Trivial Eigen3 Tensor program does not build without -On - c++

I'm trying to build a write of software with the Tensor module provided as unsupported from eigen3. I've written a simple piece of code that will build with a simple application of VectorXd (just printing it to stdout), and will also build with an analogous application of Tensor in place of the VectorXd, but WILL NOT build when I do not throw an optimization flag (-On). Note that my build is from within a conda enviromnent that is using conda-forge compilers, so the g++ in what follows is the g++ obtained from conda forge for ubuntu. It says its name in the error messages following, if that is perceived to be the issue.
I have a feeling this is not about the program I'm trying to write, but just in case I've included an mwe.cpp that seems to produce the error. The code follows:
#include <eigen3/Eigen/Dense>
#include <eigen3/unsupported/Eigen/CXX11/Tensor>
#include <iostream>
using namespace Eigen;
using namespace std;
int main(int argc, char const *argv[])
{
VectorXd v(6);
v << 1, 2, 3, 4, 5, 6;
cout << v.cwiseSqrt() << "\n";
Tensor<double, 1> t(6);
for (auto i=0; i<v.size(); i++){
t(i) = v(i);
}
cout << "\n";
for (auto i=0; i<t.size(); i++){
cout << t(i) << " ";
}
cout << "\n";
return 0;
}
If the above code is compiled without any optimizations, like:
g++ -I ~/miniconda3/envs/myenv/include/ mwe.cpp -o mwe
I get the following compiler error:
/home/myname/miniconda3/envs/myenv/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /tmp/cc2q8gj4.o: in function `Eigen::internal::(anonymous namespace)::get_random_seed()':
mwe.cpp:(.text+0x15): undefined reference to `clock_gettime'
collect2: error: ld returned 1 exit status
If instead I ask for 'n' optimization level, like the following:
g++ -I ~/miniconda3/envs/loos/include/ -On mwe.cpp -o mwe
The program builds without complaint and I get expected output:
$ ./mwe
1
1.41421
1.73205
2
2.23607
2.44949
1 2 3 4 5 6
I have no clue why this little program, or the real program I'm trying to write, would be trying to get a random seed for anything. Any advice would be appreciated. The reason why I would like to build without optimization is so that debugging is easier. I actually thought all this was being caused by debug flags, but I realized that my build tool's debug setting didn't ask for optimization and narrowed that down to the apparent cause. If I throw -g -O1 I do not see the error.
Obviously, if one were to comment out all the code that has to do with the Tensor module, that is everthing in main above 'return' and below the cwiseSqrt() line, and also the include statement, the code builds and produces expected output.

Technically, this is a linker error (g++ calls the compiler as well as the linker, depending on the command line arguments). And you get linker-errors if an externally defined function is called from somewhere, even if the code is never reached.
When compiling with optimizations enabled, g++ will optimize away uncalled functions (outside the global namespace), thus you get no linker errors. You may want to try -Og instead of -O1 for better debugging experience.
The following code should produce similar behavior:
int foo(); // externally defined
namespace { // anonymous namespace
// defined inside this module, but never called
int bar() {
return foo();
}
}
int main() {
// if you un-comment this line, the
// optimized version will fail as well:
// ::bar();
}
According to man clock_gettime you need to link with -lrt if your glibc version is older than 2.17 -- maybe that is the case for your setup:
g++ -I ~/miniconda3/envs/myenv/include/ mwe.cpp -o mwe -lrt

Related

How to run a Fortran program within GNU Octave?

I want to run a Fortran program within Octave. I would like to do this for automation purposes and use Octave for all the data processing.
Is it possible to run a Fortran program from octave using cygwin, if so, could you provide me some pointers along that direction?
Moreover, I have a gfortran compiler installed in my system, Is there a way I could make use of it to complete my task mentioned above?
Furthermore, I tried to use mex to perform the same:
mckoctfile --mex HelloWorld.f
I got the following error after trying the mex approach:
c:/octave/octave~1.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\rajan\AppData\Local\Temp/oct-qur1RF.o: in function `hi': C:\Tech Stuff\Fortran Programs/HelloWorld.f:3: undefined reference to `_gfortran_st_write'
c:/octave/octave~1.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Tech Stuff\Fortran Programs/HelloWorld.f:3: undefined reference to `_gfortran_transfer_character_write'
c:/octave/octave~1.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Tech Stuff\Fortran Programs/HelloWorld.f:3: undefined reference to `_gfortran_st_write_done'
c:/octave/octave~1.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Users\rajan\AppData\Local\Temp/oct-qur1RF.o: in function `main':C:\Tech Stuff\Fortran Programs/HelloWorld.f:6: undefined reference to `_gfortran_set_args'
c:/octave/octave~1.0/mingw64/bin/../lib/gcc/x86_64-w64-mingw32/9.2.0/../../../../x86_64-w64-mingw32/bin/ld.exe: C:\Tech Stuff\Fortran Programs/HelloWorld.f:6: undefined reference to `_gfortran_set_options'
collect2.exe: error: ld returned 1 exit status
warning: mkoctfile: building exited with failure sta
How do I resolve this error to move forward?
Obviously your particular use-case may be a lot more complex than this, but here's a simple example to get you started (or to help you decide whether it's worth going down that route at all...)
Let's start with a simple octfile which performs simple integer addition, no fortran involved for now.
// in: simple_addition.cpp
#include <octave/oct.h>
DEFUN_DLD (simple_addition, args, ,"Add two integers via C++")
{
octave_value retval = args(0).int_value() + args(1).int_value();
return retval;
}
Compile:
mkoctfile -c simple_addition.cpp # compiles a simple_addition.o file
mkoctfile -o simple_addition simple_addition.o # links .o file to named output file
In octave:
octave:1> simple_addition(1,2)
ans = 3
Now let's put this aside for a minute, and see how we might call a fortran-defined function from pure c++. First let's create a simple integer addition function:
! in fortran_addition.f90
function fortran_addition(a,b) result(Out)
integer, intent(in) :: a,b ! input
integer :: Out ! output
Out = a + b
end function fortran_addition
and compile it using gfortran:
gfortran -c fortran_addition.f90 # creates fortran_addition.o
You can see (e.g. using nm fortran_addition.o) that the generated object contains a reference to a symbol under the name fortran_addition_ (note the added underscore at the end).
Now let's create a normal (i.e. non-octave-related) c++ wrapper program which calls the function defined via this symbol:
// in generic_fortran_addition_wrapper.cpp
#include <iostream>
extern "C" { int fortran_addition_( int *, int * ); }
int main() {
int a = 1, b = 2, fortran_result;
fortran_result = fortran_addition_( &a, &b );
std::cout << a << " + " << b << " = " << fortran_result << std::endl;
}
compile:
g++ -c generic_fortran_addition_wrapper.cpp
g++ -o addints generic_fortran_addition_wrapper.o fortran_addition.o
./addints # outputs `1 + 2 = 3` on the terminal
Now we have all the ingredients to create an octfile that wraps a fortran function:
// in fortran_addition_wrapper.cpp
#include <octave/oct.h>
extern "C" { int fortran_addition_( int *, int *); }
DEFUN_DLD (fortran_addition_wrapper, args, ,"Add two integers via fortran")
{
int a, b, fortran_result;
a = args(0).int_value();
b = args(1).int_value();
fortran_result = fortran_addition_( &a, &b );
octave_value retval(fortran_result);
return retval;
}
compile with mkoctfile:
mkoctfile -c fortran_addition_wrapper.cpp
mkoctfile -o fortran_addition_wrapper fortran_addition_wrapper.o fortran_addition.o
and then in octave:
octave:1> fortran_addition_wrapper(1,2)
ans = 3
Having said all this, obviously if you have a fully defined fortran program, rather than just linkable functions, and you have a running compiled executable on your system, then you can skip all the above 'formalities' and just call your executable via the system() command from octave. Obviously in this scenario it's up to you to pass the data in an octave-agnostic way ... but presumably if you have a standalone fortran executable, then presumably it already has a way of reading input data from the operating system.
EDIT as per the comments below, I've been reminded that I got side-tracked and answered the question that was asked in the comments to the original question, and forgot to address the error messages in the original question. As mentioned in my comment there, mkoctave is a generic wrapper to the gnu compiler collection. Those messages do not sound specific to octave, but rather that the compiler/linker complains that you're missing the fortran runtime libraries that define these basic functions.

"Duplicate symbol" when attempting to compile two .cpp files (from XCode) in terminal (MacOSX)

I have two .cpp files, main.cpp and secondFile.cpp:
#include <iostream>
int main()
{
std::cout << "Hello, World!\n" << std::endl;
std::cout << "I was also able to add this line!" << std::endl;
return 0;
}
And
#include <iostream>
int main()
{
std::cout << "This was from the second file!" << std::endl;
return 0;
}
I have successfully run g++ -o main.cpp main and g++ -o secondFile.cpp secondFile, as well as run each of their corresponding executables. However when I attempt to compile them simultaneously into a single executable g++ -o main.cpp secondFile.cpp bothScripts or clang++ main.cpp secondFile.cpp -o bothScripts I receive the following error:
"duplicate symbol _main in:
/var/folders/49/38grlkzs44zcth3v_dw9m9dm0000gn/T/main-d43536.o
/var/folders/49/38grlkzs44zcth3v_dw9m9dm0000gn/T/secondfile-2bee63.o
ld: 1 duplicate symbol for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)"
Clearly something is being loaded twice, but I am unsure whether this is a library (iostream), that I've named both sections 'main', or something else entirely. There are certainly questions similar to this already, but many are convoluted and not as fundamental for new C++ members (hence my question here).
Context: My rationale is to practice building executables from multiple .cpp files. Is there a better way to go about this? (New to C++ but not to programming/code as a whole.)
The reason for your error is simple. You have 2 main() functions. As you should know, in a C++ program, the function main() generally defines the entry point of a program. When each of the files are compiled together, and have their own main() function, the compiler gets confused and throws an error. To solve this, simply change the name of the main() function in one file, and call it from the other file, if you are planning to run them together.

Programming Error, New to C++

I'm taking an intro class into C++ and we are using jgrasp. I'm doing a simple exercise right now which looks like this:
#include <iostream>
using namespace std;
int main()
{
cout << "Testing 1, 2, 3\n";
return 0;
}
though when I compile it and link it I get this error:
----jGRASP exec: g++ -c -fsyntax-only H:\COP2334\Excerises\Display 1.10
g++.exe: warning: H:\COP2334\Excerises\Display 1.10: linker input file unused because linking not done
----jGRASP: operation complete.
The option -c means "Compile or assemble the source files, but do not link."
So, of course, linking isn't performed.

Can't run to_string() function on Linux

I've got some code that I'm running on Mac OS X that can't be compiled on the Virtual Machine running Linux Mint. This is a simple example. When I run it in Mac, all is fine, but I'm getting issues when I run the same code on Linux, so I'm assuming the library I'm including is not there, but should I be getting an include error then?
Here's the example code that runs on Mac.
#include <iostream>
#include <stdlib.h>
#include <string>
#include <cstdlib>
using namespace std;
int main(){
for (int i = 0; i < 10; i++){
string test = to_string(i);
cout << test << endl;
}
cout << "done" << endl;
return 0;
}
I get no issues here but running on Linux Mint, I get this when I try to compile:
for.cpp: In function 'int main()':
for.cpp:7:28 error: 'to_string' was not declared in this scope
string test = to_string(i);
^
make: *** [for] Error 1
Am I missing something? Any help would be much appreciated!
edit
I realize I forgot to include <string> on here and I fixed it, but what I changed (<string> included) still doesn't compile on Linux. I've used to_string before. I know that much in C++. I also tried adding <cstdlib>. Once again, this DOES compile on Mac and DOES NOT compile on Linux.
Here is my OSX output:
0
1
2
3
4
5
6
7
8
9
done
Here is my output on Linux Mint (Once again, Virtual Box, g++ make):
test.cpp: In function ‘int main()’:
test.cpp:9:28: error: ‘to_string’ was not declared in this scope
string test = to_string(i);
^
make: *** [test] Error 1
You could reproduce the problem yourself if you don't believe me. It's the same code, you can see for yourself if you want.
Compile your for.cpp file like this:
g++ -std=c++11 for.cpp
and run it with:
./a.out
The support for the to_string function in the <string> header was added in the C++11 version of the language, so you need to tell GCC to use that version. You can use the c++0x flag too, for example:
g++ -std=c++0x for.cpp
And you don't have to worry about <cstdlib>, that has nothing to do with it...
to_string() is defined in <string> if you are compiling with C++11 (but is not defined, or unreliably defined as an extension feature, if you are compiling with an earlier version of C++).
Reference: http://en.cppreference.com/w/cpp/string/basic_string/to_string
SOLUTION:
I found a better solution. For some reason, I've read stdlib.h will not work on some linux systems. I used a different function to convert int to string.
on linux:
#include <stdio.h>
and then
for (int i = 0; i < 10; i++){
char buffer[10];
sprintf(buffer,"%d",i);
string stringInt = buffer;
cout << stringInt << endl;
// do whatever you want with the string
}
edit
To the person that down voted my solution to this, here's a post from six years ago basically saying the same thing.

g++ malloc error when linking with libmx and using std::stringstream

The simplest example is the following program, linked with libmx (-lmx) (for MATLAB support) on OS X Yosemite, compiled with g++4.9.1 from macports:
#include <sstream>
int main()
{
std::ostringstream ostr;
// ostr << " "; // if I un-comment this line no more malloc error
}
I realized that at ostr destruction (just before exiting the program), I get a malloc runtime error of the form:
testcpp(5362,0x7fff7d2af300) malloc: *** error for object 0x1055b6270:
pointer being freed was not allocated *** set a breakpoint in malloc_error_break to debug
If, on the other hand, I uncomment the second line in main() and write something to the ostringstream, then the program exits happily with no more error. This happens only with g++, clang++ compiles and runs it without any problems. Anyone knows if this is a g++-related issue or a libmx one?
PS: if I am not using -lmx flag on linking, then there is no more malloc error.
I guess it's better to comment on this separately. As I said, I'm having troubles reproducing your error. I'm on Ubuntu Linux 14.04 64 bits with g++ 4.8.2 and I downloaded the Matlab Compiler Runtime v83 and v84 for Linux 64 bits.
The source I am compiling is the following:
#include <sstream>
int main()
{
std::ostringstream ostr;
// ostr << " "; // if I un-comment this line no more malloc error
}
And the following commands run fine (2014 a and b):
g++ -L/opt/MATLAB/MCR/v83/runtime/glnxa64 -Wall malloc_gcc_matlab.cpp -o malloc_gcc_matlab && ./malloc_gcc_matlab
g++ -L/opt/MATLAB/MCR/v84/runtime/glnxa64 -Wall malloc_gcc_matlab.cpp -o malloc_gcc_matlab && ./malloc_gcc_matlab