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

Closed jamesblackburn closed 8 years ago

jamesblackburn commented 9 years ago

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 commented 9 years ago

Does reinstall clang-omp do any help?

jamesblackburn commented 9 years ago

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 commented 9 years ago

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 commented 9 years ago

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 commented 9 years ago

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

jamesblackburn commented 9 years ago

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`:
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  /usr/local/Library/LinkedKegs/pkg-config
  /usr/local/Library/LinkedKegs/wireshark
  /usr/local/Library/LinkedKegs/xz

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jamesblackburn commented 9 years ago

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 commented 9 years ago

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

jamesblackburn commented 9 years ago 
(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>
ghost commented 9 years ago

Try xcode-select --install in terminal.

luisremis commented 8 years ago

Thanks @ContinuedStory! That solved my issue!

MikeMcQuaid commented 8 years ago

This formula was removed.