FFTW compilation issue (autoconf for standard headers fails)

[Diehl__Martin]

Hi,

I try to compile FFTW 3.3.8 on Ubuntu 18.10 and get the following errors (note that I have remove some lines)

checking fcntl.h usability... no
checking fcntl.h presence... yes
configure: WARNING: fcntl.h: present but cannot be compiled
configure: WARNING: fcntl.h:     check for missing prerequisite headers?
checking for fcntl.h... no
checking fenv.h usability... no
checking fenv.h presence... yes
configure: WARNING: fenv.h: present but cannot be compiled
configure: WARNING: fenv.h:     check for missing prerequisite headers?
checking for fenv.h... no
checking limits.h usability... no
checking limits.h presence... yes
configure: WARNING: limits.h: present but cannot be compiled
configure: WARNING: limits.h:     check for missing prerequisite headers?
checking for limits.h... no
checking malloc.h usability... no
checking malloc.h presence... yes
configure: WARNING: malloc.h: present but cannot be compiled
configure: WARNING: malloc.h:     check for missing prerequisite headers?
checking for malloc.h... no
checking stddef.h usability... no
checking stddef.h presence... yes
configure: WARNING: stddef.h: present but cannot be compiled
configure: WARNING: stddef.h:     check for missing prerequisite headers?
checking for stddef.h... no
checking sys/time.h usability... no
checking sys/time.h presence... yes
configure: WARNING: sys/time.h: present but cannot be compiled
configure: WARNING: sys/time.h:     check for missing prerequisite headers?
checking for sys/time.h... no
checking altivec.h usability... no
checking altivec.h presence... no
checking for altivec.h... no
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... no
checking for uint32_t... no
checking for uint64_t... no
checking whether time.h and sys/time.h may both be included... no
checking for long double... no
checking for hrtime_t... no
checking size of int... 0
checking size of unsigned int... 0
checking size of long... 0
checking size of unsigned long... 0
checking size of long long... 0
checking size of unsigned long long... 0
checking size of size_t... 0
checking size of ptrdiff_t... 0
checking for ptrdiff_t... no
checking for uintptr_t... no
checking size of void *... 0
checking size of float... 0
checking size of double... 0
checking size of fftw_r2r_kind... 0
configure: error: sizeof(fftw_r2r_kind) test failed

So essentially, something with respect to the system headers went terribly wrong.

Please note that I have updated to the more recent gcc compilers 8.2

icc version 19.0.1.144 (gcc version 8.2.0 compatibility)

[Viet_H_Intel]

It could be your OS. We only support Ubuntu 18.04. Please refer to the Release Notes for System Requirements

https://software.intel.com/en-us/articles/intel-c-compiler-190-for-linux-release-notes-for-intel-parallel-studio-xe-2019#sysreq

Thanks,

[Diehl__Martin]

My mistake, I am using Ubuntu 18.04.

It works with -gcc-sys.

[Terrence_K_ · Accepted solution]

Thanks Martin.  I had the same issue. Just to be clear for others who might find this thread the configure I used was:

./configure --prefix=/usr/local CC=icc CXX=icpc FC=ifort CFLAGS="-gcc-sys"