<div dir="ltr">Hi Ian,<div><br></div><div>I have elected to get the development version and have successfully done a build only changing the osx-macports.cfg to replace the default HDF5 = line to HDF5 = BUILD, as you suggested earlier today. I am now running the static-tov test and see the beginning of reasonable output with the plots of rho max and alp looking ok. </div><div><br></div><div>Thanks for the help from you Erik, Roberto, and Frank. Should the macports version of HDF5 work compatibly with Cactus please let me know. </div><div><br></div><div>Best regards,</div><div><br></div><div>Comer</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sat, May 23, 2015 at 1:06 PM, Ian Hinder <span dir="ltr"><<a href="mailto:ian.hinder@aei.mpg.de" target="_blank">ian.hinder@aei.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><br><div><span class=""><div>On 23 May 2015, at 05:08, Erik Schnetter <<a href="mailto:schnetter@cct.lsu.edu" target="_blank">schnetter@cct.lsu.edu</a>> wrote:</div><br><blockquote type="cite"><div dir="ltr">On Fri, May 22, 2015 at 12:38 PM, Ian Hinder <span dir="ltr"><<a href="mailto:ian.hinder@aei.mpg.de" target="_blank">ian.hinder@aei.mpg.de</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><br><div><span><div>On 22 May 2015, at 18:34, Ian Hinder <<a href="mailto:ian.hinder@aei.mpg.de" target="_blank">ian.hinder@aei.mpg.de</a>> wrote:</div><br><blockquote type="cite"><div style="word-wrap:break-word"><br><div><div>On 22 May 2015, at 16:10, Roberto De Pietri <<a href="mailto:roberto.depietri@unipr.it" target="_blank">roberto.depietri@unipr.it</a>> wrote:</div><br><blockquote type="cite">Hi Ian:<br><br><br>Thanks for the answer. I followed exactly your procedure and I was very surprised of having<br>a failing compilation. Than I starting tracing back the problem. <br>* All the thorns except one were compiling correctly.<br>* The failing thorn was CarpetIOHDF5 and of the 5 source files present only 3 failed<br>* The error was very strange because the only real problem was related to <br> a system include “/opt/local/lib/gcc49/gcc/x86_64-apple-darwin14/4.9.2/include/mmintrin.h”<br> and was related to conversion using AVX intel intrinsic. The error were of the type:<br><br> error: can’t convert between vector values of different size<br> return (__m64) __builtin_ia32_vec_init_v2si (__i, 0);<br></blockquote><div><br></div><div>There is a stackoverflow post (<a href="http://stackoverflow.com/questions/19043109/gcc-4-8-1-combining-c-code-with-c11-code" target="_blank">http://stackoverflow.com/questions/19043109/gcc-4-8-1-combining-c-code-with-c11-code</a> ) 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.</div></div></div></blockquote></span></div></div></blockquote><div>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.</div><div><br></div><div>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.</div><div><br></div><div>I would try adding the line</div><div><br></div><div>#undef __attribute__</div><div><br></div><div>right after (below) any line that says</div><div><br></div><div>#include <hdf5.h></div><div><br></div><div>to undo (part of) the damage that HDF5 does. We should also complain to the HDF5 authors.</div></div></div></div></blockquote><div><br></div></span><div>So to summarise:</div><div><br></div><div><span style="white-space:pre-wrap"> </span>– HDF5 is undefining __attribute__, and this is a bug in hdf5. </div><div><span style="white-space:pre-wrap"> </span>– In the stack overflow post, argp.h is undefining __attribute__, so this is a bug in glibc</div><div><br></div><div>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.</div><div><br></div><div>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 (<a href="https://trac.macports.org/log/trunk/dports/science/hdf5/Portfile" target="_blank">https://trac.macports.org/log/trunk/dports/science/hdf5/Portfile</a>), 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.</div><div><br></div><div>The responsible commit in HDF5 seems to be this one:</div><div><br></div><div><span style="white-space:pre-wrap"> </span><a href="https://github.com/live-clones/hdf5/commit/b283f087e32fb99023650240ef8290a3f46319c5" target="_blank">https://github.com/live-clones/hdf5/commit/b283f087e32fb99023650240ef8290a3f46319c5</a></div><div><br></div><div>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? </div><div><br></div><div>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. </div><span class="HOEnZb"><font color="#888888"><div><br></div><div>-- </div></font></span></div><span class="HOEnZb"><font color="#888888"><div><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div>Ian Hinder</div><div><a href="http://members.aei.mpg.de/ianhin" target="_blank">http://members.aei.mpg.de/ianhin</a></div></div></div></div></div>
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