External libraries¶

Python¶

import numpy as np
 from numpy.linalg import inv

Python interpreter searches modules in the form *.py files, or directories with init.py files
Python interpreter searches modules in the form *.py files, or directories with __init__.py files
Search through standard paths (/usr/lib/python3.6/)
Search through path provided in an environment variable PYTHONPATH (edit .bashrc to extend the list)
can see such a list with:

import sys
 print(sys.path)

Producing executables¶

Compilation: produces .o files
Using external libraries first need to include interfaces

#include <iostream>
 #include <cmath>
 #include <gsl/gsl_sf_bessel.h>

At compilation, g++ searches through standard paths (such as /usr/bin/include)

Extending the list can be done with the option '-I':

> g++ -c -Imynew_path file.cc
+Extending the list can be done with the option '-I':> g++ -c -Imynew_path file.cc
 
 
-Link edition (Linking): produces executables/libraries from .o files and libraries with '-l' option
-
+

+ +

Link edition (Linking): produces executables/libraries from .o files and libraries with '-l' option
At compilation, g++ searches through standard paths (such as /usr/lib)

Extend the list can be done with the option '-L'

> g++ file1.o file2.o -L~/libpath/ -o exec
+Extend the list can be done with the option '-L' > g++ file1.o file2.o -L/some_path/ -lmylib -o exec

What is this error about ?

> g++ tmp.cc
 
 /usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/8/../../../x86_64-linux-gnu/Scrt1.o: in function `_start':
 (.text+0x20): undefined reference to `main'
 collect2: error: ld returned 1 exit status

What is this error about ?

#include <gsl/gsl_sf_bessel.h>
 #include <iostream>
 
 int main(void) {
   double x = 5.0;
   double y = gsl_sf_bessel_J0(x);
   std::cout << "J0(" << x << ") = " << y;
   return 0;
 }

> g++ tmp.cc
 
-/usr/bin/ld: /tmp/ccXkvsyR.o: in function `main':
+/usr/bin/ld: /tmp/ccN3AVEO.o: in function `main':
 tmp.cc:(.text+0x1b): undefined reference to `gsl_sf_bessel_J0'
 collect2: error: ld returned 1 exit status

Need to specify the "library" where the files reside

> g++ -lgsl tmp.cc

Why does this show no error at link ?

#include <cmath>
 
 int main() { return int(sqrt(2.)); }

> gcc tmp.cc
+> g++ tmp.cc

Static libraries¶

A Static libraries is a set of routines, external functions and variables which are resolved by linker/binder to produce a stand-alone executable.
Generally with extension "libXXXX.a" (e.g. /usr/lib/x86_64-linux-gnu/libm.a).
The final executable statically linked includes all the libraries (big executable file)
carry dependencies but not portable

+ +

Dynamic libraries¶

Dynamic/Shared libraries#Shared_libraries) are loaded on demand by executables.
Shared libraries can be statically linked or dynamically loaded.
libXXX.so (or libXXX.dll on windows). e.g. /usr/lib/x86_64-linux-gnu/libm.so

#include <cmath>
 #include <gsl/gsl_sf_bessel.h>
 #include <iostream>
 
 int main(void) {
   double x = 5.0;
   double y = gsl_sf_bessel_J0(x);
   std::cout << "J0(" << x << ") = " << y;
   return int(sqrt(2.));
 }

> ldd exe
 
-	linux-vdso.so.1 (0x00007ffeb9b0c000)
-	libgsl.so.23 => /lib/x86_64-linux-gnu/libgsl.so.23 (0x00007f98cd54c000)
-	libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f98cd3c9000)
-	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f98cd235000)
-	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f98cd21b000)
-	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f98cd05e000)
-	libgslcblas.so.0 => /lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007f98cd01d000)
-	/lib64/ld-linux-x86-64.so.2 (0x00007f98cd806000)
+	linux-vdso.so.1 (0x00007ffe0acfa000)
+	libgsl.so.23 => /lib/x86_64-linux-gnu/libgsl.so.23 (0x00007f434ca37000)
+	libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007f434c8b4000)
+	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f434c720000)
+	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f434c706000)
+	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f434c549000)
+	libgslcblas.so.0 => /lib/x86_64-linux-gnu/libgslcblas.so.0 (0x00007f434c508000)
+	/lib64/ld-linux-x86-64.so.2 (0x00007f434ccf1000)

Scrutinizing a library¶

What to do if you have a link error Undefined symbol
For an internal symbol: check missing inline, check missing implementation
For an external symbol: search the library file !

Listing the Symbols from a library:

> nm -DAC /lib/x86_64-linux-gnu/libm.so.6

option "-A": precede the symbol with library name
option "-D": for dynamic libraries (not needed if .o or .a files)
option "-C": demangle C++ symbols

> nm -DAC /lib/x86_64-linux-gnu/libm.so.6
+

+ +

/lib/x86_64-linux-gnu/libm.so.6:000000000000e910 W acos
 /lib/x86_64-linux-gnu/libm.so.6:0000000000011f40 W acosf
 /lib/x86_64-linux-gnu/libm.so.6:0000000000074b30 W acosf128
 /lib/x86_64-linux-gnu/libm.so.6:0000000000056b30 T __acosf128_finite
 /lib/x86_64-linux-gnu/libm.so.6:0000000000011f40 W acosf32
 ...

U: undefined symbol $\Rightarrow$ used in the library not defined
T: text symbol $\Rightarrow$ used in the library and defined in the library
W: weak symbol $\Rightarrow$ used in the library, defined but can be overloaded with a T symbol ()
W: weak symbol $\Rightarrow$ used in the library, defined but can be overloaded with a T symbol

Finding a symbol from a list of files¶

> find /usr/lib/x86_64-linux-gnu/ -name '*.so' -exec nm -DAC '{}' ';' | grep 'gsl_sf_bessel_J0'

/usr/lib/x86_64-linux-gnu/libgsl.so:0000000000164250 T gsl_sf_bessel_J0
 /usr/lib/x86_64-linux-gnu/libgsl.so:0000000000163dd0 T gsl_sf_bessel_J0_e

Advanced CMake ¶

Creating an executable¶

cmake_minimum_required (VERSION 3.1)
 project (Wonderland)
 add_executable(exe file1.cc file2.cc)

compiles file1.o and file2.o and link into an executable exe

Variables¶

set(VAR_NAME "my variable")
 # example: setting version number 
 set(Wonderland_VERSION_MAJOR 1)
 set(Wonderland_VERSION_MINOR 0))
 # variable appearing in the ccmake menu
 set(CACHED_VARIABLE CACHE STRING "a variable appearing in cmake menu")

types are BOOL, FILEPATH, PATH, STRING
using variables

message("VAR_NAME = ${VAR_NAME}")

special variables

example: ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}
-

+ +

example: ${PROJECT_BINARY_DIR} ${PROJECT_SOURCE_DIR}

Adding paths to the include search list¶

include_directories('/my_preferred_path')
 include_directories("${PROJECT_BINARY_DIR}")

Adding an external library¶

add_executable(exe file1.cc file2.cc)
 target_link_libraries (exe gsl)
 # or with full path
 target_link_libraries (exe /usr/lib/x86_64-linux-gnu/libgsl.so)

Creating a library¶

add_library(mylib file1.cc file2.cc)
-add_executable(exe)
+add_executable(exe main.cc)
 target_link_libraries (exe gsl mylib)

Making options¶

# should we use our own math functions?
 option (USE_GSL "Use gsl library" ON) 
 
 if (USE_GSL)
     target_link_libraries (exe gsl mylib)
 endif (USE_GSL)

Finding libraries¶

For the library files

set(GSL_LIBRARY_PATH CACHE PATH "library where to search libgsl")
-find_library (GSL_LIBRARY libgsl /usr/include/ ${GSL_LIBRARY_PATH})
+find_library (GSL_LIBRARY libgsl ${GSL_LIBRARY_PATH} /usr/lib)

For the include files

set(GSL_INCLUDE_PATH CACHE PATH "path where to search gsl include files")
-find_file(GSL_INCLUDE gsl_root.h /usr/include/ ${GSL_INCLUDE_PATH})
+find_path(GSL_INCLUDE gsl_root.h ${GSL_INCLUDE_PATH} /usr/include/)

Discrete Fourier Transform ¶

Taking a signal (vector of points) $(x_i)$, the Discrete Fourier Transform is gien as the signal:

$$[DFT(x)]_k = \hat{x}_k = \sum_{i=0}^{N-1} x_i \cdot e^{-\frac{2\pi i kn}{N}}$$

It forms an approximation of Fourier series complex coefficients
The inverse DFT is given with

$$[DFT^{-1}(\hat{x})]_i = x_i = \frac{1}{N}\sum_{i=0}^{N-1} \hat{x}_k \cdot e^{\frac{2\pi kin}{N}}$$

Fast Fourier Transform ¶

Hierarchical algorithm ($N \log N$)
FFTW library: mainstream library implementating the FFT transform (Fastest Fourier Transform in the West)
Documentation

example

#include <fftw3.h>
 {
   fftw_complex *in, *out;
   fftw_plan p;
   ...
   in = new fftw_complex[N];
   out = new fftw_complex[N];
   p = fftw_plan_dft_1d(N, in, out, FFTW_FORWARD, FFTW_ESTIMATE);
   ...
   fftw_execute(p); /* repeat as needed */
   ...
   fftw_destroy_plan(p);
   delete [] in;
   delete [] out;
 }

- -