Include issue with time.h/features.h in debian-7 image

[Chris Whittleston]

Hey compute engine folks, I was hoping I could get some help with an issues I've encountered with the debian-7 image. This is the compilation error itself:

In file included from /usr/include/time.h:28:0,

                 from wallclock.c:12:

/usr/include/features.h:323:26: fatal error: bits/predefs.h: No such file or directory

compilation terminated.

Looking into this - features.h includes predefs.h like this:

/* Define __STDC_IEC_559__ and other similar macros.  */

#include <bits/predefs.h>

The problem is that this path is incorrect - predefs is actually in /usr/include/x86_64-linux-gnu/bits. I'm looking for the best way to solve this issue, but am wondering if I should need to. Surely the image should be set up to not have internal include path issues like this? 

I'm hoping setting C_INCLUDE_PATH and CPLUS_INCLUDE_PATH to include /usr/include/x86_64-linux-gnu the will fix my issue? I'd appreciate some advice from someone who knows more about this sort of stuff :)

Thanks,

Chris

[Google Compute Engine Team]

Hi,

GCC should by default include /usr/include/x86_64-linux-gnu on a debian system. Google Compute Engine does not make any changes in this area so this issue is not caused by running on GCE. If you run "gcc -xc -E -v -" you should see the include directories in the output.

Do you have a custom build system that is disabling default includes? Could you include the GCC command that is causing this error?

On a fresh instance based on debian-7-wheezy-v20140415:

dnewgas@dnewgas-test-2:~$ sudo aptitude install gcc

...

dnewgas@dnewgas-test-2:~$ gcc -xc -E -v -

Using built-in specs.

COLLECT_GCC=gcc

Target: x86_64-linux-gnu

Configured with: ../src/configure -v --with-pkgversion='Debian 4.7.2-5' --with-bugurl=file:///usr/share/doc/gcc-4.7/README.Bugs --enable-languages=c,c++,go,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.7 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.7 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --with-arch-32=i586 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu

Thread model: posix

gcc version 4.7.2 (Debian 4.7.2-5) 

COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64'

 /usr/lib/gcc/x86_64-linux-gnu/4.7/cc1 -E -quiet -v -imultiarch x86_64-linux-gnu - -mtune=generic -march=x86-64

ignoring nonexistent directory "/usr/local/include/x86_64-linux-gnu"

ignoring nonexistent directory "/usr/lib/gcc/x86_64-linux-gnu/4.7/../../../../x86_64-linux-gnu/include"

#include "..." search starts here:

#include <...> search starts here:

 /usr/lib/gcc/x86_64-linux-gnu/4.7/include

 /usr/local/include

 /usr/lib/gcc/x86_64-linux-gnu/4.7/include-fixed

 /usr/include/x86_64-linux-gnu

 /usr/include

End of search list.

^C

dnewgas@dnewgas-test-2:~$ cat > test.c

#include <time.h>

int main(){return 0;}

dnewgas@dnewgas-test-2:~$ gcc test.c

dnewgas@dnewgas-test-2:~$ ./a.out 

dnewgas@dnewgas-test-2:~$

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[Chris Whittleston]

Thanks for getting back to me.

I've checked my include paths using the command you suggested and I do indeed have that directory included. Here is some more detail of the build - I'm trying to compile a version of the AMBER molecular mechanics package (http://ambermd.org/) which is a mix of C and Fortran90.

When I initially tried to compile, I got the following error from wallclock.c:

gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32  -o wallclock.o wallclock.c

wallclock.c:12:22: fatal error: sys/time.h: No such file or directory

compilation terminated.

I bypassed this by making the following change in wallclock.c:

Old

#include <sys/time.h>

New

#include <time.h>

After this, the error changes to:

gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32  -o wallclock.o wallclock.c

In file included from /usr/include/time.h:28:0,

                 from wallclock.c:12:

/usr/include/features.h:323:26: fatal error: bits/predefs.h: No such file or directory

compilation terminated.

This is the original error I posted. Does anything here jump out at you?

Best,

Chris

[Google Compute Engine Team]

Hello,

This is somewhat out of scope of Google Compute Engine as I believe you are having an issue with AMBER's build system. I suggest you see if that project has any advice for you.

The only pointer I can give you is that "-m32" is directing gcc to generate 32 bit code. The x86_64-linux-gnu  directory is for 64 bit specific headers.  You may need to install a full 32 bit build system or direct AMBER to build in 64 bit.

To view this discussion on the web visit https://groups.google.com/d/msgid/gce-discussion/10097b27-4d5b-4b00-8de7-a77d3dd3712d%40googlegroups.com.

[Chris Whittleston]

Thanks - the 32/64 bit mismatch seems like a good place to start the debugging. There are a few ex AMBER developers in my building so I might grab one of them tomorrow to pick their brains.

Since my initial post, I've managed to get it compiling and running using cmake, so happily I can continue my benchmarking while I look into the gcc issue.

Thanks again for the responses.

Chris