catastrophic error: cannot open source file "stdio.h" on Mac

Turnquist__Brian · ‎09-10-2019

Hello,

I have just installed 2019 version 4 of Intel® Parallel Studio XE Composer Edition for C++ macOS. I am trying to build a program (Szip 2.1.1) and have the following issue

conftest.c(11): catastrophic error: cannot open source file "stdio.h"
  #include <stdio.h>
                    ^

compilation aborted for conftest.c (code 4)
configure:3543: $? = 4
configure:3550: ./conftest
./configure: line 3552: ./conftest: No such file or directory
configure:3554: $? = 127
configure:3561: error: in `/Users/brianturnquist/Downloads/szip-2.1.1':
configure:3563: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.

It appears the installer has not included the header files that come with CommandLineTools. However, I thought the initialization with

source /opt/intel/bin/compilervars.sh intel64

would cover that issue. How do I fix this and make sure I am linking to all necessary header files?

Thank you. Also, the entire config.log is posted below.

Brian

This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by SZIP configure 2.1.1, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure --prefix=/usr/local/Intel-compiled/szip-2.1.1 --enable-shared --enable-static

## --------- ##
## Platform. ##
## --------- ##

hostname = Brians-MacBook-Pro-2.local
uname -m = x86_64
uname -r = 18.7.0
uname -s = Darwin
uname -v = Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64

/usr/bin/uname -p = i386
/bin/uname -X     = unknown

/bin/arch              = unknown
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo      = Mach kernel version:
         Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64
Kernel configured for up to 8 processors.
4 processors are physically available.
8 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3 4 5 6 7
Primary memory available: 16.00 gigabytes
Default processor set: 414 tasks, 1751 threads, 8 processors
Load average: 1.29, Mach factor: 6.69
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /Library/Frameworks/Python.framework/Versions/3.7/bin
PATH: /usr/local/openmpi-4.0.1/bin
PATH: /Library/Frameworks/Python.framework/Versions/3.6/bin
PATH: /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
PATH: /usr/bin
PATH: /opt/local/sbin
PATH: /opt/local/bin
PATH: /usr/local/openmpi-4.0.1/bin
PATH: /bin
PATH: /usr/bin
PATH: /usr/local/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:2330: checking for a BSD-compatible install
configure:2398: result: /usr/bin/install -c
configure:2409: checking whether build environment is sane
configure:2464: result: yes
configure:2615: checking for a thread-safe mkdir -p
configure:2654: result: bin/install-sh -c -d
configure:2661: checking for gawk
configure:2691: result: no
configure:2661: checking for mawk
configure:2691: result: no
configure:2661: checking for nawk
configure:2691: result: no
configure:2661: checking for awk
configure:2677: found /usr/bin/awk
configure:2688: result: awk
configure:2699: checking whether make sets $(MAKE)
configure:2721: result: yes
configure:2750: checking whether make supports nested variables
configure:2767: result: yes
configure:2894: checking whether to enable maintainer-specific portions of Makefiles
configure:2903: result: no
configure:2921: checking build system type
configure:2935: result: x86_64-apple-darwin18.7.0
configure:2955: checking host system type
configure:2968: result: x86_64-apple-darwin18.7.0
configure:3030: checking for config x86_64-apple-darwin18.7.0
configure:3038: result: no
configure:3030: checking for config x86_64-apple-darwin18.7.0
configure:3038: result: no
configure:3030: checking for config apple-darwin18.7.0
configure:3038: result: no
configure:3030: checking for config apple-darwin18.7.0
configure:3038: result: no
configure:3030: checking for config x86_64-darwin18.7.0
configure:3038: result: no
configure:3030: checking for config x86_64-darwin18.7.0
configure:3038: result: no
configure:3030: checking for config x86_64-apple
configure:3038: result: no
configure:3030: checking for config darwin18.7.0
configure:3038: result: no
configure:3030: checking for config darwin18.7.0
configure:3038: result: no
configure:3030: checking for config apple
configure:3038: result: no
configure:3030: checking for config x86_64
configure:3038: result: no
configure:3095: checking for gcc
configure:3122: result: icc-19.0.4.233
configure:3351: checking for C compiler version
configure:3360: icc-19.0.4.233 --version >&5
icc-19_0_4_233 (ICC) 19.0.4.233 20190416
Copyright (C) 1985-2019 Intel Corporation.  All rights reserved.

configure:3371: $? = 0
configure:3360: icc-19.0.4.233 -v >&5
icc-19.0.4.233 version 19.0.4.233 (gcc version 4.9.0 compatibility)
configure:3371: $? = 0
configure:3360: icc-19.0.4.233 -V >&5
Intel(R) C Intel(R) 64 Compiler for applications running on Intel(R) 64, Version 19.0.4.233 Build 20190416
Copyright (C) 1985-2019 Intel Corporation.  All rights reserved.

configure:3371: $? = 0
configure:3360: icc-19.0.4.233 -qversion >&5
icc-19_0_4_233: command line warning #10006: ignoring unknown option '-qversion'
icc-19_0_4_233: command line error: no files specified; for help type "icc-19_0_4_233 -help"
configure:3371: $? = 1
configure:3391: checking whether the C compiler works
configure:3413: icc-19.0.4.233    conftest.c  >&5
configure:3417: $? = 0
configure:3465: result: yes
configure:3468: checking for C compiler default output file name
configure:3470: result: a.out
configure:3476: checking for suffix of executables
configure:3483: icc-19.0.4.233 -o conftest    conftest.c  >&5
configure:3487: $? = 0
configure:3509: result: 
configure:3531: checking whether we are cross compiling
configure:3539: icc-19.0.4.233 -o conftest    conftest.c  >&5
conftest.c(11): catastrophic error: cannot open source file "stdio.h"
  #include <stdio.h>
                    ^

compilation aborted for conftest.c (code 4)
configure:3543: $? = 4
configure:3550: ./conftest
./configure: line 3552: ./conftest: No such file or directory
configure:3554: $? = 127
configure:3561: error: in `/Users/brianturnquist/Downloads/szip-2.1.1':
configure:3563: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_build=x86_64-apple-darwin18.7.0
ac_cv_env_CC_set=set
ac_cv_env_CC_value=icc-19.0.4.233
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_LT_SYS_LIBRARY_PATH_set=
ac_cv_env_LT_SYS_LIBRARY_PATH_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_host=x86_64-apple-darwin18.7.0
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=awk
ac_cv_prog_ac_ct_CC=icc-19.0.4.233
ac_cv_prog_make_make_set=yes
am_cv_make_support_nested_variables=yes

## ----------------- ##
## Output variables. ##
## ----------------- ##

ACLOCAL='${SHELL} /Users/brianturnquist/Downloads/szip-2.1.1/bin/missing aclocal-1.15'
AMDEPBACKSLASH=''
AMDEP_FALSE=''
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AR=''
AUTOCONF='${SHELL} /Users/brianturnquist/Downloads/szip-2.1.1/bin/missing autoconf'
AUTOHEADER='${SHELL} /Users/brianturnquist/Downloads/szip-2.1.1/bin/missing autoheader'
AUTOMAKE='${SHELL} /Users/brianturnquist/Downloads/szip-2.1.1/bin/missing automake-1.15'
AWK='awk'
CC='icc-19.0.4.233'
CCDEPMODE=''
CFLAGS=''
CPP=''
CPPFLAGS=''
CYGPATH_W='echo'
DEFS=''
DEPDIR=''
DLLTOOL=''
DSYMUTIL=''
DUMPBIN=''
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP=''
EXEEXT=''
FGREP=''
GREP=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
LD=''
LDFLAGS=''
LIBOBJS=''
LIBS=''
LIBTOOL=''
LIPO=''
LN_S=''
LTLIBOBJS=''
LT_SYS_LIBRARY_PATH=''
MAINT='#'
MAINTAINER_MODE_FALSE=''
MAINTAINER_MODE_TRUE='#'
MAKEINFO='${SHELL} /Users/brianturnquist/Downloads/szip-2.1.1/bin/missing makeinfo'
MANIFEST_TOOL=''
MKDIR_P='bin/install-sh -c -d'
NM=''
NMEDIT=''
OBJDUMP=''
OBJEXT=''
OTOOL64=''
OTOOL=''
PACKAGE='szip'
PACKAGE_BUGREPORT='help@hdfgroup.org'
PACKAGE_NAME='SZIP'
PACKAGE_STRING='SZIP 2.1.1'
PACKAGE_TARNAME='szip'
PACKAGE_URL=''
PACKAGE_VERSION='2.1.1'
PATH_SEPARATOR=':'
RANLIB=''
SED=''
SET_MAKE=''
SHELL='/bin/sh'
STRIP=''
VERSION='2.1.1'
ac_ct_AR=''
ac_ct_CC='icc-19.0.4.233'
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE=''
am__fastdepCC_FALSE=''
am__fastdepCC_TRUE=''
am__include=''
am__isrc=''
am__leading_dot='.'
am__nodep=''
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-apple-darwin18.7.0'
build_alias=''
build_cpu='x86_64'
build_os='darwin18.7.0'
build_vendor='apple'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host='x86_64-apple-darwin18.7.0'
host_alias=''
host_cpu='x86_64'
host_os='darwin18.7.0'
host_vendor='apple'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /Users/brianturnquist/Downloads/szip-2.1.1/bin/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local/Intel-compiled/szip-2.1.1'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

/* confdefs.h */
#define PACKAGE_NAME "SZIP"
#define PACKAGE_TARNAME "szip"
#define PACKAGE_VERSION "2.1.1"
#define PACKAGE_STRING "SZIP 2.1.1"
#define PACKAGE_BUGREPORT "help@hdfgroup.org"
#define PACKAGE_URL ""
#define PACKAGE "szip"
#define VERSION "2.1.1"

configure: exit 1

Turnquist__Brian · ‎09-10-2019

Okay, I got it to build. After installing 2019 version 4 of Intel® Parallel Studio XE Composer Edition for C++ macOS, I then installed Xcode's CommandLineTools as suggested in https://github.com/frida/frida/issues/338#issuecomment-426777849

chiniwar__santosh · ‎09-14-2019

Anyone found solution?

I got same problem on MacBook Pro 2019, on MacBook Air 2014 model, ICC works fine.

I wrote simple Hello.c program and I got

" catastrophic error: cannot open source file "stdio.h"

#include <stdio.h>

^ "

Any suggestion would be appreciated. .. Thank You!

chiniwar__santosh · ‎09-14-2019

Anyone found solution?

I got same problem on MacBook Pro 2019, on MacBook Air 2014 model, ICC works fine.

I wrote simple Hello.c program and I got

" catastrophic error: cannot open source file "stdio.h"

#include <stdio.h>

^ "

chiniwar__santosh · ‎09-14-2019

Solved!!

I installed intel complier then Xcode, again.