MATLAB_R2013b.app/sys/openscenegraph/lib/maci64
PATH=/usr/bin:/bin:/usr/sbin:/sbin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/texbin
__CHECKFIX1436934=1
XFILESEARCHPATH=/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/locale/%L/%T/%N%S:
DYLD_FRAMEWORK_PATH=/Applications/MATLAB_R2013b.app/sys/os/maci64:/Applications/MATLAB_R2013b.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2013b.app/bin/maci64:/Applications/MATLAB_R2013b.app/extern/lib/maci64:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./native_threads:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./server:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./lib/jli
SHLVL=1
__KMP_REGISTERED_LIB_33586=0x124404710-cafeb339-libiomp5.dylib
DYLD_LIBRARY_PATH=/Applications/MATLAB_R2013b.app/sys/os/maci64:/Applications/MATLAB_R2013b.app/bin/maci64/../../Contents/MacOS:/Applications/MATLAB_R2013b.app/bin/maci64:/Applications/MATLAB_R2013b.app/extern/lib/maci64:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./native_threads:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./server:/Applications/MATLAB_R2013b.app/sys/java/jre/maci64/jre/lib/./lib/jli
If you take a look at the error message, MATLAB uses libtiff to call pdftops, but only has version 6.0.0. It says it needs version 8.0.0 or later. There has been a case where this happened before here on StackOverflow. Someone was trying to install mexopencv and has encountered the same error that you're talking about: Compiling mexopencv in OS X 10.9 with Xcode 5 and Matlab R2013b
Though this is unrelated to what you're doing, they encountered the libtiff error that you speak of. They provide two solutions how to fix this error:
Go into MATLAB's root directory, then go bin/os directory where os is the directory of the operating system you are using (in my case, it's maci64). To get into the root directory, in the command prompt do this: cd/(matlabroot). Once you're here, locate the libtiff.5.dylib file and rename it to something like libtiff.5.dylib.bak so that the libtiff libraries that are used are the ones that are default to your system rather than what MATLAB is using internally in the program.
Force MATLAB to point to the library that is part of the system rather than using the one built into MATLAB. As such, in MATLAB's command prompt, run this command:
setenv('DYLD_INSERT_LIBRARIES','/opt/local/lib/libtiff.5.dylib');
Once you do this, you may get further errors that are similar but are with other libraries. As such, you need to keep appending these libraries in the second parameter of setenv and colon-delimiting them until you resolve the issues. You need to make sure that you're pointing to the ones on your system rather than the ones installed with MATLAB. In your case, you have to do:
setenv('DYLD_INSERT_LIBRARIES', ...
'/opt/local/lib/libtiff.5.dylib:/opt/local/lib/libcurl.4.dylib');
Glad this helped!
I have compiled Mex file successfully on my laptop. But when I am running it, it says Invalid mex file 'c:\newfolder\filename.mexw32' The specified module could not be found.
System specification:
OS: windows 7
MATLAB 2010a
Microsoft Visual Studio 2008.
The same mex file is compiled and run successfully on my PC under XP SP3.
This MathWorks support link suggests two possible reasons to your problem:
You do not have all of the necessary libraries that the MEX-function is dependent upon.
You are running a MEX-file on a different version of MATLAB than it was compiled on.
Either way, to locate the source of this error it says that you need to list all dependent library files and verify their existence in the system you're trying to run the MEX file on, and also recommends the Dependecy Walker as the tool to to do that.
Do you you the mex file on another system than the one it is created on?
If so, then you need to install the Microsoft Visual C++ Redistributable on that machine.
I had this problem also when upgrading from Matlab2010a/VS2008 to Matlab2013a/VS2010.
All my environment variables were sent correctly.
A reboot fixed problems with OpenCV dlls not being found, I assume that it was still trying to link to the OpenCV dlls for VS2008 (even though I had changed the path). However still my mex file could not find libmex.dll.
When I installed Matlab2013a, I did not uninstall the old version (in case I wanted to go back).
However that was the cause of my problem.
Once I uninstalled the old version of Matlab and rebooted again, the problem was gone.
I had a similar problem. I was only linking against 1 'lib' so I simply copied that lib into the same folder as the mexw64 and it worked.
I have not poked around for the correct place to tell MATLAB to add the lib's real location to whatever path it's looking at.
I am trying to execute some example code from a MATLAB toolkit, 'oscmex'. This toolkit allows for communication using the OSC protocol over MATLAB. I presume this question is non-specific; it should apply to any toolkit that is set-up in the manner that this one is.
Reasons aside, I'm having some simple trouble getting the toolkit up and running. The toolkit comes with no documentation whatsoever; just a set of six DLL files (in one directory), and a set of four MATLAB '.m' example code files (in another directory). Every toolkit I've used in the past has either been a built-in kit or has had an intuitive (semi-automated) install procedure.
After downloading the toolkit, the first thing I tried was to simply run one of the '.M' example codes. This failed as the first line of the code contained the function osc(), which is not (currently) recognised by MATLAB.
So, I figured maybe I need to move the '.M' files into the same folder as the DLLs; perhaps MATLAB would see the functions inside the DLLs. No dice.
So, I realise that I have to somehow link MATLAB to the DLLs on startup. I tried adding the DLLs to a folder and adding an entry to that in the 'pathdef.m' file. This also failed.
I've read somewhere I can load a DLL file by using the loadlibrary() function. So, I tried doing this for the DLL files. This failed on the first file:
>> loadlibrary('osc_free_address.dll')
Error using loadlibrary>lFullPath (line 587)
Could not find file osc_free_address.h.
I'm starting to run out of options... How can I get this set of DLLs up and running?
Browsing this library's web page it would seems these DLLs are just old form of mex files.
Therefore, they should not be used in the context of shared library (e.g., using loadlibrary and calllib), but rather compiled directly to mex files.
To do so, I would suggest the following steps:
Make sure you have a working mex compiler configured for your Matlab.
In matlab, type:
>> mex -setup
this will guide you through the configuration process. I understand that you are working on a windows machine, I usually work with visual studio compiler - works best for me.
This library's README file suggests that OSC
requires liblo 0.22 or later. See http://plugin.org.uk/liblo/
Make sure you have this library and it is located in you LD_LIBRARY_PATH (see e.g., this question for details, or the mex docs).
Get the source code for OSC library from their repository.
Compile the sources in matlab using
>> mex -O -largeArrayDims osc_free_address.c
>> mex -O -largeArrayDims osc_free_server.c
and so on for all 7 c source files. After mex-ing the c files you'll have mex files that you can run from Matlab as if they were regular functions.
You may find it useful to use the library's make file, as suggested by Andrew Mao.
Good luck,
If you look at the build for that software, it is compiling mex files, not DLLs (shared libraries): http://sourceforge.net/p/oscmex/code/4/tree/trunk/src/osc_make.m.
I would try using the mex commands instead of the dll commands (perhaps the files are just misnamed.) Even better, I would compile the files yourself with mex using the build file in source.
Note that the instructions also say that you need liblo-0.22 in order to run the library, so make sure you have that accessible as well.
I took a look at your OSC Toolkit. It seems they have been compiled by MATLAB mex. But, it is not mentioned for which kind of architecture they have been built. You can type mexext at MATLAB command prompt to find the extension for your MATLAB mex files. Then, change the DLL extensions to the given extension. If the original mex is compatible with your matlab, the DLL can be easily accessed by MATLAB. Just make sure to add the folder to your MATLAB path.
Try changing the extension from .dll to .mexw32 (in win32), or .wexw64 (in win64). It's a long shot but it might work.
The Shared Libraries cannot be used directly. As you have mentioned, you need to load them into MATLAB using loadlibrary. According to the documentation, loadlibrary takes two arguments (at least). The first argument is the name of the file, and the second one is the header file which contains definition of functions and external variables. If you do not provide the header file, the MATLAB looks for the a file with the same name as the DLL. Having said that, you need to have access to the header file or at least if you know how the function looks like, you need to write a header for the DLL.
I have worked with the DLLs in MATLAB. The MATLAB is not very user-friendly as long as DLL is concerned. Especially, if the DLL is written in a language other than C (or C++) you will have trouble loading the function into MATLAB.
Besides, MATLAB can only support some specific DLLs. Based, on your version of MATLAB, you need to find out whether or not the shared library is supported by MATLAB. Have a look at Here
In a nutshell, it is not easy to load a DLL into MATLAB. You need to have some information from DLL.
I seem to have wiped out my path environment variable a while back. I've been slowly restoring things. I have both MATLAB and the MATLAB compiler installed. DLL's I've created from the MATLAB compiler won't run because they can't find the MATLAB compiler runtime dlls. While I did find the particular files that are my immediate problem. I'm wondering if there is a MATLAB *.bat file or command I can type that will restore my path variable to what it was after MATLAB and the Compiler were installed. I'm hoping to forestall future problems.
In case it's version specific I'm running MATLAB R2010b, I'm running a 32 bit version on a 64 bit machine.
[Edit]
I thought I would add that the path I need for running the compiled version was:
C:\Program Files (x86)\MATLAB\MATLAB Compiler Runtime\v714\runtime\win32
With luck, that one along with the two suggested in the answer will get me back to the original state.
restoredefaultpath might recover your MATLAB installation. Consider the use of startup.m, in order to easily undo changes to your environment.
You want to have these two directories on the PATH (I think the order is important):
C:\Program Files\MATLAB\R2010b\runtime\win32
C:\Program Files\MATLAB\R2010b\bin
Obviously you need to adjust the path to match your setup and architecture (those are on a WinXP 32-bit)
If you have a current software maintenance contract for your MATLAB, it may well be that the easy thing to do is just upgrade to the next version of MATLAB since R2011a is out now (unless there is some compelling reason why you must develop on R2010b. Running the software installer should recreate the default environment for MATLAB. I am, of course, assuming that you have Administrator access on your PC and have permission to install software.