On 23 May 2015, at 05:08, Erik Schnetter <[email protected]> wrote:
> On Fri, May 22, 2015 at 12:38 PM, Ian Hinder <[email protected]> wrote: > > On 22 May 2015, at 18:34, Ian Hinder <[email protected]> wrote: > >> >> On 22 May 2015, at 16:10, Roberto De Pietri <[email protected]> >> wrote: >> >>> Hi Ian: >>> >>> >>> Thanks for the answer. I followed exactly your procedure and I was very >>> surprised of having >>> a failing compilation. Than I starting tracing back the problem. >>> * All the thorns except one were compiling correctly. >>> * The failing thorn was CarpetIOHDF5 and of the 5 source files present only >>> 3 failed >>> * The error was very strange because the only real problem was related to >>> a system include >>> “/opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2/include/mmintrin.h” >>> and was related to conversion using AVX intel intrinsic. The error were of >>> the type: >>> >>> error: can’t convert between vector values of different size >>> return (__m64) __builtin_ia32_vec_init_v2si (__i, 0); >> >> There is a stackoverflow post >> (http://stackoverflow.com/questions/19043109/gcc-4-8-1-combining-c-code-with-c11-code >> ) which describes a similar problem, which I haven't studied in depth, but >> they seem to suggest that it's a bug in gcc, and that setting --std=gnu++11 >> instead of --std=c++11 in CXXFLAGS will work around the problem. > > Yes, it seems that this describes the problem we're having. GCC uses > __attribute__ to provide certain language extensions, e.g. for vectorization. > These are not optional declarations -- these modify function definition and > can't just be omitted. > > And HDF5 does just that: it #defines __attribute__ to be empty (file > H5api_adpt.h, near the beginning) if the file is included from C++. I have no > idea why they would think this is legal, or why they would think this is even > a good idea. We use __attribute__ in Cactus (after checking via autoconf > whether it is supported) for a variety of optimizations and security checks. > > I would try adding the line > > #undef __attribute__ > > right after (below) any line that says > > #include <hdf5.h> > > to undo (part of) the damage that HDF5 does. We should also complain to the > HDF5 authors. So to summarise: – HDF5 is undefining __attribute__, and this is a bug in hdf5. – In the stack overflow post, argp.h is undefining __attribute__, so this is a bug in glibc Is that correct? My suggestion to try --std=gnu++11 in CXXFLAGS won't fix the problem in the HFD5 header; it would only affect the argp.h problem, which doesn't apply to us. Digging a bit deeper, it seems that we have been bitten (again) by trying to track a moving target. The HDF5 MacPorts port was updated from 1.8.14 to 1.8.15 on 16-May-2015 (https://trac.macports.org/log/trunk/dports/science/hdf5/Portfile), 2 days before the ET release, and after the release branches had been created and the final testing had been done. Note that this also happened with OpenMPI a few days before, introducing a critical regression which we were able to work around in time. The responsible commit in HDF5 seems to be this one: https://github.com/live-clones/hdf5/commit/b283f087e32fb99023650240ef8290a3f46319c5 They were previously undefining __attribute__ only in H5private.h, which is included by hdf5 source files, but not from the public api used by user code, and this commit moves this definition into a public header file included by user code. Erik, do you want to contact the developers, since you understand this better than I do? I think the most sensible workaround for us would be set HDF5_DIR = BUILD in osx-macports.cfg, since the current macports version is broken. MacPorts has a single tree, they don't split into stable and unstable branches, presumably due to lack of resources. The same is true of homebrew; presumably they will also update to 1.8.15 at some point, so maybe we should build HDF5 for homebrew as well. The Cactus-provided version in ExternalLibraries is 1.8.14. -- Ian Hinder http://members.aei.mpg.de/ianhin
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