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clang-omp not finding <stdio.h> / <omp.h> #40391

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jamesblackburn opened this issue Jun 4, 2015 · 12 comments
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clang-omp not finding <stdio.h> / <omp.h> #40391

jamesblackburn opened this issue Jun 4, 2015 · 12 comments
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Clear out Legacy

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@jamesblackburn
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Hi

I've installed clang-omp but there seem to be issues with it picking up built-in headers.

It is installed locally, but running tests doesn't work:

(arctic)JB-MacBook:arctic james$ brew install clang-omp
Warning: clang-omp-2015-04-01 already installed
(arctic)JB-MacBook:arctic james$ brew test clang-omp
Testing clang-omp
==> /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp -liomp5 -fopenmp test.c -o test

test.c:3:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^
1 error generated.
Error: clang-omp: failed
Failed executing: /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp -liomp5 -fopenmp test.c -o test
/usr/local/Library/Homebrew/formula.rb:885:in `block in system'
/usr/local/Library/Homebrew/formula.rb:842:in `open'
/usr/local/Library/Homebrew/formula.rb:842:in `system'
/usr/local/Library/Formula/clang-omp.rb:76:in `block in <class:ClangOmp>'
/usr/local/Library/Homebrew/formula.rb:785:in `block in run_test'
/usr/local/Library/Homebrew/extend/fileutils.rb:17:in `mktemp'
/usr/local/Library/Homebrew/formula.rb:781:in `run_test'
/usr/local/Library/Homebrew/test.rb:28:in `block in <main>'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/timeout.rb:66:in `timeout'
/usr/local/Library/Homebrew/test.rb:27:in `<main>'

If I try a the simple test from:
https://clang-omp.github.io
It find omp.h but not sodlib.h:

(arctic)JB-MacBook:arctic james$ cat test_clang.c 
#include <omp.h>
#include <stdio.h>
int main() {
#pragma omp parallel
printf("Hello from thread %d, nthreads %d\n", omp_get_thread_num(), omp_get_num_threads());
}
(arctic)JB-MacBook:arctic james$ /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp test_clang.c -liomp5 -fopenmp 
In file included from test_clang.c:1:
/usr/local/opt/libiomp/include/libiomp/omp.h:134:13: fatal error: 'stdlib.h' file not found
#   include <stdlib.h>
            ^
1 error generated.

Current system:

(arctic)JB-MacBook:arctic james$ uname -a
Darwin JB-MacBook.local 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_64
(arctic)JB-MacBook:arctic james$ clang --version
Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)
Target: x86_64-apple-darwin14.3.0
Thread model: posix

Any ideas?
@xu-cheng
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xu-cheng commented Jun 5, 2015

Does reinstall clang-omp do any help?

@jamesblackburn
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Doesn't seem to:

JB-MacBook:local james$ brew remove clang-omp
Uninstalling /usr/local/Cellar/clang-omp/2015-04-01... (1396 files, 378M)
JB-MacBook:local james$ brew install clang-omp
==> Downloading https://homebrew.bintray.com/bottles/clang-omp-2015-04-01.yosemite.bottle.2.tar.gz
Already downloaded: /Library/Caches/Homebrew/clang-omp-2015-04-01.yosemite.bottle.2.tar.gz
==> Pouring clang-omp-2015-04-01.yosemite.bottle.2.tar.gz
🍺  /usr/local/Cellar/clang-omp/2015-04-01: 1396 files, 378M
JB-MacBook:local james$ brew test clang-omp
Testing clang-omp
==> /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp -liomp5 -fopenmp test.c -o test

test.c:3:10: fatal error: 'omp.h' file not found
#include <omp.h>
         ^
1 error generated.
acError: clang-omp: failed
Failed executing: /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp -liomp5 -fopenmp test.c -o test
/usr/local/Library/Homebrew/formula.rb:885:in `block in system'
/usr/local/Library/Homebrew/formula.rb:842:in `open'
/usr/local/Library/Homebrew/formula.rb:842:in `system'
/usr/local/Library/Formula/clang-omp.rb:76:in `block in <class:ClangOmp>'
/usr/local/Library/Homebrew/formula.rb:785:in `block in run_test'
/usr/local/Library/Homebrew/extend/fileutils.rb:17:in `mktemp'
/usr/local/Library/Homebrew/formula.rb:781:in `run_test'
/usr/local/Library/Homebrew/test.rb:28:in `block in <main>'
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/lib/ruby/2.0.0/timeout.rb:66:in `timeout'
/usr/local/Library/Homebrew/test.rb:27:in `<main>'

Did you mean something else?

@xu-cheng
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xu-cheng commented Jun 5, 2015

Ok in this case, can you try reinstall libiomp? Both of formulae have been updated some time ago. I suspect you may install a old version for one of them.

@jamesblackburn
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I only recently installed brew for this package, so it's all new for -- I don't think it's a stale package issue. I'm on Yosemite with the latest Xcode.

(arctic)JB-MacBook:arctic james$ brew remove libiomp
Uninstalling /usr/local/Cellar/libiomp/20150401... (8 files, 548K)
(arctic)JB-MacBook:arctic james$ brew install libiomp
==> Downloading https://homebrew.bintray.com/bottles/libiomp-20150401.yosemite.bottle.tar.gz
Already downloaded: /Library/Caches/Homebrew/libiomp-20150401.yosemite.bottle.tar.gz
==> Pouring libiomp-20150401.yosemite.bottle.tar.gz
🍺  /usr/local/Cellar/libiomp/20150401: 8 files, 548K
(arctic)JB-MacBook:arctic james$ brew test clang-omp
Testing clang-omp
==> /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp -liomp5 -fopenmp test.c -o test

test.c:3:10: fatal error: 'omp.h' file not found
...

@xu-cheng
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xu-cheng commented Jun 5, 2015

Can you paste the output of brew config and brew doctor?

@jamesblackburn
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Attached below... I notice a complaint about pig-config -- I wonder if that's the issue!
(The warning about GCC is probably less important as I'm installing that in another terminal in the hope I can use that...)

(arctic)JB-MacBook:arctic james$ brew config
HOMEBREW_VERSION: 0.9.5
ORIGIN: https://github.com/Homebrew/homebrew
HEAD: 0099e5e5da718a4608fe78f0b9a5d34068308059
Last commit: 6 days ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: quad-core 64-bit broadwell
OS X: 10.10.3-x86_64
Xcode: 6.3.2
CLT: N/A
Clang: 6.1 build 602
MacPorts/Fink: /opt/local/bin/port, /sw/bin/fink
X11: 2.7.7 => /opt/X11
System Ruby: 2.0.0-p481
Perl: /opt/local/bin/perl => /opt/local/bin/perl5.12
Python: /Users/james/pyenvs/arctic/bin/python
Ruby: /usr/bin/ruby
Java: 1.8.0_25
(arctic)JB-MacBook:arctic james$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Broken symlinks were found. Remove them with `brew prune`:
  /usr/local/etc/pkcs11/pkcs11.conf.example
  /usr/local/lib/pkgconfig/geoip.pc
  /usr/local/lib/pkgconfig/gio-2.0.pc
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  /usr/local/lib/pkgconfig/gmodule-no-export-2.0.pc
  /usr/local/lib/pkgconfig/gnutls.pc
  /usr/local/lib/pkgconfig/gobject-2.0.pc
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  /usr/local/lib/pkgconfig/hogweed.pc
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  /usr/local/share/locale/zh_CN/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/zh_HK/LC_MESSAGES/glib20.mo
  /usr/local/share/locale/zh_TW/LC_MESSAGES/glib20.mo
  /usr/local/Library/LinkedKegs/autoconf
  /usr/local/Library/LinkedKegs/automake
  /usr/local/Library/LinkedKegs/boost
  /usr/local/Library/LinkedKegs/geoip
  /usr/local/Library/LinkedKegs/glib
  /usr/local/Library/LinkedKegs/gnutls
  /usr/local/Library/LinkedKegs/libgcrypt
  /usr/local/Library/LinkedKegs/libgpg-error
  /usr/local/Library/LinkedKegs/libtasn1
  /usr/local/Library/LinkedKegs/libtool
  /usr/local/Library/LinkedKegs/nettle
  /usr/local/Library/LinkedKegs/p11-kit
  /usr/local/Library/LinkedKegs/pkg-config
  /usr/local/Library/LinkedKegs/wireshark
  /usr/local/Library/LinkedKegs/xz

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:

  /opt/local/bin/apr-1-config
  /opt/local/bin/apu-1-config
  /opt/local/bin/curl-config
  /opt/local/bin/freetype-config
  /opt/local/bin/krb5-config
  /opt/local/bin/libpng-config
  /opt/local/bin/libpng15-config
  /opt/local/bin/ncurses5-config
  /opt/local/bin/ncursesw5-config
  /opt/local/bin/neon-config
  /opt/local/bin/pcre-config
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  /opt/local/bin/python2-config
  /opt/local/bin/python2.5-config
  /opt/local/bin/python2.7-config
  /opt/local/bin/xml2-config
  /sw/bin/apt-config
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  /sw/bin/gdlib-config
  /sw/bin/glib-config
  /sw/bin/libpng-config
  /sw/bin/libpng12-config
  /sw/bin/libusb-config
  /sw/bin/libwww-config
  /sw/bin/netpbm-config
  /sw/bin/octave-config
  /sw/bin/pdflib-config
  /sw/bin/pkg-config

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This can cause trouble. You don't have to uninstall them, but you may want to
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Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libflickcurl.0.dylib
    /usr/local/lib/libMonoPosixHelper.dylib
    /usr/local/lib/librtmp.dylib
    /usr/local/lib/libSFFileMonitor.32.dylib
    /usr/local/lib/libSFIPC.32.dylib
    /usr/local/lib/libSFIPC.I.dylib
    /usr/local/lib/libSFsqlite3.7.4.dylib
    /usr/local/lib/libSFSyncEngine.I.dylib
    /usr/local/lib/libumem.0.0.0.dylib
    /usr/local/lib/libumem_malloc.0.0.0.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
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Unexpected header files:
    /usr/local/include/flickcurl.h
    /usr/local/include/node/ares.h
    /usr/local/include/node/ares_version.h
    /usr/local/include/node/eio-emul.h
    /usr/local/include/node/ev-emul.h
    /usr/local/include/node/node.h
    /usr/local/include/node/node_buffer.h
    /usr/local/include/node/node_object_wrap.h
    /usr/local/include/node/node_version.h
    /usr/local/include/node/uv-private/eio.h
    /usr/local/include/node/uv-private/ev.h
    /usr/local/include/node/uv-private/ngx-queue.h
    /usr/local/include/node/uv-private/tree.h
    /usr/local/include/node/uv-private/uv-unix.h
    /usr/local/include/node/uv-private/uv-win.h
    /usr/local/include/node/uv.h
    /usr/local/include/node/v8-debug.h
    /usr/local/include/node/v8-preparser.h
    /usr/local/include/node/v8-profiler.h
    /usr/local/include/node/v8-testing.h
    /usr/local/include/node/v8.h
    /usr/local/include/node/v8stdint.h
    /usr/local/include/sys/vmem.h
    /usr/local/include/umem.h

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Unexpected static libraries:
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    /usr/local/lib/libumem.a
    /usr/local/lib/libumem_malloc.a

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Error: Failed to import: scantailor
version '{"0.9.11"=>Formulary::Formulae::Scantailor::Version}' should be a string

Warning: Your Homebrew is outdated.
You haven't updated for at least 24 hours. This is a long time in brewland!
To update Homebrew, run `brew update`.

@jamesblackburn
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it's not pkg-config:

(arctic)JB-MacBook:arctic james$ export PATH=/usr/local/bin/:$PATH
(arctic)JB-MacBook:arctic james$ which pkg-config
/usr/local/bin//pkg-config
(arctic)JB-MacBook:arctic james$ brew test clang-omp
Testing clang-omp
==> /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp -liomp5 -fopenmp test.c -o test

test.c:3:10: fatal error: 'omp.h' file not found
#include <omp.h>

@tdsmith
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tdsmith commented Jun 5, 2015

Can you pass -v when you try and build the example to see what the include search path is?

@jamesblackburn
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(arctic)JB-MacBook:arctic james$ /usr/local/Cellar/clang-omp/2015-04-01/bin/clang-omp -v test.c
clang version 3.5.0 
Target: x86_64-apple-darwin14.3.0
Thread model: posix
 "/usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/clang-3.5" -cc1 -triple x86_64-apple-macosx10.10.0 -emit-obj -mrelax-all -disable-free -main-file-name test.c -mrelocation-model pic -pic-level 2 -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -v -dwarf-column-info -resource-dir /usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/../lib/clang/3.5.0 -fdebug-compilation-dir /Users/james/Projects/arctic -ferror-limit 19 -fmessage-length 134 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.10.0 -fencode-extended-block-signature -fdiagnostics-show-option -fcolor-diagnostics -o /var/folders/nv/854ddzmx43z7g6qm0m4p2bh80000gn/T/test-e88e22.o -x c test.c
clang -cc1 version 3.5.0 based upon LLVM 3.5.0svn default target x86_64-apple-darwin14.3.0
ignoring nonexistent directory "/usr/local/Cellar/clang-omp/2015-04-01/libexec/usr/include"
ignoring nonexistent directory "/usr/include"
#include "..." search starts here:
#include <...> search starts here:
 /usr/local/include
 /usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/../lib/clang/3.5.0/include
 /usr/local/opt/libiomp/include/libiomp
 /usr/local/Cellar/clang-omp/2015-04-01/libexec/include/c++/v1
 /System/Library/Frameworks (framework directory)
 /Library/Frameworks (framework directory)
End of search list.
test.c:1:10: fatal error: 'stdio.h' file not found
#include <stdio.h>

@jamesblackburn jamesblackburn mentioned this issue Jun 16, 2015
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@AdrianTeng AdrianTeng mentioned this issue Jul 13, 2015
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@ghost
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ghost commented Jul 26, 2015

Try xcode-select --install in terminal.

@luisremis
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Thanks @continuedstory! That solved my issue!

@apjanke apjanke modified the milestone: Clear out Legacy May 3, 2016
@arunsrinivasan arunsrinivasan mentioned this issue May 6, 2016
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@MikeMcQuaid
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This formula was removed.

@Homebrew Homebrew locked and limited conversation to collaborators Aug 18, 2016
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