File format not recognized error while installing CBLAS on a Ubuntu machine - lapack

I need to install CBLAS on an Ubuntu 16.04.4 machine. The following values have been set in the Makefile.in file of CBLAS:
SHELL = /bin/sh
PLAT = LINUX
BLLIB = /home/ubuntu/BLAS-3.8.0/blas_LINUX.a
CBLIB = /home/ubuntu/CBLAS/lib/cblas_LINUX.a
CC = gcc
FC = gfortran
LOADER = $(FC)
CFLAGS = -O3 -DADD_ -fPIC
FFLAGS = -O3 -fPIC
ARCH = gcc
ARCHFLAGS = -shared -o
RANLIB = ranlib
However, while running the make command I run into following error:
ranlib: /home/ubuntu/CBLAS/lib/cblas_LINUX.a: File format not recognized
The following is the stack trace:
Can someone suggest how this can be resolved?

CBLAS shared libraries : sudo apt install libatlas3-base libatlas-base-dev
libatlas3-base provides
/usr/lib/atlas-base/atlas/libblas.so.3
/usr/lib/atlas-base/atlas/libblas.so.3.0
/usr/lib/atlas-base/atlas/liblapack.so.3
/usr/lib/atlas-base/atlas/liblapack.so.3.0
/usr/lib/atlas-base/libatlas.so.3
/usr/lib/atlas-base/libatlas.so.3.0
/usr/lib/atlas-base/libcblas.so.3
/usr/lib/atlas-base/libcblas.so.3.0
/usr/lib/atlas-base/libf77blas.so.3
/usr/lib/atlas-base/libf77blas.so.3.0
/usr/lib/atlas-base/liblapack_atlas.so.3
/usr/lib/atlas-base/liblapack_atlas.so.3.0
/usr/lib/libatlas.so.3
/usr/lib/libcblas.so.3 ← ←
/usr/lib/libf77blas.so.3
/usr/lib/liblapack_atlas.so.3
libatlas-base-dev provides
/usr/lib/atlas-base/atlas/libblas.a
/usr/lib/atlas-base/atlas/libblas.so
/usr/lib/atlas-base/atlas/liblapack.a
/usr/lib/atlas-base/atlas/liblapack.so
/usr/lib/atlas-base/libatlas.a
/usr/lib/atlas-base/libatlas.so
/usr/lib/atlas-base/libcblas.a
/usr/lib/atlas-base/libcblas.so
/usr/lib/atlas-base/libf77blas.a
/usr/lib/atlas-base/libf77blas.so
/usr/lib/atlas-base/liblapack_atlas.a
/usr/lib/atlas-base/liblapack_atlas.so
/usr/lib/libatlas.a
/usr/lib/libatlas.so
/usr/lib/libcblas.a
/usr/lib/libcblas.so ← ←
/usr/lib/libf77blas.a
/usr/lib/libf77blas.so
/usr/lib/liblapack_atlas.a
/usr/lib/liblapack_atlas.so

Related

MATLAB mex linking error using clang and external library fftw3

My question is about linking errors I get when compiling with external libraries using mex. I'm trying to compile C++ code using the external library fftw3 using Matlab's mex on MacOS using clang++. Here is an example
main.cpp
#include "fftw3.h"
int main(){
double * test = (double *) fftw_malloc(10*sizeof(double));
}
compiling this works
$ clang++ main.cpp -L/usr/local/lib -lfftw3
Now I try something similar with mex
mex.cpp
#include "math.h"
#include "matrix.h"
#include "mex.h"
#include "fftw3.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
double * test = (double *) fftw_malloc(10*sizeof(double));
}
in MATLAB
>> mex -setup C++;
>> mex -L/usr/local/lib -lfftw3 CXXFLAGS='-L/usr/local/lib -lfftw3' mex.cpp
Building with 'Xcode Clang++'.
Error using mex
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
using the -v flag I get more detailed errors
Verbose mode is on.
Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require the use of
-largeArrayDims and remove the -compatibleArrayDims option.
For more information:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-api.html.
... Looking for compiler 'Xcode Clang++' ...
... Looking for environment variable 'DEVELOPER_DIR' ...No.
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer' ...Yes.
... Executing command 'which xcrun' ...Yes ('/usr/bin/xcrun').
... Looking for folder '/usr/bin' ...Yes.
... Executing command 'defaults read com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...No.
... Executing command 'defaults read /Library/Preferences/com.apple.dt.Xcode IDEXcodeVersionForAgreedToGMLicense' ...Yes ('7.1.1').
... Executing command '
agreed=7.1.1
if echo $agreed | grep -E '[\.\"]' >/dev/null; then
lhs=`expr "$agreed" : '\([0-9]*\)[\.].*'`
rhs=`expr "$agreed" : '[0-9]*[\.]\(.*\)$'`
if echo $rhs | grep -E '[\."]' >/dev/null; then
rhs=`expr "$rhs" : '\([0-9]*\)[\.].*'`
fi
if [ $lhs -gt 4 ] || ( [ $lhs -eq 4 ] && [ $rhs -ge 3 ] ); then
echo $agreed
else
exit 1
fi
fi' ...Yes ('7.1.1').
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes.
... Executing command 'xcode-select -print-path' ...Yes ('/Applications/Xcode.app/Contents/Developer').
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.7.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk' ...No.
... Looking for folder '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk' ...Yes.
... Executing command 'echo /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk | rev | cut -c1-10 | rev | egrep -oh '[0-9]+\.[0-9]+'' ...Yes ('10.11').
Found installed compiler 'Xcode Clang++'.
Options file details
-------------------------------------------------------------------
Compiler location: /Applications/Xcode.app/Contents/Developer
Options file: ~/.matlab/R2014b/mex_C++_maci64.xml
CMDLINE100 : /usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
CMDLINE200 : /usr/bin/xcrun -sdk macosx10.11 clang++ -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" -O -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map" /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat -o mex.mexmaci64
CMDLINE300 : rm -f /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
CXX : /usr/bin/xcrun -sdk macosx10.11 clang++
DEFINES : -DMX_COMPAT_32 -DMATLAB_MEX_FILE
MATLABMEX : -DMATLAB_MEX_FILE
CXXFLAGS : -L/usr/local/lib -lfftw3
INCLUDE : -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include"
CXXOPTIMFLAGS : -O2 -DNDEBUG
CXXDEBUGFLAGS : -g
LDXX : /usr/bin/xcrun -sdk macosx10.11 clang++
LDFLAGS : -Wl,-twolevel_namespace -undefined error -arch x86_64 -mmacosx-version-min=10.11 -Wl,-syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk -framework Cocoa -bundle -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map"
LDBUNDLE : -bundle
LINKEXPORT : -Wl,-exported_symbols_list,"/Applications/MATLAB_R2014b.app/extern/lib/maci64/mexFunction.map"
LINKLIBS : -lfftw3 -L/usr/local/lib -L"/Applications/MATLAB_R2014b.app/bin/maci64" -lmx -lmex -lmat
LDOPTIMFLAGS : -O
LDDEBUGFLAGS : -g
OBJEXT : .o
LDEXT : .mexmaci64
DEVELOPER_DIR_CHECK :
XCODE_DIR : /Applications/Xcode.app/Contents/Developer
XCRUN_DIR : /usr/bin
XCODE_AGREED_VERSION : 7.1.1
ISYSROOT : /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
SDKVER : 10.11
MATLABROOT : /Applications/MATLAB_R2014b.app
ARCH : maci64
SRC : /path/to/file/mex.cpp
OBJ : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
OBJS : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
SRCROOT : /path/to/file/mex
DEF : /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.def
EXP : mex.exp
LIB : mex.lib
EXE : mex.mexmaci64
ILK : mex.ilk
MANIFEST : mex.mexmaci64.manifest
TEMPNAME : mex
EXEDIR :
EXENAME : mex
OPTIM : -O2 -DNDEBUG
LINKOPTIM : -O
-------------------------------------------------------------------
Building with 'Xcode Clang++'.
/usr/bin/xcrun -sdk macosx10.11 clang++ -c -DMX_COMPAT_32 -DMATLAB_MEX_FILE -I"/Applications/MATLAB_R2014b.app/extern/include" -I"/Applications/MATLAB_R2014b.app/simulink/include" -L/usr/local/lib -lfftw3 -O2 -DNDEBUG /path/to/file/mex.cpp -o /var/folders/09/dysbhb1d5zn98sq8lzkwpn5r0000gn/T//mex_291104578803706_45753/mex.o
Error using mex
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
The warnings
clang: warning: -lfftw3: 'linker' input unused
clang: warning: argument unused during compilation: '-L/usr/local/lib'
are there because you are setting CXXFLAGS to contain these flags. This variable is for compiler flags, but -L and -l are linker flags. Simply remove the CXXFLAGS definition from your mex command.
The error
/path/to/file/mex.cpp:4:10:
fatal error: 'fftw3.h' file not found
#include "fftw3.h"
^
1 error generated.
is because the compiler cannot find the fftw4.h header file. You need to tell the compiler where to find it:
mex -I/usr/local/include -L/usr/local/lib -lfftw3 mex.cpp
Note that in your first case, where you call clang++ directly, it is likely that CLang is configured to look for header files in /usr/local/include, it's a standard place. But when mex invokes your compiler (I don't even know if it's the same one?) apparently this location is not added to the search path.

How to compile uefi application using gnu-efi?

I tried to compile uefi code using gnu-efi. But I don't understand how to compile my uefi application code.
I get gnu-efi 3.0.2, decompress and type make && make install. I write hello world code:
#include <efi.h>
#include <efilib.h>
EFI_STATUS efi_main (EFI_HANDLE ImageHandle, EFI_SYSTEM_TABLE *SystemTable) {
InitializeLib(ImageHandle, SystemTable);
Print(L"Hello, world!\n");
return EFI_SUCCESS;
}
My OS is Ubuntu 15.04.
Include the gnu-efi files
#include <efi.h>
#include <efilib.h>
it looks like your includes where removed by SO
create the make file;
If you were building a "Hello, World" program for Linux in a Linux
environment, you could compile it without a Makefile. Building the
program in Linux for EFI, though, is essentially a cross-compilation
operation. As such, it necessitates using unusual compilation and
linker options, as well as a post-linking operation to convert the
program into a form that the EFI will accept. Although you could type
all the relevant commands by hand, a Makefile helps a lot.
ARCH = $(shell uname -m | sed s,i[3456789]86,ia32,)
OBJS = main.o
TARGET = hello.efi
EFIINC = /usr/include/efi
EFIINCS = -I$(EFIINC) -I$(EFIINC)/$(ARCH) -I$(EFIINC)/protocol
LIB = /usr/lib64
EFILIB = /usr/lib64/gnuefi
EFI_CRT_OBJS = $(EFILIB)/crt0-efi-$(ARCH).o
EFI_LDS = $(EFILIB)/elf_$(ARCH)_efi.lds
CFLAGS = $(EFIINCS) -fno-stack-protector -fpic \
-fshort-wchar -mno-red-zone -Wall
ifeq ($(ARCH),x86_64)
CFLAGS += -DEFI_FUNCTION_WRAPPER
endif
LDFLAGS = -nostdlib -znocombreloc -T $(EFI_LDS) -shared \
-Bsymbolic -L $(EFILIB) -L $(LIB) $(EFI_CRT_OBJS)
all: $(TARGET)
hello.so: $(OBJS)
ld $(LDFLAGS) $(OBJS) -o $# -lefi -lgnuefi
%.efi: %.so
objcopy -j .text -j .sdata -j .data -j .dynamic \
-j .dynsym -j .rel -j .rela -j .reloc \
--target=efi-app-$(ARCH) $^ $#
reference:
http://www.rodsbooks.com/efi-programming/hello.html
In Ubuntu 18.04, these two lines:
LIB = /usr/lib64
EFILIB = /usr/lib64/gnuefi
need to be changed to:
LIB = /usr/lib
EFILIB = /usr/lib

Cannot compile MEX LAPACK example

Summary
I am trying to write some MEX files that use LAPACK, and I thought I'd start by looking through the examples provided by MathWorks.
However, I am having some trouble compiling them. After copying the matrixDivide.c example from [MATLAB root]/extern/examples/refbook into a working directory, I tried to build a mex file, but it failed with error undefined reference to `dgesv_' (where dgesv is the name of the LAPACK routine being called).
I was able to build a different mex example (timestwo.c) that doesn't use LAPACK.
So what's going on? What's the deal with the trailing underscore? What about this memcpy warning?
More info
I think this is fairly similar to the issues encountered by this user:
How can I use CLAPACK,BLAS or LAPACK in a mex file?
I've tried this with MATLAB R2013b and R2014b. I am running on 64-bit Linux (RHEL 6) and my compiler is gcc 4.4.7 (which is not the MathWorks recommended version, but is the newest version I can get).
Here are the relevant portions of the code I'm trying to compile:
1 /*=========================================================
2 * matrixDivide.c - Example for illustrating how to use
3 * LAPACK within a C MEX-file.
4 *
5 * X = matrixDivide(A,B) computes the solution to a
6 * system of linear equations A * X = B
7 * using LAPACK routine DGESV, where
8 * A is an N-by-N matrix
9 * X and B are N-by-1 matrices.
10 *
11 * This is a MEX-file for MATLAB.
12 * Copyright 2009-2010 The MathWorks, Inc.
13 *=======================================================*/
14 /* $Revision: 1.1.6.3 $ $Date: 2011/01/28 18:11:56 $ */
15
16 #if !defined(_WIN32)
17 #define dgesv dgesv_
18 #endif
19
20 #include "mex.h"
21 #include "lapack.h"
22
23 void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
24 {
[ snip ]
73 /* Call LAPACK */
74 dgesv(&m,&n,A2,&m,iPivot,B2,&p,&info);
75 /* plhs[0] now holds X */
76
77 mxDestroyArray(Awork);
78 mxDestroyArray(mxPivot);
79 }
Here is the output of the failed mex build:
>> mex -v -largeArrayDims matrixDivide.c
-> mexopts.sh sourced from directory (DIR = $MATLAB/bin)
FILE = /sw/matlab/R2013b/bin/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /sw/matlab/R2013b
-> CC = gcc
-> CC flags:
CFLAGS = -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread
CDEBUGFLAGS = -g
COPTIMFLAGS = -O -DNDEBUG
CLIBS = -Wl,-rpath-link,/sw/matlab/R2013b/bin/glnxa64 -L/sw/matlab/R2013b/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
arguments =
-> CXX = g++
-> CXX flags:
CXXFLAGS = -ansi -D_GNU_SOURCE -fPIC -fno-omit-frame-pointer -pthread
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O -DNDEBUG
CXXLIBS = -Wl,-rpath-link,/sw/matlab/R2013b/bin/glnxa64 -L/sw/matlab/R2013b/bin/glnxa64 -lmx -lmex -lmat -lm
arguments =
-> FC = gfortran
-> FC flags:
FFLAGS = -fexceptions -fbackslash -fPIC -fno-omit-frame-pointer
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -Wl,-rpath-link,/sw/matlab/R2013b/bin/glnxa64 -L/sw/matlab/R2013b/bin/glnxa64 -lmx -lmex -lmat -lm
arguments =
-> LD = gcc
-> Link flags:
LDFLAGS = -pthread -shared -Wl,--version-script,/sw/matlab/R2013b/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexa64
arguments =
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments =
----------------------------------------------------------------
-> gcc -c -I/sw/matlab/R2013b/extern/include -I/sw/matlab/R2013b/simulink/include -DMATLAB_MEX_FILE -ansi -D_GNU_SOURCE -fexceptions -fPIC -fno-omit-frame-pointer -pthread -O -DNDEBUG "matrixDivide.c"
In file included from matrixDivide.c:21:
/sw/matlab/R2013b/extern/include/lapack.h:6907:1: warning: "dgesv" redefined
matrixDivide.c:17:1: warning: this is the location of the previous definition
matrixDivide.c: In function `mexFunction':
matrixDivide.c:64: warning: incompatible implicit declaration of built-in function ?memcpy?
-> gcc -O -pthread -shared -Wl,--version-script,/sw/matlab/R2013b/extern/lib/glnxa64/mexFunction.map -Wl,--no-undefined -o "matrixDivide.mexa64" matrixDivide.o -Wl,-rpath-link,/sw/matlab/R2013b/bin/glnxa64 -L/sw/matlab/R2013b/bin/glnxa64 -lmx -lmex -lmat -lm -lstdc++
matrixDivide.o: In function `mexFunction':
matrixDivide.c:(.text+0x1c6): undefined reference to `dgesv_'
collect2: ld returned 1 exit status
mex: link of ' "matrixDivide.mexa64"' failed.
After some more messing around, I figured out my (rather elementary) mistake.
You need to specify the -lmwlapack option (and/or -lmwblas, as appropriate) to the linker:
mex -largeArrayDims -lmwlapack matrixDivide.c
It even says so on the MathWorks page I was trying to follow along on. RTFM!

mex linker not finding mexFunction symbol

Up until recently I've been able to compile mex functions fine on my mac osx 10.8.4
but now it gives me the error as follows (for convenience I have included the entire -v invocation):
**************************************************************************
Warning: Neither -compatibleArrayDims nor -largeArrayDims is selected.
Using -compatibleArrayDims. In the future, MATLAB will require
the use of -largeArrayDims and remove the -compatibleArrayDims
option. For more information, see:
http://www.mathworks.com/help/matlab/matlab_external/upgrading-mex-files-to-use-64-bit-
api.html
**************************************************************************
-> mexopts.sh sourced from directory (DIR = .)
FILE = /Users/munanxu/Dropbox/Code/CUDA/mexThomasTDM/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /Applications/MATLAB_R2013a.app
-> CC = xcrun -sdk macosx10.7 clang
-> CC flags:
CFLAGS = -fno-common -arch x86_64 -isysroot
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOS
X10.7.sdk -mmacosx-version-min=10.7 -fexceptions
CDEBUGFLAGS = -g
COPTIMFLAGS = -O2 -DNDEBUG
CLIBS = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -
lstdc++
arguments = -DMX_COMPAT_32
-> CXX = xcrun -sdk macosx10.7 clang++
-> CXX flags:
CXXFLAGS = -fno-common -fexceptions -arch x86_64 -isysroot
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX
10.7.sdk -mmacosx-version-min=10.7
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O2 -DNDEBUG
CXXLIBS = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -
lstdc++
arguments = -DMX_COMPAT_32
-> FC = gfortran
-> FC flags:
FFLAGS = -fexceptions -m64 -fbackslash
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx -lmex -lmat -L
-lgfortran -L -lgfortranbegin
arguments = -DMX_COMPAT_32
-> LD = xcrun -sdk macosx10.7 clang
-> Link flags:
LDFLAGS = -arch x86_64 -Wl,-
syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/
SDKs/MacOSX10.7.sdk -mmacosx-version-min=10.7 -bundle -Wl,-
exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/mexFunction.map
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexmaci64
arguments =
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments =
----------------------------------------------------------------
-> xcrun -sdk macosx10.7 clang -g -arch x86_64 -Wl,-
syslibroot,/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/
SDKs/MacOSX10.7.sdk -mmacosx-version-min=10.7 -bundle -Wl,-
exported_symbols_list,/Applications/MATLAB_R2013a.app/extern/lib/maci64/mexFunction.map -o
"inputsTest.mexmaci64" "inputsTest.o" -L/Applications/MATLAB_R2013a.app/bin/maci64 -lmx
-lmex -lmat -lstdc++
Undefined symbols for architecture x86_64:
"_mexFunction", referenced from:
-exported_symbol[s_list] command line option
ld: symbol(s) not found for architecture x86_64
I had copied the original mexopts.sh file to the local directory to ensure that the mex compiler was using the correct version. I had also previously compiled my cpp file using g++ just to make sure the code was compiled natively for the x86_64 architecture. However, the same result occurs when I attempt to use the mex compiler to do compilation and linking.
Any ideas on what might be going on here? It seems that people have had this issue before, but mostly with missing libraries or definitions. I have definitely defined a mexFunction in my source file.
I think Amro is correct, I would put this as a comment, but it's a bit large, I find this for clang command line options to select target CPU
Registered Targets:
alpha - Alpha [experimental]
arm - ARM
bfin - Analog Devices Blackfin [experimental]
c - C backend ... ...
mblaze - MBlaze
mips - Mips ...
msp430 - MSP430 [experimental] ...
thumb - Thumb
x86 - 32-bit X86: Pentium-Pro and above
x86-64 - 64-bit X86: EM64T and AMD64
xcore - XCoreI'm thinking Amro is correct:
So is -arch x86-64 the right command line switch, rather than x86_64

Changing pg_config

I'm facing a very similar problem as I'm trying to install psycopg2 onto Mac OS 10.6.3; it claims it can't find "stdarg.h" but I can see it's there; what should I do? (except I'm on OS X 10.7 and PostgreSQL v 9.0.5), and I'm thinking about changing my psql config c-compiler.
When I type pg_config in terminal I get:
BINDIR = /usr/bin
DOCDIR = /usr/share/doc/postgresql
HTMLDIR = /Library/WebServer/Documents/postgresql
INCLUDEDIR = /usr/include
PKGINCLUDEDIR = /usr/include/postgresql
INCLUDEDIR-SERVER = /usr/include/postgresql/server
LIBDIR = /usr/lib
PKGLIBDIR = /usr/lib/postgresql
LOCALEDIR = /usr/share/locale
MANDIR = /usr/share/man
SHAREDIR = /usr/share/postgresql
SYSCONFDIR = /private/etc/postgresql
PGXS = /usr/lib/postgresql/pgxs/src/makefiles/pgxs.mk
CONFIGURE = '--mandir=/usr/share/man' '--infodir=/usr/share/info' '--disable-dependency-tracking' '--prefix=/usr' '--sbindir=/usr/libexec' '--sysconfdir=/private/etc' '--localstatedir=/var/pgsql' '--htmldir=/Library/WebServer/Documents/postgresql' '--enable-thread-safety' '--enable-dtrace' '--with-tcl' '--with-perl' '--with-python' '--with-gssapi' '--with-krb5' '--with-pam' '--with-ldap' '--with-bonjour' '--with-openssl' '--with-libxml' '--with-libxslt' '--with-system-tzdata=/usr/share/zoneinfo' 'CFLAGS=-arch x86_64 -arch i386 -pipe -Os -g -Wall -Wno-deprecated-declarations' 'LDFLAGS=-arch x86_64 -arch i386 -pipe -Os -g -Wall -Wno-deprecated-declarations' 'LDFLAGS_EX=-mdynamic-no-pic'
CC = gcc
CPPFLAGS = -I/usr/include/libxml2
CFLAGS = -arch x86_64 -arch i386 -pipe -Os -g -Wall -Wno-deprecated-declarations -Wall -Wmissing-prototypes -Wpointer-arith -Wdeclaration-after-statement -Wendif-labels -fno-strict-aliasing -fwrapv
CFLAGS_SL =
LDFLAGS = -arch x86_64 -arch i386 -pipe -Os -g -Wall -Wno-deprecated-declarations -Wl,-dead_strip_dylibs
LDFLAGS_EX = -mdynamic-no-pic
LDFLAGS_SL =
LIBS = -lpgport -lxslt -lxml2 -lpam -lssl -lcrypto -lgssapi_krb5 -lz -lreadline -lm
VERSION = PostgreSQL 9.0.5
I'm wondering how to change pg_config (so I can set CC = gcc-4.2) or something along those lines.
pg_config is just a util that provides information, it is not a "config" in the typical sense that you can edit properties. If you want to change a value that pg_config provides, you will need to manually do so outside of the util (in your case, you will need to install a new C compiler).