[FLASH-USERS] Problems compiling Flash3

Wed Aug 6 12:59:47 EDT 2008

Good day Flash3 users:

I have some compilation problems that I haven't been able to solve.

$ make, at the object directory and it displays:
*
-L/mraosw/data1/krause/lib/mpich-1.2.4/lib
/home/krause/dataw/lib/mpich-1.2.4/lib/libmpich.a(p4_secure.o)(.text+0x91):
In function `start_slave'
:
: warning: Using 'getpwuid' in statically linked applications requires at
runtime the shared librarie
s from the glibc version used for linking
/mraosw/data1/krause/lib/hdf/5-1.6.5-amd-icc/lib/libhdf5.a(H5FDstream.o)(.text+0x723):
In function `H
5FD_stream_open_socket':
: warning: Using 'gethostbyname' in statically linked applications requires
at runtime the shared lib
raries from the glibc version used for linking
Grid_bcApplyToRegionSpecialized.o(.text+0x5ac): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32
simulation_data_mp_sim_counter1_
Grid_bcApplyToRegionSpecialized.o(.text+0x5c7): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32 simulation_data_mp_sim_numepis_
Grid_bcApplyToRegionSpecialized.o(.text+0x5e2): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32 simulation_data_mp_sim_tinit_
Grid_bcApplyToRegionSpecialized.o(.text+0x5f0): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32 simulation_data_mp_sim_tjet_
Grid_bcApplyToRegionSpecialized.o(.text+0x600): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32
simulation_data_mp_sim_counter1_
Grid_bcApplyToRegionSpecialized.o(.text+0x629): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32
simulation_data_mp_sim_counter1_
Grid_bcApplyToRegionSpecialized.o(.text+0x943): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32
simulation_data_mp_sim_jetradius_
Grid_bcApplyToRegionSpecialized.o(.text+0x9a1): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32 simulation_data_mp_sim_jetvel_
Grid_bcApplyToRegionSpecialized.o(.text+0x9fc): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32 simulation_data_mp_sim_gamma_
Grid_bcApplyToRegionSpecialized.o(.text+0xa4b): In function
`grid_bcapplytoregionspecialized_':
: relocation truncated to fit: R_X86_64_PC32 simulation_data_mp_sim_gamma_
Grid_conserveField.o(.text+0xe): In function `grid_conservefield_':
: additional relocation overflows omitted from the output
/home/krause/dataw/lib/mpich-1.2.4/lib/libpmpich.a(getpname.o)(.text+0x1b):
In function `PMPI_Get_pro
cessor_name':
: undefined reference to `MPID_Node_name'
make: *** [flash3] Error 1*

My make file (taken from my working flash2.5 for the same machine):

*LD_LIBRARY_PATH =
$LD_LIBRARY_PATH:/mraosw/data1/krause/lib/hdf/szip2.0-amd-enc/lib
#HDF4_PATH = /usr/local/hdf4
HDF5_PATH = /mraosw/data1/krause/lib/hdf/5-1.6.5-amd-icc
#hdf/hdf5-1.6.5/hdf5/
#PAPI_PATH = /usr/papi

#PAPI_FLAGS = -c -fast -I$(PAPI_PATH)/include

#----------------------------------------------------------------------------
# Compiler and linker commands
#
#   Use the MPICH wrappers around the compilers -- these will automatically
#   load the proper libraries and include files.  Version of MPICH prior
#   to 1.2.2 (?) do not recognize .F90 as a valid Fortran file extension.
#   You need to edit mpif90 and add .F90 to the test of filename extensions,
#   or upgrade your MPICH.
#----------------------------------------------------------------------------
FCOMP   = /mraosw/data1/krause/lib/mpich-1.2.4/bin//mpif90
CCOMP   = /mraosw/data1/krause/lib/mpich-1.2.4/bin//mpicc
CPPCOMP = /mraosw/data1/krause/lib/mpich-1.2.4/bin//mpicc
LINK    = /mraosw/data1/krause/lib/mpich-1.2.4/bin//mpif90 -static
#FCOMP   = /mraosw/data1/krause/lib/mpich2-1.0.4p1/bin/mpif90
#CCOMP   = /mraosw/data1/krause/lib/mpich2-1.0.4p1/bin/mpicc
#CPPCOMP = /mraosw/data1/krause/lib/mpich2-1.0.4p1/bin/mpicc
#LINK    = /mraosw/data1/krause/lib/mpich2-1.0.4p1/bin/mpif90 -static
# pre-processor flag
PP      = -D

#----------------------------------------------------------------------------
# Compilation flags
#
#  Three sets of compilation/linking flags are defined: one for optimized
#  code, one for testing, and one for debugging.  The default is to use the
#  _OPT version.  Specifying -debug to setup will pick the _DEBUG version,
#  these should enable bounds checking.  Specifying _TEST is used for
#  flash_test, and is set for quick code generation, and (sometimes)
#  profiling.  The Makefile generated by setup will assign the generic token
#  (ex. FFLAGS) to the proper set of flags (ex. FFLAGS_OPT).
#----------------------------------------------------------------------------

#FFLAGS_OPT = -c -fast -r8 -i4
#FFLAGS_DEBUG = -g -c -Mbounds -r8 -i4
#FFLAGS_TEST = -c -r8 -i4 -Mprof=lines
FFLAGS_OPT = -c -r8 -i4 -O3
-I/home/krause/mpich2-0.971/mpich2-install/include
FFLAGS_DEBUG = -g -c -Mbounds -double
FFLAGS_TEST = -c -double  -Mprof=lines

F90FLAGS = -w -v -mismatch -dusty

# if we are using HDF5, we need to specify the path to the include files
CFLAGS_HDF5 = -I $(HDF5_PATH)/include

CFLAGS_OPT =   -O3 -c
CFLAGS_DEBUG = -g -c
CFLAGS_TEST = -c

#----------------------------------------------------------------------------
# Linker flags
#
#  There is a seperate version of the linker flags for each of the _OPT,
#  _DEBUG, and _TEST cases.
#----------------------------------------------------------------------------

LFLAGS_OPT = -o
LFLAGS_DEBUG = -g -o
LFLAGS_TEST = -Mprof=lines -o

#----------------------------------------------------------------------------
# Library specific linking
#
#  If a FLASH module has a 'LIBRARY xxx' line in its Config file, we need to
#  create a macro in this Makefile.h for LIB_xxx, which will be added to the
#  link line when FLASH is built.  This allows us to switch between
different
#  (incompatible) libraries.  We also create a _OPT, _DEBUG, and _TEST
#  library macro to add any performance-minded libraries (like fast math),
#  depending on how FLASH was setup.
#----------------------------------------------------------------------------

#LIB_MPI  = -L/mraosw/data1/krause/lib/mpich-1.2.4/lib
LIB_MPI  = -L/mraosw/data1/krause/lib/mpich-1.2.6/lib
LIB_HDF4 = -L$(HDF4_PATH)/lib -lmfhdf -ldf -ljpeg -lz
LIB_HDF5 = -L$(HDF5_PATH)/lib -lhdf5 -lz -lhdf5_fortran
# SZ with path to be included if v1.6.3 is used (not recommended)
#LIB_PAPI = $(PAPI_PATH)/lib/libpapi.a
LIB_MATH = -ldfftw -ldrfftw

#LIB_OPT = -L/home/krause/mpich2-0.971/mpich2-install/lib

LIB_DEBUG =
LIB_TEST =

#----------------------------------------------------------------------------
# Additional machine-dependent object files
#
#  Add any machine specific files here -- they will be compiled and linked
#  when FLASH is built.
#----------------------------------------------------------------------------

MACHOBJ =

#----------------------------------------------------------------------------
# Additional commands
#----------------------------------------------------------------------------

MV = mv -f
AR = ar -r
RM = rm -f
CD = cd
RL = ranlib
ECHO = echo
*
Do you have any hints?

Thank you.

-- 
Martin Huarte-Espinosa
PhD Student, Astrophysics Group,
Physics Department, University of Cambridge
mh475 at cam.ac.uk
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