[gmx-users] Regarding installation problem

SOUVIK MONDAL m.souvik at iitkgp.ac.in
Tue Feb 23 11:10:56 CET 2016 

The CmakeErroor.log file have following things

Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_bf3f2/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_bf3f2.dir/build.make CMakeFiles/cmTC_bf3f2.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_bf3f2.dir/src.c.o
/usr/bin/cc    -DCFLAGS_EXCESS_PREC -fexcess-precision=fast   -o CMakeFiles/cmTC_bf3f2.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
cc1: error: unrecognized command line option "-fexcess-precision=fast"
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake[1]: *** [CMakeFiles/cmTC_bf3f2.dir/src.c.o] Error 1
gmake: *** [cmTC_bf3f2/fast] Error 2

Source file was:
int main(void) { return 0; }
Performing C++ SOURCE FILE Test CXXFLAGS_EXCESS_PREC failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_2e3fd/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_2e3fd.dir/build.make CMakeFiles/cmTC_2e3fd.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_2e3fd.dir/src.cxx.o
/usr/bin/c++     -DCXXFLAGS_EXCESS_PREC -fexcess-precision=fast   -o CMakeFiles/cmTC_2e3fd.dir/src.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx
cc1plus: error: unrecognized command line option "-fexcess-precision=fast"
gmake[1]: *** [CMakeFiles/cmTC_2e3fd.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_2e3fd/fast] Error 2

Source file was:
int main() { return 0;}
Determining if files io.h exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_c44f7/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_c44f7.dir/build.make CMakeFiles/cmTC_c44f7.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_c44f7.dir/CheckIncludeFiles.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter     -o CMakeFiles/cmTC_c44f7.dir/CheckIncludeFiles.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckIncludeFiles.c
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckIncludeFiles.c:2:16: error: io.h: No such file or directory
gmake[1]: *** [CMakeFiles/cmTC_c44f7.dir/CheckIncludeFiles.c.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_c44f7/fast] Error 2

Source:
/* */
#include <io.h>


int main(void){return 0;}

Determining if the memalign exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_bf2d4/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_bf2d4.dir/build.make CMakeFiles/cmTC_bf2d4.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_bf2d4.dir/CheckSymbolExists.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function     -o CMakeFiles/cmTC_bf2d4.dir/CheckSymbolExists.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8: error: ‘memalign’ was not declared in this scope
gmake[1]: *** [CMakeFiles/cmTC_bf2d4.dir/CheckSymbolExists.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_bf2d4/fast] Error 2

File /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <stdlib.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef memalign
  return ((int*)(&memalign))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the _aligned_malloc exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_956e1/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_956e1.dir/build.make CMakeFiles/cmTC_956e1.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_956e1.dir/CheckSymbolExists.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function     -o CMakeFiles/cmTC_956e1.dir/CheckSymbolExists.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8: error: ‘_aligned_malloc’ was not declared in this scope
gmake[1]: *** [CMakeFiles/cmTC_956e1.dir/CheckSymbolExists.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_956e1/fast] Error 2

File /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <stdlib.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef _aligned_malloc
  return ((int*)(&_aligned_malloc))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the _fileno exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_c09ea/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_c09ea.dir/build.make CMakeFiles/cmTC_c09ea.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_c09ea.dir/CheckSymbolExists.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function     -o CMakeFiles/cmTC_c09ea.dir/CheckSymbolExists.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8: error: ‘_fileno’ was not declared in this scope
gmake[1]: *** [CMakeFiles/cmTC_c09ea.dir/CheckSymbolExists.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_c09ea/fast] Error 2

File /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <stdio.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef _fileno
  return ((int*)(&_fileno))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the _commit exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_a9cfb/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_a9cfb.dir/build.make CMakeFiles/cmTC_a9cfb.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_a9cfb.dir/CheckSymbolExists.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function     -o CMakeFiles/cmTC_a9cfb.dir/CheckSymbolExists.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:2:16: error: io.h: No such file or directory
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8: error: ‘_commit’ was not declared in this scope
gmake[1]: *** [CMakeFiles/cmTC_a9cfb.dir/CheckSymbolExists.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_a9cfb/fast] Error 2

File /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <io.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef _commit
  return ((int*)(&_commit))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the rsqrt exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_f9a6b/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_f9a6b.dir/build.make CMakeFiles/cmTC_f9a6b.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_f9a6b.dir/CheckSymbolExists.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function     -o CMakeFiles/cmTC_f9a6b.dir/CheckSymbolExists.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8: error: ‘rsqrt’ was not declared in this scope
gmake[1]: *** [CMakeFiles/cmTC_f9a6b.dir/CheckSymbolExists.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_f9a6b/fast] Error 2

File /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <math.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef rsqrt
  return ((int*)(&rsqrt))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the rsqrtf exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_b3e92/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_b3e92.dir/build.make CMakeFiles/cmTC_b3e92.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_b3e92.dir/CheckSymbolExists.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function     -o CMakeFiles/cmTC_b3e92.dir/CheckSymbolExists.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx: In function ‘int main(int, char**)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:8: error: ‘rsqrtf’ was not declared in this scope
gmake[1]: *** [CMakeFiles/cmTC_b3e92.dir/CheckSymbolExists.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_b3e92/fast] Error 2

File /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.cxx:
/* */
#include <math.h>

int main(int argc, char** argv)
{
  (void)argv;
#ifndef rsqrtf
  return ((int*)(&rsqrtf))[argc];
#else
  (void)argc;
  return 0;
#endif
}

Determining if the system is big endian passed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_2b7fc/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_2b7fc.dir/build.make CMakeFiles/cmTC_2b7fc.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_2b7fc.dir/TestEndianess.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter     -o CMakeFiles/cmTC_2b7fc.dir/TestEndianess.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/TestEndianess.c
Linking C executable cmTC_2b7fc
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2b7fc.dir/link.txt --verbose=1
/usr/bin/cc   -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter      CMakeFiles/cmTC_2b7fc.dir/TestEndianess.c.o  -o cmTC_2b7fc -rdynamic 
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'

TestEndianess.c:
/* A 16 bit integer is required. */
typedef unsigned short cmakeint16;

/* On a little endian machine, these 16bit ints will give "THIS IS LITTLE ENDIAN."
   On a big endian machine the characters will be exchanged pairwise. */
const cmakeint16 info_little[] =  {0x4854, 0x5349, 0x4920, 0x2053, 0x494c, 0x5454, 0x454c, 0x4520, 0x444e, 0x4149, 0x2e4e, 0x0000};

/* on a big endian machine, these 16bit ints will give "THIS IS BIG ENDIAN."
   On a little endian machine the characters will be exchanged pairwise. */
const cmakeint16 info_big[] =     {0x5448, 0x4953, 0x2049, 0x5320, 0x4249, 0x4720, 0x454e, 0x4449, 0x414e, 0x2e2e, 0x0000};

#ifdef __CLASSIC_C__
int main(argc, argv) int argc; char *argv[];
#else
int main(int argc, char *argv[])
#endif
{
  int require = 0;
  require += info_little[argc];
  require += info_big[argc];
  (void)argv;
  return require;
}


Determining if the pthread_create exist failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_6c74e/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_6c74e.dir/build.make CMakeFiles/cmTC_6c74e.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_6c74e.dir/CheckSymbolExists.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter     -o CMakeFiles/cmTC_6c74e.dir/CheckSymbolExists.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTC_6c74e
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6c74e.dir/link.txt --verbose=1
/usr/bin/cc   -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter      CMakeFiles/cmTC_6c74e.dir/CheckSymbolExists.c.o  -o cmTC_6c74e -rdynamic 
CMakeFiles/cmTC_6c74e.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0xc): undefined reference to `pthread_create'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_6c74e] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_6c74e/fast] Error 2

File /root/Downloads/gromacs-5.1.2/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: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_95ca6/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_95ca6.dir/build.make CMakeFiles/cmTC_95ca6.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_95ca6.dir/CheckFunctionExists.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DCHECK_FUNCTION_EXISTS=pthread_create   -o CMakeFiles/cmTC_95ca6.dir/CheckFunctionExists.c.o   -c /usr/local/share/cmake-3.4/Modules/CheckFunctionExists.c
Linking C executable cmTC_95ca6
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_95ca6.dir/link.txt --verbose=1
/usr/bin/cc   -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DCHECK_FUNCTION_EXISTS=pthread_create    CMakeFiles/cmTC_95ca6.dir/CheckFunctionExists.c.o  -o cmTC_95ca6 -rdynamic -lpthreads 
/usr/bin/ld: cannot find -lpthreads
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_95ca6] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_95ca6/fast] Error 2


Performing C SOURCE FILE Test _isfinite_compile_ok failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_808f2/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_808f2.dir/build.make CMakeFiles/cmTC_808f2.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_808f2.dir/src.c.o
/usr/bin/cc   -I/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/math.h  -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -D_isfinite_compile_ok   -o CMakeFiles/cmTC_808f2.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c: In function ‘main’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:4: warning: implicit declaration of function ‘_isfinite’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:5: warning: control reaches end of non-void function
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:4: warning: ‘f’ is used uninitialized in this function
Linking C executable cmTC_808f2
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_808f2.dir/link.txt --verbose=1
/usr/bin/cc   -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -D_isfinite_compile_ok    CMakeFiles/cmTC_808f2.dir/src.c.o  -o cmTC_808f2 -rdynamic -lm 
CMakeFiles/cmTC_808f2.dir/src.c.o: In function `main':
src.c:(.text+0x16): undefined reference to `_isfinite'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_808f2] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_808f2/fast] Error 2

Source file was:
#include <math.h>
int main(void) {
  float f;
  _isfinite(f);
}
Performing C SOURCE FILE Test _finite_compile_ok failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_3fecf/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_3fecf.dir/build.make CMakeFiles/cmTC_3fecf.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_3fecf.dir/src.c.o
/usr/bin/cc   -I/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/float.h  -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -D_finite_compile_ok   -o CMakeFiles/cmTC_3fecf.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c: In function ‘main’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:4: warning: implicit declaration of function ‘_finite’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:5: warning: control reaches end of non-void function
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:4: warning: ‘f’ is used uninitialized in this function
Linking C executable cmTC_3fecf
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_3fecf.dir/link.txt --verbose=1
/usr/bin/cc   -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -D_finite_compile_ok    CMakeFiles/cmTC_3fecf.dir/src.c.o  -o cmTC_3fecf -rdynamic 
CMakeFiles/cmTC_3fecf.dir/src.c.o: In function `main':
src.c:(.text+0x16): undefined reference to `_finite'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_3fecf] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_3fecf/fast] Error 2

Source file was:
#include <float.h>
int main(void) {
  float f;
  _finite(f);
}
Performing C++ SOURCE FILE Test GMX_CXX11_SUPPORTED failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_9fa68/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_9fa68.dir/build.make CMakeFiles/cmTC_9fa68.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_9fa68.dir/src.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -DGMX_CXX11_SUPPORTED -std=c++0x   -o CMakeFiles/cmTC_9fa68.dir/src.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:10: sorry, unimplemented: cannot expand ‘Tail ...’ into a fixed-length argument list
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:11: error: ‘int’ is not a class type
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:11: error: ‘ListType’ in class ‘int’ does not name a type
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:11: error: template argument 2 is invalid
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:11: error: expected ‘::’ before ‘ListType’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:13: error: only declarations of constructors can be ‘explicit’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In copy constructor ‘A::A(const A&)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:4:   instantiated from ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Tp*, _Args&& ...) [with _Args = A, _Tp = A]’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:95:   instantiated from ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = A, _Tp = A, _Alloc = std::allocator<A>]’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:747:   instantiated from ‘void std::vector<_Tp, _Alloc>::push_back(_Tp&&) [with _Tp = A, _Alloc = std::allocator<A>]’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:20:   instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:214: error: deleted function ‘std::unique_ptr<_Tp, _Tp_Deleter>::unique_ptr(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = int, _Tp_Deleter = std::default_delete<int>]’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:4: error: used here
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++allocator.h:34,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/allocator.h:48,
                 from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector:62,
                 from /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:1:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h: In member function ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Tp*, _Args&& ...) [with _Args = A, _Tp = A]’:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/ext/new_allocator.h:111: note: synthesized method ‘A::A(const A&)’ first required here 
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h: In member function ‘A& A::operator=(const A&)’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:4:   instantiated from ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(__gnu_cxx::__normal_iterator<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type::pointer, std::vector<_Tp, _Alloc> >, _Args&& ...) [with _Args = A, _Tp = A, _Alloc = std::allocator<A>]’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:100:   instantiated from ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = A, _Tp = A, _Alloc = std::allocator<A>]’
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/stl_vector.h:747:   instantiated from ‘void std::vector<_Tp, _Alloc>::push_back(_Tp&&) [with _Tp = A, _Alloc = std::allocator<A>]’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:20:   instantiated from here
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/unique_ptr.h:219: error: deleted function ‘std::unique_ptr<_Tp, _Tp_Deleter>& std::unique_ptr<_Tp, _Tp_Deleter>::operator=(const std::unique_ptr<_Tp, _Tp_Deleter>&) [with _Tp = int, _Tp_Deleter = std::default_delete<int>]’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:4: error: used here
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/vector:69,
                 from /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:1:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(__gnu_cxx::__normal_iterator<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type::pointer, std::vector<_Tp, _Alloc> >, _Args&& ...) [with _Args = A, _Tp = A, _Alloc = std::allocator<A>]’:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/bits/vector.tcc:314: note: synthesized method ‘A& A::operator=(const A&)’ first required here 
gmake[1]: *** [CMakeFiles/cmTC_9fa68.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_9fa68/fast] Error 2

Source file was:
#include <vector>
#include <memory>
#include <utility>
struct A {
  A(int *i=NULL) : p(i) {} ;
  std::unique_ptr<int> p;
};
template <typename Head, typename... Tail>
struct VarList {
  typedef VarList<Tail...> VarListTail;
  typedef std::pair<Head, typename VarListTail::ListType> ListType;
};
class a { explicit operator bool() {return true;} };
int main() {
  typedef std::unique_ptr<int> intPointer;
  intPointer p(new int(10));
  std::vector<intPointer> v;
  v.push_back(std::move(p));
  std::vector<A> v2;
  v2.push_back(A());  //requires default move constructor
  v2.push_back(A(new int(5))); //detects bug in ICC
}
Determining if the include file regex exists failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_906d5/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_906d5.dir/build.make CMakeFiles/cmTC_906d5.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_906d5.dir/CheckIncludeFile.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function     -o CMakeFiles/cmTC_906d5.dir/CheckIncludeFile.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx
In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/regex:35,
                 from /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/CheckIncludeFile.cxx:1:
/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/c++0x_warning.h:31:2: error: #error This file requires compiler and library support for the upcoming ISO C++ standard, C++0x. This support is currently experimental, and must be enabled with the -std=c++0x or -std=gnu++0x compiler options.
gmake[1]: *** [CMakeFiles/cmTC_906d5.dir/CheckIncludeFile.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_906d5/fast] Error 2


Performing C SOURCE FILE Test C_FLAG_march_core_avx2 failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_7715e/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_7715e.dir/build.make CMakeFiles/cmTC_7715e.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_7715e.dir/src.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DC_FLAG_march_core_avx2 -march=core-avx2   -o CMakeFiles/cmTC_7715e.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:1: error: bad value (core-avx2) for -march= switch
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:1: error: bad value (core-avx2) for -mtune= switch
gmake[1]: *** [CMakeFiles/cmTC_7715e.dir/src.c.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_7715e/fast] Error 2

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test C_FLAG_mavx2 failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_146f4/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_146f4.dir/build.make CMakeFiles/cmTC_146f4.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_146f4.dir/src.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DC_FLAG_mavx2 -mavx2   -o CMakeFiles/cmTC_146f4.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
cc1: error: unrecognized command line option "-mavx2"
gmake[1]: *** [CMakeFiles/cmTC_146f4.dir/src.c.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_146f4/fast] Error 2

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test C_FLAG_arch_AVX failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_34e1f/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_34e1f.dir/build.make CMakeFiles/cmTC_34e1f.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_34e1f.dir/src.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DC_FLAG_arch_AVX /arch:AVX   -o CMakeFiles/cmTC_34e1f.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
cc: /arch:AVX: No such file or directory
gmake[1]: *** [CMakeFiles/cmTC_34e1f.dir/src.c.o] Error 1
gmake[1]: *** Deleting file `CMakeFiles/cmTC_34e1f.dir/src.c.o'
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_34e1f/fast] Error 2

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test C_FLAG_hgnu failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_c4b7a/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_c4b7a.dir/build.make CMakeFiles/cmTC_c4b7a.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_c4b7a.dir/src.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DC_FLAG_hgnu -hgnu   -o CMakeFiles/cmTC_c4b7a.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
cc: unrecognized option '-hgnu'
Linking C executable cmTC_c4b7a
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_c4b7a.dir/link.txt --verbose=1
/usr/bin/cc   -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DC_FLAG_hgnu -hgnu    CMakeFiles/cmTC_c4b7a.dir/src.c.o  -o cmTC_c4b7a -rdynamic 
cc: unrecognized option '-hgnu'
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'

Source file was:
int main(void) { return 0; }
Performing C SOURCE FILE Test C_SIMD_COMPILES_FLAG_ failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_413ec/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_413ec.dir/build.make CMakeFiles/cmTC_413ec.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_413ec.dir/src.c.o
/usr/bin/cc    -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter  -DC_SIMD_COMPILES_FLAG_   -o CMakeFiles/cmTC_413ec.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c: In function ‘main’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:2: error: ‘__m256i’ undeclared (first use in this function)
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:2: error: (Each undeclared identifier is reported only once
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:2: error: for each function it appears in.)
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:2: error: expected ‘;’ before ‘x’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:2: error: ‘x’ undeclared (first use in this function)
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:2: warning: implicit declaration of function ‘_mm256_add_epi32’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c:2: warning: implicit declaration of function ‘_mm256_movemask_epi8’
gmake[1]: *** [CMakeFiles/cmTC_413ec.dir/src.c.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_413ec/fast] Error 2

Source file was:
#include<immintrin.h>
                              int main(){__m256i x=_mm256_set1_epi32(5);x=_mm256_add_epi32(x,x);return _mm256_movemask_epi8(x);}
Performing C++ SOURCE FILE Test CXX_FLAG_march_core_avx2 failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_201e9/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_201e9.dir/build.make CMakeFiles/cmTC_201e9.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_201e9.dir/src.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -DCXX_FLAG_march_core_avx2 -march=core-avx2   -o CMakeFiles/cmTC_201e9.dir/src.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:1: error: bad value (core-avx2) for -march= switch
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:1: error: bad value (core-avx2) for -mtune= switch
gmake[1]: *** [CMakeFiles/cmTC_201e9.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_201e9/fast] Error 2

Source file was:
int main() { return 0;}
Performing C++ SOURCE FILE Test CXX_FLAG_mavx2 failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_e71b8/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_e71b8.dir/build.make CMakeFiles/cmTC_e71b8.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_e71b8.dir/src.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -DCXX_FLAG_mavx2 -mavx2   -o CMakeFiles/cmTC_e71b8.dir/src.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx
cc1plus: error: unrecognized command line option "-mavx2"
gmake[1]: *** [CMakeFiles/cmTC_e71b8.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_e71b8/fast] Error 2

Source file was:
int main() { return 0;}
Performing C++ SOURCE FILE Test CXX_FLAG_arch_AVX failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_abed8/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_abed8.dir/build.make CMakeFiles/cmTC_abed8.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_abed8.dir/src.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -DCXX_FLAG_arch_AVX /arch:AVX   -o CMakeFiles/cmTC_abed8.dir/src.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx
c++: /arch:AVX: No such file or directory
gmake[1]: *** [CMakeFiles/cmTC_abed8.dir/src.cxx.o] Error 1
gmake[1]: *** Deleting file `CMakeFiles/cmTC_abed8.dir/src.cxx.o'
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_abed8/fast] Error 2

Source file was:
int main() { return 0;}
Performing C++ SOURCE FILE Test CXX_FLAG_hgnu failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_00366/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_00366.dir/build.make CMakeFiles/cmTC_00366.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_00366.dir/src.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -DCXX_FLAG_hgnu -hgnu   -o CMakeFiles/cmTC_00366.dir/src.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx
c++: unrecognized option '-hgnu'
Linking CXX executable cmTC_00366
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_00366.dir/link.txt --verbose=1
/usr/bin/c++    -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -DCXX_FLAG_hgnu -hgnu    CMakeFiles/cmTC_00366.dir/src.cxx.o  -o cmTC_00366 -rdynamic 
c++: unrecognized option '-hgnu'
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'

Source file was:
int main() { return 0;}
Performing C++ SOURCE FILE Test CXX_SIMD_COMPILES_FLAG_ failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_1c2c7/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_1c2c7.dir/build.make CMakeFiles/cmTC_1c2c7.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_1c2c7.dir/src.cxx.o
/usr/bin/c++     -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function  -DCXX_SIMD_COMPILES_FLAG_   -o CMakeFiles/cmTC_1c2c7.dir/src.cxx.o -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx: In function ‘int main()’:
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:2: error: ‘__m256i’ was not declared in this scope
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:2: error: expected ‘;’ before ‘x’
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:2: error: ‘x’ was not declared in this scope
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:2: error: ‘_mm256_add_epi32’ was not declared in this scope
/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.cxx:2: error: ‘_mm256_movemask_epi8’ was not declared in this scope
gmake[1]: *** [CMakeFiles/cmTC_1c2c7.dir/src.cxx.o] Error 1
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_1c2c7/fast] Error 2

Source file was:
#include<immintrin.h>
                                int main(){__m256i x=_mm256_set1_epi32(5);x=_mm256_add_epi32(x,x);return _mm256_movemask_epi8(x);}

----- Original Message -----
From: "SOUVIK MONDAL" <m.souvik at iitkgp.ac.in>
To: "gromacs org gmx-users" <gromacs.org_gmx-users at maillist.sys.kth.se>
Sent: Tuesday, February 23, 2016 11:55:18 AM
Subject: [gmx-users] Regarding installation problem

Hi
  I have found the following problem regarding gromacs 5.1.2 installation. I have installes cmake and ffftw before. Can you help me out?
-- Configuring incomplete, errors occurred!


See also "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeOutput.log".
See also "/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeError.log"

when I opened that two log files it shows 
Performing C SOURCE FILE Test CFLAGS_EXCESS_PREC failed with the following output:
Change Dir: /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/gmake" "cmTC_bf3f2/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_bf3f2.dir/build.make CMakeFiles/cmTC_bf3f2.dir/build
gmake[1]: Entering directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_bf3f2.dir/src.c.o
/usr/bin/cc    -DCFLAGS_EXCESS_PREC -fexcess-precision=fast   -o CMakeFiles/cmTC_bf3f2.dir/src.c.o   -c /root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp/src.c
cc1: error: unrecognized command line option "-fexcess-precision=fast"
gmake[1]: Leaving directory `/root/Downloads/gromacs-5.1.2/build/CMakeFiles/CMakeTmp'
gmake[1]: *** [CMakeFiles/cmTC_bf3f2.dir/src.c.o] Error 1
gmake: *** [cmTC_bf3f2/fast] Error 2

Source file was:
int main(void) { return 0; }
Performing C++ SOURCE FILE Test CXXFLAGS_EXCESS_PREC failed with the following output:
"CMakeError.log" 624L, 40593C

-- 
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