[FLASH-USERS] Segfault in libhdf5 on Debian

[Sean Lynch]

Hello,

I'm trying to get Flash3 running on a Debian machine with an Intel Core 2 Duo. I installed gfortran, mpich2, and hdf5 libraries (and associated files) using apt.

I first tried to get the Sedov simulation running. It compiles fine but when I ran it, with
mpirun -np 2 ./flash3
I don't get any errors to stdout, but I get the following errors in my /var/log/mpd.log
kernel: [ 2910.672295] flash3[3296]: segfault at 0 ip b769394f sp bfffcd70 error 4 in libhdf5.so.6.0.3[b7307000+407000]
kernel: [ 2910.673413] flash3[3295]: segfault at 0 ip b76d994f sp bfffd2f0 error 4 in libhdf5.so.6.0.3[b734d000+407000]

Has anyone seen these errors before? I'm assuming it has something to do with my hdf5 installation, but I'm not sure why that would cause a segfault.

Thanks,
Sean Lynch

For reference, my Makefile.h file contains:
#--------------------------------------------------------------------------
# Makefile.h
#--------------------------------------------------------------------------
HDF4_PATH =
HDF5_PATH = /usr

ZLIB_PATH  =

PAPI_PATH  =
PAPI_FLAGS =

NCMPI_PATH =
MPE_PATH   =

FCOMP   = mpif90
CCOMP   = mpicc
CPPCOMP = mpicxx
LINK    = mpif90

PP      = -D

FFLAGS_OPT = -c -O2 -fdefault-real-8 -fdefault-double-8 -ffree-line-length-none
FFLAGS_DEBUG = -g -c -fdefault-real-8 -fdefault-double-8 -ffree-line-length-none
FFLAGS_TEST = -c -fdefault-real-8 -fdefault-double-8 -ffree-line-length-none

F90FLAGS =

CFLAGS_OPT = -O2  -c -I/usr/include
CFLAGS_DEBUG = -g -c -I/usr/include
CFLAGS_TEST = -c

CFLAGS_HDF5 = -I ${HDF5_PATH}/include

CFLAGS_NCMPI =

LFLAGS_OPT   = -o
LFLAGS_DEBUG = -g -o
LFLAGS_TEST  = -o

LIB_OPT   =
LIB_DEBUG =
LIB_TEST  =

LIB_HDF4  = 
LIB_HDF5 = -L ${HDF5_PATH}/lib -lhdf5 -lz

LIB_PAPI  =
LIB_MATH  = 

LIB_MPI   =
LIB_NCMPI = 
LIB_MPE   =

MACHOBJ =

MV = mv -f
AR = ar -r
RM = rm -f
CD = cd
RL = ranlib
ECHO = echo
#--------------------------------------------------------------------------
# End Makefile.h
#--------------------------------------------------------------------------