Hi, I found something else (I know, I should stop :)). I am not entirely sure but it seems that when H5detect fails it writes "unable to calculate alignment for long double" on stderr so this message should be observable on build logs (although buried by other warnings). The packages on debian sid and testing for both i386 and x86-64 seem to be affected:
https://buildd.debian.org/status/fetch.php?pkg=hdf5&arch=amd64&ver=1.8.11-3%2Bb1&stamp=1377024563 https://buildd.debian.org/status/fetch.php?pkg=hdf5&arch=i386&ver=1.8.11-3%2Bb1&stamp=1377025110 But here's the exciting part: look what I found http://www.unidata.ucar.edu/mailing_lists/archives/gembud/2010/msg00052.html It's a build log from 2010 for HDF5 v1.6.5 and gcc-4.4.3 that says "unable to calculate alignment for long double". If my understanding is correct, nor 1.8.11 or gcc 4.8.0 would be the problem and it would be that piece of code just doesn't work properly. Best wishes, Andrea On 4 September 2013 08:00, Andrea Bedini <andrea.bed...@gmail.com> wrote: > Hi Ray, > > thanks for giving it a look. Antonio made me notice that something else > might be at work since the macro DETECT_F already zeroes the structure > right before anything else: > > memset(&INFO, 0, sizeof(INFO)); #L299 > > so I don't understand how the perm fields need to be zeroed again around > line #L308. This still considering the "Byte Order" loop as a black box. > > As a side question: isn't there a more portable way of doing this? I am > pretty sure H5detect.c might invoke a bunch of undefined behaviours given > the amount of warning the compiler generates and of bit trickery. > > Best wishes, > Andrea > > > > > On 4 September 2013 05:43, Raymond Lu <songy...@hdfgroup.org> wrote: > >> Andrea, >> >> We've verified that your solution is correct. We're putting your fix >> into the library. Thanks for helping us. >> >> Ray >> >> On Sep 3, 2013, at 3:32 AM, Andrea Bedini wrote: >> >> Hi there, >> >> I think I have found the problem. The issue is in H5detect.c. >> Macros DETECT_F and DETECT_I do not initialize properly the perm field in >> the detected_t struct. As a result the routine fix_order is passed some >> uninitialized memory which makes it fail. I have a small patch against >> H5detect.c which fixes the problem by simply initializing the perm field >> with zeros. Valgrind's tool memcheck would have exposed the problem. >> >> Best wishes, >> Andrea >> >> >> >> On 3 September 2013 15:30, Andrea Bedini <andrea.bed...@gmail.com> wrote: >> >>> Hi, >>> >>> I am experiencing the following issue with hdf5 and gcc 4.8.0 >>> >>> Consider this very simple test >>> >>> #include <hdf5.h> >>> >>> int main() { >>> switch (H5Tget_order(H5T_NATIVE_LDOUBLE)) { >>> case H5T_ORDER_LE: >>> printf("H5Tget_order(H5T_NATIVE_LDOUBLE) = H5T_ORDER_LE\n"); >>> break; >>> case H5T_ORDER_BE: >>> printf("H5Tget_order(H5T_NATIVE_LDOUBLE) = H5T_ORDER_BE\n"); >>> break; >>> case H5T_ORDER_VAX: >>> printf("H5Tget_order(H5T_NATIVE_LDOUBLE) = H5T_ORDER_VAX\n"); >>> break; >>> case H5T_ORDER_MIXED: >>> printf("H5Tget_order(H5T_NATIVE_LDOUBLE) = H5T_ORDER_MIXED\n"); >>> break; >>> case H5T_ORDER_NONE: >>> printf("H5Tget_order(H5T_NATIVE_LDOUBLE) = H5T_ORDER_NONE\n"); >>> break; >>> default: >>> printf("here are dragons\n"); >>> } >>> return 0; >>> } >>> >>> on the same x86_64 GNU/Linux machine I get >>> >>> $ hdf5-1.8.11-gcc-4.7.0/my_test # compiled with gcc 4.7.0 >>> H5Tget_order(H5T_NATIVE_LDOUBLE) = H5T_ORDER_LE >>> >>> $ hdf5-1.8.11-gcc-4.8.0/my_test # compiled with gcc 4.8.0 >>> H5Tget_order(H5T_NATIVE_LDOUBLE) = H5T_ORDER_VAX >>> >>> So H5T_NATIVE_LDOUBLE is mis-detected. I tried to dig deeper and >>> basically the fault must be in src/H5detect.c which is used to generate the >>> definitions in src/H5Tinit.c >>> I could not figure out what H5detect.c does wrong (it is not very >>> readable, given its extensive use of macros) but the compiler does emit a >>> lot of warnings (see https://gist.github.com/andreabedini/6419975). >>> >>> I think this must be related to the failure of dt_arith long double test >>> observed recently. >>> >>> Any suggestion on how to fix this ? >>> >>> Best wishes, >>> Andrea >>> >>> >>> -- >>> Andrea Bedini <andrea.bed...@gmail.com> >>> >> >> >> >> -- >> Andrea Bedini <andrea.bed...@gmail.com> >> <hdf5_uninitialized.patch>_______________________________________________ >> Hdf-forum is for HDF software users discussion. >> Hdf-forum@lists.hdfgroup.org >> >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> Hdf-forum@lists.hdfgroup.org >> >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> >> > > > -- > Andrea Bedini <andrea.bed...@gmail.com> > -- Andrea Bedini <andrea.bed...@gmail.com>
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