HDF5 1.8.12 test is segfaulting with ifort 14.0.1

valery_w_ — Wed, 04 Dec 2013 10:09:31 GMT

Dear All

HDF5 1.8.12 segfault with ifort 14.0.1 (worked fine with 13.1.2). The tests fortranlib_test_F03 (segfault see bellow) and fortranlib_test (not shown) dont work properly.

The conf and compilation steps are:

ifort -V
Intel(R) Fortran Intel(R) 64 Compiler XE for applications running on Intel(R) 64, Version 14.0.1.106 Build 20131008
Copyright (C) 1985-2013 Intel Corporation. All rights reserved.
FOR NON-COMMERCIAL USE ONLY

wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.12.tar.gz

tar xvfz hdf5-1.8.12.tar.gz

mkdir tmp

cd tmp

../hdf5-1.8.12/configure --prefix=/home/vwe/libs/hdf5/1.8.12-intel-14.0.1 --enable-fortran --enable-fortran2003 --enable-static-execs=yes --enable-shared=no CC=icc FC='ifort -O0 -g -traceback'

[...]

make -j 4

[...]

cd fortran/test

./fortranlib_test_F03
                        ==============================
                              FORTRAN 2003 tests
                        ==============================
FORTRANLIB_TEST is linked with HDF5 Library version 1.8 release 12

Testing 1-D Array of Compound Datatypes Functionality                  PASSED
Testing 1-D Array of Compound Array Datatypes Functionality            PASSED
Testing 3-D array by dataset, using C_LOC                              PASSED
Testing writing/reading enum dataset, using C_LOC                      PASSED
Testing enumeration conversions                                        PASSED
Testing writing/reading bitfield dataset, using C_LOC                  PASSED
Testing writing/reading opaque datatypes, using C_LOC                  PASSED
Testing writing/reading object references, using C_LOC                 PASSED
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source
fortranlib_test_F 000000000071AED9 Unknown               Unknown Unknown
fortranlib_test_F 0000000000719850 Unknown               Unknown Unknown
fortranlib_test_F 00000000006D75C2 Unknown               Unknown Unknown
fortranlib_test_F 00000000006A7FE3 Unknown               Unknown Unknown
fortranlib_test_F 00000000006AB9AB Unknown               Unknown Unknown
libpthread.so.0    0000003FC900F000 Unknown               Unknown Unknown
fortranlib_test_F 0000000000430A9C Unknown               Unknown Unknown
fortranlib_test_F 0000000000425A8D h5s_mp_h5sselect_        1332 H5Sff.f90
fortranlib_test_F 0000000000419624 t_regref_                2028 tH5T_F03.f90
fortranlib_test_F 00000000004042BD MAIN__                     96 fortranlib_test_F03.f90
fortranlib_test_F 0000000000403F76 Unknown               Unknown Unknown
libc.so.6          0000003FC8C21A05 Unknown               Unknown Unknown
fortranlib_test_F 0000000000403E69 Unknown               Unknown Unknown

I have had nothing but

Casey — Thu, 05 Dec 2013 06:46:18 GMT

I have had nothing but problems with hdf5 1.8.x compile with the 14.x versions of ifort. My problems vary from test-cases never finishing and exhausting memory to corrupt output in production code. There is a thread a month or two old that goes into a bit more detail, but never received much attention. I've gone back to gfortran until ifort can remember how to compile hdf5.

This was probably caused by

Michael_B_10 — Thu, 18 Dec 2014 16:22:33 GMT

This was probably caused by this bug in the Intel Fortran compiler:

https://software.intel.com/en-us/forums/topic/498698

which they fixed. But alas, Version 15.0 again breaks HDF5 when the --enable-fortran2003 option is specified...*sigh*.

I'll update the 15.0 situation in another thread.

topic I have had nothing but in Intel® Fortran Compiler

HDF5 1.8.12 test is segfaulting with ifort 14.0.1

I have had nothing but

This was probably caused by