meaning of ld error message "duplicate version tag" - matlab

I'm compiling some C++ functionality into Matlab by using Mex compilation to produce a .mexa64 binary.
Honestly I don't know much about the guts of the symbols created in the .mexa64 binary and how it allows Matlab to call C++, but I'm starting with a simple question related to the error I eventually get when the command mex calls ld.
The ld error is:
/usr/bin/ld.real: duplicate version tag `MEX'
The question is, what does this ld error "duplicate version tag" mean? Other appreciated perspectives are: what does it mean in relation to the Matlab compilation I'm trying to do specifically; and where can I find comprehensive ld error message documentation?
This latter point, the comprehensive ld documentation, I've found particularly hard to find. The manual page for ld didn't seem to be helpful for this.
requested to post the mex config file:
<config Name="g++" ShortName="g++" Manufacturer="GNU" Version="" Language="C++" Priority="A" Location="$GCC_DIR">
<Details CompilerExecutable="$CXX" CompilerDefines="$DEFINES" CompilerFlags="$CXXFLAGS" OptimizationFlags="$CXXOPTIMFLAGS" DebugFlags="$CXXDEBUGFLAGS" IncludeFlags="$INCLUDE" LinkerLibraries="$LINKLIBS" LinkerOptimizationFlags="$LDOPTIMFLAGS" LinkerDebugFlags="$LDDEBUGFLAGS" CompilerDefineFormatter="-D%s" LinkerLibrarySwitchFormatter="-l%s" LinkerPathFormatter="-L%s"/>
<vars CMDLINE1="$CXX -c $DEFINES $INCLUDE $CXXFLAGS $OPTIM $SRC -o $OBJ" CMDLINE2="$LDXX $LDFLAGS $LDTYPE $LINKOPTIM $LINKEXPORT $OBJS $CXXLIBS $LINKLIBS -o $EXE" CMDLINE3="rm -f $OBJ" CXX="$GCC" DEFINES="-D_GNU_SOURCE $MATLABMEX" MATLABMEX="-DMATLAB_MEX_FILE " CXXFLAGS="-ansi -fexceptions -fPIC -fno-omit-frame-pointer -pthread -std=c++11" INCLUDE="-I"$MATLABROOT/extern/include" -I"$MATLABROOT/simulink/include"" CXXOPTIMFLAGS="-O -DNDEBUG" CXXDEBUGFLAGS="-g" LDXX="$CXX" LDFLAGS="-pthread -Wl,--no-undefined " LDTYPE="-shared" LINKEXPORT="-Wl,--version-script,"$MATLABROOT/extern/lib/$ARCH/mexFunction.map"" LINKLIBS="-Wl,-rpath-link,$MATLABROOT/bin/$ARCH -L"$MATLABROOT/bin/$ARCH" -lmx -lmex -lmat -lm -lstdc++" LDOPTIMFLAGS="-O" LDDEBUGFLAGS="-g" OBJEXT=".o" LDEXT=".mexa64"> </vars>
<client>
<engine LINKLIBS="$LINKLIBS -leng" LINKEXPORT="" LDEXT="" LDTYPE=""/>
<mbuild DEFINES="-D_GNU_SOURCE $MATLABMEX -DUNIX -DX11 -DGLNXA64 -DGCC" CXXFLAGS="-ansi -pthread -std=c++11" INCLUDE="$INCLUDE -I"$MATLABROOT/extern/include/cpp"" LDFLAGS="-pthread -Wl,-rpath-link,$MATLABROOT/bin/$ARCH" LINKEXPORT="" LINKLIBS="-L"$MATLABROOT/runtime/$ARCH" -lm -lmwmclmcrrt" LDEXT="" MATLABMEX="" LDTYPE=""/>
</client>
<locationFinder>
<GCC>
<cmdReturns name="which g++"/>
</GCC>
<CPPLIB_DIR>
<cmdReturns name="g++ -print-file-name=libstdc++.so" diagnostic="GCC appears to be installed, but supporting C++ libraries were not found. You must first install the gcc-c++ packge, or similiar, to complete this action."/>
</CPPLIB_DIR>
</locationFinder>
</config>

Related

Recompile with -fPIC

I write this command:
gcc drr.c -o drr -pthread -lcdsl -L./../synch_implementations -I./../synch_implementations
And I can't understand why I get this response:
usr/bin/ld: ./../synch_implementations/libcdsl.a(cdsl_queue_list.o): relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC
usr/bin/ld: ./../synch_implementations/libcdsl.a(cdsl_deque_list.o): relocation R_X86_64_32S against symbol `cdsl_deque_list_lock_based_pthread_push_tail' can not be used when making a PIE object; recompile with -fPIC
usr/bin/ld: ./../synch_implementations/libcdsl.a(cdsl_lock.o): relocation R_X86_64_32S against symbol `cdsl_pthread_lock_request' can not be used when making a PIE object; recompile with -fPIC
usr/bin/ld: final link failed: Nonrepresentable section on output
ollect2: error: ld returned 1 exit status
Can anyone help me understand what is wrong?
Notes:
1)I use ubuntu (via VirtualBox).
2)I am very inexperienced, so probably this is not a very bright question.
Solution:
When you compile ./../synch_implementations/libcdsl.a you need to add an extra "-fPIC" flag to produce position-independent-code (see comments above).
Note:
The PIC flag is in general needed when producing library object code since it creates objects relative to a global offset table (GOT) which subsequently allows to link library objects with your code.

Error in ./configure step in installation of libpqxx

this is a bit of a long shot but:
I'm following this guide: https://www.tutorialspoint.com/postgresql/postgresql_c_cpp.htm
But when running ./configure I get the following error:
(previous checking lines omitted for brevity)
checking for main in -lpq... yes
checking for PQexec in -lpq... yes
checking for correct C++ linkage of basic libpq functions...
sed: character class syntax is [[:space:]], not [:space:]
configure: error:
Linking a call to libpq failed in C++, even though it succeeded in C. If your
C and C++ compilers are very different beasts, this may mean that we do not have
the right options for linking with it after all.
Read the config.log file for more detailed information. Look for the last error
message, which may be several pages up from the end of the file.
And the configure.log file looks like this:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by libpqxx configure 4.0, which was
generated by GNU Autoconf 2.68. Invocation command line was
$ ./configure
## --------- ##
## Platform. ##
## --------- ##
(some lines omitted)
configure:3039: g++ -V >&5
g++: error: unrecognized command line option '-V'
g++: fatal error: no input files
compilation terminated.
configure:3050: $? = 1
configure:3039: g++ -qversion >&5
g++: error: unrecognized command line option '-qversion'; did you mean '--version'?
g++: fatal error: no input files
compilation terminated.
(some lines omitted)
configure:7629: gcc -E conftest.c
conftest.c:11:10: fatal error: ac_nonexistent.h: No such file or directory
#include <ac_nonexistent.h>
^~~~~~~~~~~~~~~~~~
compilation terminated.
(some lines omitted)
configure:8319: gcc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5
cc1: warning: command line option '-fno-rtti' is valid for C++/ObjC++ but not for C
(some lines omitted)
configure:16424: g++ -o conftest -g -O2 -L/usr/lib/x86_64-linux-gnu conftest.cpp >&5
/tmp/ccfFBf4K.o: In function `main':
/home/peter/libpqxx-4.0/conftest.cpp:44: undefined reference to `PQexec'
collect2: error: ld returned 1 exit status
(some liens omitted)
I don't believe I have any packages missing. I have the newest version of g++, psql and libpqxx installed.
I have updated and upgraded all packages on my system.
I have crawled the web for solutions to this error, but I have no clue what is wrong.
Do you have an idea where I can go from here?
There hasn't been a tarball release of libpqxx at the old spot in a long time, so the tutorial you used with its wget command to download the tarball is very outdated.
The issue you encountered looks related to this issue and appears to have been fixed in this commit:
commit 85e9336740475be25ed19924cca0961f7d844c4b
Author: Jeroen Vermeulen <jtvjtv#gmail.com>
Date: Thu Jun 1 11:39:08 2017 +0700
Fix #13: not linking to libpq.
This was that annoying interaction between autoconf, m4, GNU sed syntax,
and the shell which broke the "remove redundant -lpq options" code in
the configure script.
Solution: forget about GNU sed's "[[:space:]]" syntax, and just look for
a literal space. There aren't going to be any tabs, newlines,
non-breaking spaces, etc. there in even a moderately sane world.

mutt installaiton error on CentOS 6.7

I'm trying to install mutt on CentOS 6.7 and ./configure --prefix=$HOME/local runs fine but at make install step, I run into this error below that I don't know how to solve. I tried with mutt 1.6.1 and 1.6.0 and this same error came up so it's probably some system setting that wasn't correct. How could I fix it?
gcc -std=gnu99 -Wall -pedantic -Wno-long-long -g -O2 -o mutt addrbook.o alias.o attach.o base64.o browser.o buffy.o color.o crypt.o cryptglue.o commands.o complete.o compose.o copy.o curs_lib.o curs_main.o date.o edit.o enter.o flags.o init.o filter.o from.o getdomain.o group.o handler.o hash.o hdrline.o headers.o help.o hook.o keymap.o main.o mbox.o menu.o mh.o mx.o pager.o parse.o pattern.o postpone.o query.o recvattach.o recvcmd.o rfc822.o rfc1524.o rfc2047.o rfc2231.o rfc3676.o score.o send.o sendlib.o signal.o sort.o status.o system.o thread.o charset.o history.o lib.o muttlib.o editmsg.o mbyte.o mutt_idna.o url.o ascii.o crypt-mod.o safe_asprintf.o patchlist.o conststrings.o pgp.o pgpinvoke.o pgpkey.o pgplib.o gnupgparse.o pgpmicalg.o pgppacket.o crypt-mod-pgp-classic.o smime.o crypt-mod-smime-classic.o resize.o -lncursesw -lidn
/opt/gnu/bin/ld: curs_lib.o: undefined reference to symbol 'wtimeout'
/lib64/libtinfo.so.5: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
make[2]: *** [mutt] Error 1
OK, I somehow fixed it.. not really understand why this fixed it.
After configure, in the Makefile, change the LDFLAGS = line to LDFLAGS = -lncurses -ltinfo, then make install and it solved the issue.
Credit to this post: http://www.pclinuxos.com/forum/index.php?topic=129566.0, Tara-Rain-9.5ß's answer

MEX cuda code with dynamic parallelism - unable to compile

I have a code by name mexCodeCuda.cu which uses dynamic parallelism. In the matlab interface, when I try to execute the following commands, I get the following error :
system('nvcc --compile mexCodeCuda.cu -o mexCodeCuda.o --compiler-options -fPIC -m64 -rdc=true -gencode arch=compute_35,code=sm_35 -O3 -lineinfo -use_fast_math -lcudadevrt -I/cm/shared/apps/MATLAB/extern/include')
system('nvcc -arch=sm_35 -dlink mexCodeCuda.o -o dlink.o')
eval('mex mexCodeCuda.o dlink.o -L'CUDA_LIB_PATH '-lcudart')
It gives the following error :
Error using mex
/usr/bin/ld: dlink.o: relocation R_X86_64_32S against `__nv_module_id' can
not be used when making a shared object; recompile with -fPIC
dlink.o: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
Can anyone help me ?
Thanks in advance...
A few changes:
Add -fPIC to the second nvcc command (using --compiler-options, just as you did with the first nvcc).
Specify the cudadevrt runtime option on the mex command (-lcudadevrt), just as you have with the first nvcc call.
And you may need to add -fPIC to the mex linking via LDCXXFLAGS or LDFLAGS. Not sure.

Eclipse/C++ Configuration Issue

I am trying to configure Eclipse/Helios on a Win7/64 Professional with CDT and MinGW. When I try and compile:
#include <iostream>
using namespace std ;
int main() {
cout << "What a lovely day\n" ;
return(0) ;
}
I get the output/error:
make all
Building file: ../SeeProgram.cpp
Invoking: Cross G++ Compiler
C:\Tools\MinGW\bin\g++ -O0 -g3 -Wall -c -fmessage-length=0 -MMD -MP -MF"SeeProgram.d" -MT"SeeProgram.d" -o"SeeProgram.o" "../SeeProgram.cpp"
/bin/sh: C:ToolsMinGWbing++: command not found
make: *** [SeeProgram.o] Error 127 .
In the next-to-last line, it should have read C:\Tools\MinGW\bin\g++, but it left out the back-slashes. I have not seen any other discussion of this, and have tried numerous approaches, but I am stumped at the moment. Any thoughts?
Many thanks.
Have you tried escaping the backslashes when you enter the location, e.g.:
C:\\Tools\\MingGW\\bin\\g++
This setup seems similar to yours, maybe it could provide a hint:
http://max.berger.name/howto/cdt/ar01s03.jsp#wincompiler