Hello Kyle,
I'm having the same problem, not only in Scientific Linux 6.4, but also
on Fedora 19.
First I thought that it was related to the fact that I was using both
distributions on virtual machine (Virtual Box).
I got to compile everything fine ONCE, after re-installing Scientific
Linux, but since then, the same error happens all the time and I was
unable to reproduce the "success".
I figured out what is the problem, but not the cause of it.
First, with some changes in the makefile to create a trace, I get this.
============================
Fortran API: fortranlib_test Test Log
============================
==========================
FORTRAN tests
==========================
FORTRANLIB_TEST is linked with HDF5 Library version 1.8 release 11
Mounting test PASSED
Reopen test PASSED
File open/close test
PASSED
File free space test
PASSED
Dataset test PASSED
Extendible dataset test
PASSED
Basic dataspace test
PASSED
Reference to object test
PASSED
Reference to dataset region test
PASSED
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
lt-fortranlib_tes 000000000049BC99 Unknown Unknown Unknown
lt-fortranlib_tes 000000000049A610 Unknown Unknown Unknown
lt-fortranlib_tes 00000000004703C2 Unknown Unknown Unknown
lt-fortranlib_tes 00000000004562D3 Unknown Unknown Unknown
lt-fortranlib_tes 000000000042C95B Unknown Unknown Unknown
libpthread.so.0 0000003B1C40EFA0 Unknown Unknown Unknown
libhdf5_fortran.s 00007FB43829BAAC h5sselect_hypersl 993 H5Sf.c
libhdf5_fortran.s 00007FB43828F547 h5s_mp_h5sselect_ 1332 H5Sff.f90
lt-fortranlib_tes 000000000041EC68 test_basic_select 905
tH5Sselect.f90
lt-fortranlib_tes 000000000040D567 MAIN__ 129
fortranlib_test.f90
lt-fortranlib_tes 000000000040D1B6 Unknown Unknown Unknown
libc.so.6 0000003B1BC21B75 Unknown Unknown Unknown
lt-fortranlib_tes 000000000040D0A9 Unknown Unknown Unknown
Than, with some more tests, I found that the soubroutine
nh5sselect_hyperslab_c, during the test that causes the SIGSEGV, is
being called twice, but shouldn't (at least I think). The second time it
is executed (a thread problem?) , the "stride" array is not defined,
causing the error.
I tried to use the --disable-production and a new error happened, this
time when testing the C library:
============================
Testing testhdf5
============================
testhdf5 Test Log
============================
For help use: /home/user/Work/hdf5-1.8.11/test/.libs/lt-testhdf5 -help
Linked with hdf5 version 1.8 release 11
Testing -- Configure definitions (config)
Testing -- Encoding/decoding metadata (metadata)
Testing -- Checksum algorithm (checksum)
Testing -- Ternary Search Trees (tst)
Testing -- Memory Heaps (heap)
Testing -- Skip Lists (skiplist)
Testing -- Reference Counted Strings (refstr)
Testing -- Low-Level File I/O (file)
Testing -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
Testing -- Attributes (attr)
Testing -- Selections (select)
Testing -- Time Datatypes (time)
Testing -- References (reference)
Testing -- Variable-Length Datatypes (vltypes)
Testing -- Variable-Length Strings (vlstrings)
Testing -- Group & Attribute Iteration (iterate)
Testing -- Array Datatypes (array)
Testing -- Generic Properties (genprop)
Testing -- UTF-8 Encoding (unicode)
Testing -- User-Created Identifiers (id)
Testing -- Miscellaneous (misc)
*** UNEXPECTED VALUE from H5Gopen2 should be -1, but is 33554432 at line
4935 in tmisc.c
!!! 1 Error(s) were detected !!!
So... Seems that something is not working here...
I'm assuming that probably is something with the intel fortran 14...
For example, --enable-fortran2003 do not works for sure with intel
fortran 14...
Em 06-11-2013 20:16, kyle kanos escreveu:
On my University's cluster, I've built HDF5 1.8.7 using the Intel
11.1 and Intel 12.0 suites without any issue. On my personal computer,
running Scientific Linux 6.4, I have Intel 14.0 and cannot built
either 1.8.7 or 1.8.11. On both versions, I get the same error under
the Fortran tests. I compile it with zlib, and properly exporting the
Intel compilers (export CC=icc && export FC=ifort && export FCC=icpc),
using
$> ./configure --enable-fortran --with-zlib=/usr/local/zlib-1.8.7
I have also tried different permutations involving --enable-cxx,
--disable-shared, and removing the --with-zlib flags, but nothing has
changed the SIGSEGV error I get:
==========================
FORTRAN tests
==========================
FORTRANLIB_TEST is linked with HDF5 Library version 1.8 release 11
Mounting test PASSED
Reopen test PASSED
File open/close test PASSED
File free space test PASSED
Dataset test PASSED
Extendible dataset test PASSED
Basic dataspace test PASSED
Reference to object test PASSED
Reference to dataset region test PASSED
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
fortranlib_test 0000000000713379 Unknown Unknown Unknown
fortranlib_test 0000000000711CF0 Unknown Unknown Unknown
fortranlib_test 00000000006E7AA2 Unknown Unknown Unknown
fortranlib_test 00000000006CD9B3 Unknown Unknown Unknown
fortranlib_test 00000000006A403B Unknown Unknown Unknown
libpthread.so.0 0000003CBDC0F500 Unknown Unknown Unknown
fortranlib_test 000000000043676C Unknown Unknown Unknown
fortranlib_test 0000000000429D3D Unknown Unknown Unknown
fortranlib_test 0000000000417B0B Unknown Unknown Unknown
fortranlib_test 0000000000404CEC Unknown Unknown Unknown
fortranlib_test 00000000004048D6 Unknown Unknown Unknown
libc.so.6 0000003CBD41ECDD Unknown Unknown Unknown
fortranlib_test 00000000004047C9 Unknown Unknown Unknown
I have zero issues if I install this using the gcc compilers, but my
code needs the Intel compilers. Is this an error related to the newer
version of the Intel compiler, or is this something that I've done wrong?
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