I am running glmnet package on MATLAB 2019a in macOS 10.14.5. I have also installed Xcode in my laptop.
I got the error like the following:
Invalid MEX-file '/Users/Desktop/Research/Paper Code/glmnet/glmnetMex.mexmaci64' : dlopen(/Users/Desktop/Research/Paper Code/glmnet/glmnetMex.mexmaci64,
6): Library not loaded: #loader_path/libmex.dylib
Referenced from: /Users/Desktop/Research/Paper Code/glmnet/glmnetMex.mexmaci64
I have tried the code mex -setup and got
MEX configured to use 'Xcode with Clang' for C language compilation.
Warning: The MATLAB C and Fortran API has changed to support MATLAB variables with more than 2^32-1 elements.
In the near future you will be required to update your code to utilize the new API.
You can find more information about this at: http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
I've found some advice from mathworks specific to mex but I am not sure whether this can solve my problem. I stopped here since I am not sure if I should follow this answer to delete something.
Any ideas?
The glmnetMex MEX file included with the Glmnet download looks busticated on newer versions of macOS because it was compiled on a much older version of macOS (OS X 10.8, according to their website), and the DLL library loading mechanism has changed since then. (It should be using #rpath instead of #loader_path.) You will need to rebuild the MEX file yourself, or contact the Glmnet maintainers and ask them to provide a new build.
To rebuild the MEX file:
Set up Matlab with mex -setup to use a compiler that can compile Fortran MEX files. (I don't actually know how to do this.)
In Matlab, cd to the glmnet_matlab directory, !rm glmnetMex.mexmaci64, and then run mex glmnetMex.F
I would consider this a bug in the Glmnet distribution; I have reported it upstream to the Glmnet maintainers.
(I can reproduce this issue with a fresh download of Glmnet on my macOS 10.14.6 box running Matlab R2019a, too.)
Here's a similar problem with another Matlab library's pre-built MEX file: Library not loaded: #loader_path/libmex.dylib in matlab. Next time try Googling for various parts of your error message; searching for "Library not loaded: #loader_path/libmex.dylib" will pull up that question.
#Andrew Janke's answer worked well, except for the second step where I needed to compile using
mex FFLAGS='-fdefault-real-8 -ffixed-form -compatibleArrayDims' glmnetMex.F GLMnet.f
See also here: https://github.com/growlix/glmnet_matlab
I am running MATLAB 2019a with MacOS 10.15.3.
Related
I am trying to learn Fortran programming language, as a test I wrote a simple program like this:
!Fortran Program
program first
print *, "Hello World"
end program first
Then I threw this code file in to mac terminal and run gfortran first.f95 which then gave me an output of a.out as expected.
However, when I try to run the output in terminal by navigating into the output directory and typing ./a.out. It gave me this error output:
dyld: Library not loaded: #rpath/libgfortran.3.dylib
Referenced from: /Users/liang/Desktop/Programs/Fortran/Test/a.out
Reason: image not found
liang is my username.
I had the same problem, and my problem was caused because the library was not in default path and instead "anaconda" got in the path so that's why the compiler could not load it. I am a pure amateur user so I may explain not accurate in terms of technical words.
What I did was, I uninstalled my anaconda and deleted the folder in my Mac. Installed gcc "brew install gcc" again, and it worked! and then after, I installed my anaconda again, so now everything seemingly is ok.
My situation
I am also just learning, and I had a similar error message after compiling MUMPS library (http://mumps-solver.org).
I compiled the sequential version of MUMPS manually after brew installing the dependencies. When I ran the test examples, I got the same error message that libgfortran.3.dylib could not be loaded.
My brew gnu compiler is gcc version 9 and it is invoked by gcc-9, g++-9 and gfortran-9 (for C, C++ and Fortran respectively). Meanwhile gcc, g++ and gfortran invoke the compilers installed by anaconda.
How I solve it
I recompiled MUMPS using gcc-9 and gfortran-9 instead of gcc-9 and gfortran, and now everything works.
I need to call some Fortran code from within MATLAB. I did some research and read about the mex command and how to use it. Sadly I'm already failing at getting the Fortran compiler to work.
First of all, here's my setup:
macOS Sierra 10.12.1 (latest version)
MATLAB R2016b (latest version)
gfortran 4.9.2 (installed via .dmg from official GNU site)
According to the MATLAB documentation, I can use mex -setup FORTRAN to prepare mex for building a mex-file from Fortran. However, running the command in verbose mode yields the following output: mex -setup -v FORTRAN
Verbose mode is on.
... Looking for compiler 'Intel Fortran Composer XE' ...
... Looking for environment variable 'IFORT_COMPILER16' ...No.
... Looking for environment variable 'IFORT_COMPILER15' ...No.
... Looking for environment variable 'IFORT_COMPILER14' ...No.
... Looking for environment variable 'IFORT_COMPILER13' ...No.
... Executing command 'which ifort' ...No.
Did not find installed compiler 'Intel Fortran Composer XE'.
Error using mex
No supported compiler or SDK was found. For options, visit
http://www.mathworks.com/support/compilers/R2016b/maci64.html.
Following the link, one can see that MATLAB does support GNU gfortran 4.9.x on Linux. On Mac however, only Intel's commercial compilers are listed as supported. That's what mex seems to be looking for as well.
Since Mac can also use gfortran to compile Fortran code I thought it'd be possible to get it to work with MATLAB. I've also googled alot and found questions like this one on the MathWorks forum, which suggests that MATLAB should be able to use gfortran, even on Mac.
That's what I think is strange, my MATLAB isn't even looking for a gfortran compiler. All it does is look for an Intel compiler, can't find one and then throws above stated error message.
Regarding my gfortran installation. It is definitely 4.9.2 (which is listed as supported under Linux), which gfortran returns /usr/local/bin and I can successfully compile programs via Terminal.
By the way, mex -setup ANY successfully lists the compilers for C and C++ but no Fortran.
MEX configured to use 'Xcode with Clang' for C language compilation.
Warning: The MATLAB C and Fortran API has changed to support MATLAB
variables with more than 2^32-1 elements. In the near future
you will be required to update your code to utilize the
new API. You can find more information about this at:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
MEX configured to use 'Xcode Clang++' for C++ language compilation.
Warning: The MATLAB C and Fortran API has changed to support MATLAB
variables with more than 2^32-1 elements. In the near future
you will be required to update your code to utilize the
new API. You can find more information about this at:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
To choose a different C compiler, select one from the following:
Xcode with Clang mex -setup:'/Users/Lennart/Library/Application Support/MathWorks/MATLAB/R2016b/mex_C_maci64.xml' C
Xcode Clang++ mex -setup:'/Users/Lennart/Library/Application Support/MathWorks/MATLAB/R2016b/mex_C++_maci64.xml'
I also had a look at those .xml files mentioned at the very end of the last output. There was no file for anything having to do with Fortran and I wasn't able to successfully write one myself. I'm not even sure whether that's the problem...
So simply put my question is: How can I get MATLAB to actually look for and then of course also find my gfortran compiler to use it to compile mex files?
Appreciate your help!
Thanks to hsuyaa and the provided link I was able to resolve my problem. As it needed some more experimenting by myself, I'd like to post how exactly I was able to get gfortran to work.
Look at this link and the accepted answer. Although the MathWorks Team explicitly states that the instructions are specifically written for xCode 7.0 and MATLAB R2015b, I got everything to work with xCode 8.1, MATLAB R2016b and macOS Sierra 10.12.
MATLAB seems to be storing the compiler configuration details in .xml-files as mentioned before. You can find the directory in MATLAB by entering
cd( fullfile( matlabroot, 'bin', 'maci64', 'mexopts' ) );
I did perform a fresh install of MATLAB before but at that location, only three files where located, one for Clang, one for Clang++, one for Intel's Fortran. The gfortran one was simply missing.
The solution author at MathWorks appended all of these .xml-files to his post. I downloaded the files and copied gfortran.xml to the above mentioned folder. This granted partial success in that it made MATLAB actually look for gfortran when running the mex setup.
However, since the files are not up-to-date, I had to add a few lines. I don't exactly understand how the configuration files work, but I noticed that some lines where referring to older macOS versions. Download the file gfortran.xml behind the above link and then add the following:
Wherever you see
<dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk" />
or
<cmdReturns name="find $$ -name MacOSX10.11.sdk" />
also add
<dirExists name="$$/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk" />
or
<cmdReturns name="find $$ -name MacOSX10.12.sdk" />
macOS 10.12 is Sierra. Saving the file and running mex -setup FORTRAN again successfully identified gfortran and set it as the fortran compiler for mex.
Your matlab version is not able to detect the supported compilers. May be this Link can help.
I'm trying to Install BLAS on my Mac, but every time I run make I get this error (shown below the link). I was trying to follow the instructions on this website:
gfortran -O3 -c isamax.f -o isamax.o
make: gfortran: No such file or directory
make: *** [isamax.o] Error 1
I have no idea what this means or how to fix it so any help would be appreciated. Also I'm trying to install CBLAS and LAPACK so any tips/instructions for that would be nice if you know of a good source...Everything I've found so far is pretty confusing. Also I tried to install ATLAS but it kept not working.
This error is caused because gfortran is apparently not installed, so you'll need to download an installer package for OS X Yosemite 10.10 and install it:
gfortran 5.1 or
gfortran 4.9.2 (info)
Once installed run the make command in the BLAS directory.
How to install Blas/Lapack: don't.
These libraries are the textbook example of enormous performance differences between simple and optimized code. And by optimizations I don't mean compiler: I mean algorithm transformations.
So you definitely do not want to download the "reference blas/lapack" from netlib or another location. If your system doesn't already come with an optimized version (Mac OS X does), see if you can get Intel's MKL library (free for students on Linux?), and otherwise get BLIS or OpenBlas or Atlas which are all open source optimized implementations.
I've done everything, and it's payed off.
Trying to compile a mex file from MATLAB using the Windows 7.1 SDK.
~ I've created an compiled my C source code on GCC
~ I've created a MEX file that links and compiles fine via GCC on both Linux and OS X. Does not crash MATLAB, gateway function works fine
~ After much confusion, I switched my dev platform form 64-bit to x86 Win7
~ I've found .dll built files, but they do not link. Linking libs in MATLAB using MATLAB's linker flags will default to .lib, so...
~ I've found--after much googling--simple, pre-compiled x86 GSL .lib's and source files and linked them with MATLAB, eliminating any gsl_blas.h-and-it's-dependencies unrecognized external symbol errors
~ I've re-written every single variable declaration in my source code such that it is C89 standard compatible
~ I've set linker flags appropriately to avoid LIBCMT and any other LIB conflicts
~ I've installed the 2010 and 2012 VC C Runtime libraries
~ I've checked to make sure I have msvcrt.dll and msvcp60.dll in my System files
~ I've followed multiple tutorials online on how supposedly link everything together, most of which had nothing broken links or un-replicable results. I didn't find much to go off of for Cygwin or MinGW.
~ I've tried using the Lcc-win32 2.4.1 compiler
If I was doing basic matrix and vector operations, I'd be set, but unfortunately the various decomposition routines I'm utilizing require parts from the cblas library, which I linked as well, but I get ~30 errors all reporting the same thing...
cblas.lib(ctrsv.obj) : error LNK2001: unresolved external symbol __libm_sse2_sqrt_precise
Here's my MATLAB command.
mex -largeArrayDims -IC:\gsl\include -LC:\gsl\lib -lgsl -lcblas LINKFLAGS="$LINKFLAGS /NODEFAULTLIB:libcmt.lib" file1.c file2.c
So, out of options and frustrated out of my mind, I (naturally) come to stack overflow. Anyone have any idea how to solve this one? The only thing I've foudn on google points to wineHQ errors, not very helpful.
And, if possible, I'd rather not try to compile first on VS201X. I have access to whatever version I need, if necessary, but to me that just seems like a redundant step. Maybe I'm spoiled with Unix-based file system management and linking, though.
It's easy to compile the GSL library under MinGW, in fact the process of compiling from sources is exactly identical to that in Linux. Here are the steps I took:
Setup MinGW for Windows. I am using MinGW-w64 but there is also the popular TDM-GCC distribution which comes with a friendly web-installer.
Obtain GSL sources, and extract the tarball (gsl-1.16.tar.gz is the latest as of now)
Compile as usual, I've used the following commands:
$ ./configure --host=x86_64-w64-mingw32 --prefix=/mingw/local --enable-shared --enable-static
$ make
$ make install
It should take several minutes to finish. Maybe you can enable parallel builds to speed up compilation (make -j)
You'll end up with the necessary files installed in /mingw/local with the usual structure underneath (bin, lib, include).
Finally you can compile an example program with:
$ export PATH=/mingw/local:$PATH
$ gcc `gsl-config --cflags` -o main main.c `gsl-config --libs`
Of course if you prefer using Visual C++ as compiler, people out there have prepared solutions to build GSL using Visual Studio (either manually created project files, or using a build system like CMake and the like). See this question for such projects.
A third option is using Cygwin.
I am trying to run FFTW code in a mex file. This is strictly for the purpose of development and testing. After some googling, I see that others have tried to do something similar and have had related problems, but I have not found any solutions. When attempting to run the mex file, Matlab tells me:
??? Error using ==>
chirpTransform.mxCta Invalid MEX-file
'\removed\my\directory\+chirpTransform\mxCta.mexw32':
The specified procedure could not be
found.
.
I am using gnumex with MinGW to build the mex file because LCC seems to have some issues. I have tried using the 32 bit DLL from the FFTW site (http://www.fftw.org/install/windows.html). I have tried using the fftwf3.dll in the Matlab 2009b bin directory. I built the dll from source using Msys/MinGW. In all cases, the results are the same. In all cases I did the following to generate the lib file.
c:\gnumex\mexdlltool.exe -d
libfftw3f-3.def -D libfftw3f-3.dll -l
libfftw3f.lib --as C:\MinGW\bin\as.exe
I also tried using the visual studio lib.exe tool and experimented with various mexdlltool flags.
It appears that I can directly call functions in the fftwf3-3.dll using Matlab's loadlibrary functionality. Since the DLL appears not to be the problem, I tried building a static version of fftwf3 and linking it directly into the mex file. I got the same results! If I remove the FFTW code, the mex file runs fine. I have just about given up at this point, and I am tyring to come up with alternative methods of testing.
I've run into this issue with other mex functions. In my experience, it typically means that there is a dependency issue. Some dependency is not located.
Here is a link to TMW's documentation on this issue:
Invalid MEX-File Error
Give it a read, and then try using dependency walker to diagnose the problem.
It's been a long time, and my setup has changed, but this works for me now. I suspect hoogamaphone was right. I probably didn't have the fftw dll in the same directory as the mex dll (and it wasn't in my path). In fact, 64 bit Matlab 2016a still gives you a warning about not being able to find the mex file when, in fact, it's a dependency that's missing.
My current setup is using the Visual Studio 2013 C++ compiler by default. As mentioned on the fftw web site, you need to generate a lib file for linking. You can run the Visual Studio command prompt from a regular command prompt like so:
"%VS120COMNTOOLS%VsDevCmd.bat"
Then run the following in the directory with the def file.
lib /machine:x64 /def:libfftw3f-3.def
And compile.
mex mxCta.c cta.c -I../fftw -L../fftw -llibfftw3f-3.lib
Perhaps another possibility is that gnumex introduced some dependency into the mex dll. I no longer recall whether I had used gnumex successfully testing other code. When using cygwin, if you don't use the mingw compiler (x86_64-w64-mingw32-gcc), you'll end up with a dependency on the cygwin1.dll.
Finally, if you use more than one compiler, make sure all the compiler flags are the same (same function calling conventions, ABI, etc). Also, Mathworks has changed the mex build procedure. In a recent project, I copied mexconfig.xml to my local directory from
C:\Users\myuser\AppData\Roaming\MathWorks\MATLAB\R2016a\mex_C_win64.xml
and edited the compiler flags like so:
COMPFLAGS="/Zp8 /GR /W3 /EHs /nologo /MD /Gz /TC"
If you use a custom build file, use the -f option.
mex mxCustom.c custom.lib -f mexconfig.xml