trouble building trilininos using cmake - cmake

Question

I am trying to build trilinos in fedora25 guest (virtualbox). Followed procedure described here:
http://iltabiai.github.io/peridynamics/fedora/tips/2016/04/20/Peridigm141-Fedora23.html
I had to adapt the build script from above link so that it could find Netcdf and HDF5 on my system.
trilinos builds with these errors in CMakeError.log :
Performing C++ SOURCE FILE Test FINITE_VALUE_HAVE_GLOBAL_ISNAN failed with the following output:
Change Dir: /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_44df3/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_44df3.dir/build.make CMakeFiles/cmTC_44df3.dir/build
gmake[1]: Entering directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_44df3.dir/src.cxx.o
/usr/lib64/mpich/bin/mpicxx -O2 -ansi -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DFINITE_VALUE_HAVE_GLOBAL_ISNAN -o CMakeFiles/cmTC_44df3.dir/src.cxx.o -c /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx: In function ‘int main()’:
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:6:10: error: ‘isnan’ was not declared in this scope
isnan(x);
^
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:6:10: note: suggested alternative:
In file included from /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:2:0:
/usr/include/c++/6.3.1/cmath:662:5: note: ‘std::isnan’
isnan(_Tp __x)
^~~~~
CMakeFiles/cmTC_44df3.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_44df3.dir/src.cxx.o' failed
gmake[1]: *** [CMakeFiles/cmTC_44df3.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_44df3/fast' failed
gmake: *** [cmTC_44df3/fast] Error 2
Source file was:
#include <cmath>
int main()
{
double x = 1.0;
isnan(x);
return 0;
}
Performing C++ SOURCE FILE Test FINITE_VALUE_HAVE_GLOBAL_ISINF failed with the following output:
Change Dir: /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_4cb6e/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_4cb6e.dir/build.make CMakeFiles/cmTC_4cb6e.dir/build
gmake[1]: Entering directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_4cb6e.dir/src.cxx.o
/usr/lib64/mpich/bin/mpicxx -O2 -ansi -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DFINITE_VALUE_HAVE_GLOBAL_ISINF -o CMakeFiles/cmTC_4cb6e.dir/src.cxx.o -c /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx: In function ‘int main()’:
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:6:10: error: ‘isinf’ was not declared in this scope
isinf(x);
^
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:6:10: note: suggested alternative:
In file included from /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:2:0:
/usr/include/c++/6.3.1/cmath:635:5: note: ‘std::isinf’
isinf(_Tp __x)
^~~~~
CMakeFiles/cmTC_4cb6e.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_4cb6e.dir/src.cxx.o' failed
gmake[1]: *** [CMakeFiles/cmTC_4cb6e.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_4cb6e/fast' failed
gmake: *** [cmTC_4cb6e/fast] Error 2
Source file was:
#include <cmath>
int main()
{
double x = 1.0;
isinf(x);
return 0;
}
Determining if the pthread_create exist failed with the following output:
Change Dir: /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_78ecb/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_78ecb.dir/build.make CMakeFiles/cmTC_78ecb.dir/build
gmake[1]: Entering directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_78ecb.dir/CheckSymbolExists.c.o
/usr/lib64/mpich/bin/mpicc -o CMakeFiles/cmTC_78ecb.dir/CheckSymbolExists.c.o -c /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTC_78ecb
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_78ecb.dir/link.txt --verbose=1
/usr/lib64/mpich/bin/mpicc -rdynamic CMakeFiles/cmTC_78ecb.dir/CheckSymbolExists.c.o -o cmTC_78ecb
/usr/bin/ld: CMakeFiles/cmTC_78ecb.dir/CheckSymbolExists.c.o: undefined reference to symbol 'pthread_create##GLIBC_2.2.5'
/usr/lib64/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_78ecb.dir/build.make:97: recipe for target 'cmTC_78ecb' failed
gmake[1]: *** [cmTC_78ecb] Error 1
gmake[1]: Leaving directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_78ecb/fast' failed
gmake: *** [cmTC_78ecb/fast] Error 2
File /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include <pthread.h>
int main(int argc, char** argv)
{
(void)argv;
#ifndef pthread_create
return ((int*)(&pthread_create))[argc];
#else
(void)argc;
return 0;
#endif
}
Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_5fb6c/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_5fb6c.dir/build.make CMakeFiles/cmTC_5fb6c.dir/build
gmake[1]: Entering directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_5fb6c.dir/CheckFunctionExists.c.o
/usr/lib64/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_5fb6c.dir/CheckFunctionExists.c.o -c /usr/share/cmake/Modules/CheckFunctionExists.c
Linking C executable cmTC_5fb6c
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_5fb6c.dir/link.txt --verbose=1
/usr/lib64/mpich/bin/mpicc -DCHECK_FUNCTION_EXISTS=pthread_create -rdynamic CMakeFiles/cmTC_5fb6c.dir/CheckFunctionExists.c.o -o cmTC_5fb6c -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_5fb6c.dir/build.make:97: recipe for target 'cmTC_5fb6c' failed
gmake[1]: *** [cmTC_5fb6c] Error 1
gmake[1]: Leaving directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_5fb6c/fast' failed
gmake: *** [cmTC_5fb6c/fast] Error 2
Performing C++ SOURCE FILE Test HAVE_TEUCHOS_LAPACKLARND failed with the following output:
Change Dir: /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_93b6d/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_93b6d.dir/build.make CMakeFiles/cmTC_93b6d.dir/build
gmake[1]: Entering directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_93b6d.dir/src.cxx.o
/usr/lib64/mpich/bin/mpicxx -O2 -ansi -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DHAVE_TEUCHOS_LAPACKLARND -o CMakeFiles/cmTC_93b6d.dir/src.cxx.o -c /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx: In function ‘int main()’:
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: error: narrowing conversion of ‘0.0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing]
int seed[4] = { 0.0, 0.0, 0.0, 1.0 };
^
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: error: narrowing conversion of ‘0.0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing]
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: error: narrowing conversion of ‘0.0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing]
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:12:38: error: narrowing conversion of ‘1.0e+0’ from ‘double’ to ‘int’ inside { } [-Wnarrowing]
CMakeFiles/cmTC_93b6d.dir/build.make:65: recipe for target 'CMakeFiles/cmTC_93b6d.dir/src.cxx.o' failed
gmake[1]: *** [CMakeFiles/cmTC_93b6d.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_93b6d/fast' failed
gmake: *** [cmTC_93b6d/fast] Error 2
Return value: 1
Source file was:
#define F77_BLAS_MANGLE(name,NAME) name ## _
#define DLARND_F77 F77_BLAS_MANGLE(dlarnd,DLARND)
extern "C" { double DLARND_F77(const int* idist, int* seed); }
int main()
{
const int idist = 1;
int seed[4] = { 0.0, 0.0, 0.0, 1.0 };
double val = DLARND_F77(&idist, seed);
return (val < 0.0 ? 1 : 0);
}
Performing C++ SOURCE FILE Test HAVE_CXX_PRAGMA_WEAK failed with the following output:
Change Dir: /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_21bab/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_21bab.dir/build.make CMakeFiles/cmTC_21bab.dir/build
gmake[1]: Entering directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_21bab.dir/src.cxx.o
/usr/lib64/mpich/bin/mpicxx -O2 -ansi -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DHAVE_CXX_PRAGMA_WEAK -o CMakeFiles/cmTC_21bab.dir/src.cxx.o -c /home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx: In function ‘int main()’:
/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp/src.cxx:14:22: warning: the address of ‘void A::theFunction()’ will never be NULL [-Waddress]
if (A::theFunction != NULL) {
^
Linking CXX executable cmTC_21bab
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_21bab.dir/link.txt --verbose=1
/usr/lib64/mpich/bin/mpicxx -O2 -ansi -pedantic -ftrapv -Wall -Wno-long-long -std=c++11 -DHAVE_CXX_PRAGMA_WEAK -rdynamic CMakeFiles/cmTC_21bab.dir/src.cxx.o -o cmTC_21bab
CMakeFiles/cmTC_21bab.dir/src.cxx.o: In function `main':
src.cxx:(.text.startup+0x25): undefined reference to `A::theFunction()'
collect2: error: ld returned 1 exit status
CMakeFiles/cmTC_21bab.dir/build.make:97: recipe for target 'cmTC_21bab' failed
gmake[1]: *** [cmTC_21bab] Error 1
gmake[1]: Leaving directory '/home/peri/packages/trilinos-12.10.1-Source/build/CMakeFiles/CMakeTmp'
Makefile:126: recipe for target 'cmTC_21bab/fast' failed
gmake: *** [cmTC_21bab/fast] Error 2
Source file was:
#include <iostream>
namespace A {
// theFunction never gets defined, because we
// don't link with a library that defines it.
// That's OK, because it's weak linkage.
#pragma weak theFunction
extern void theFunction ();
}
int main() {
std::cout << "Hi! I am main." << std::endl;
if (A::theFunction != NULL) {
// Should never be called, since we don't link
// with a library that defines A::theFunction.
A::theFunction ();
}
return 0;
}
how can these errors be eliminated?