Hi Ben,
> Hmm... I cannot seem to repeat this. Could you please post the output
> from ./configure and your Make.common file?
>
configure:
---------------------------------------------
----------- Configuring libMesh -------------
---------------------------------------------
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking target system type... i686-pc-linux-gnu
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
<<< C++ compiler is gcc-3.3 >>>
checking how to run the C++ preprocessor... g++ -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for short int... yes
checking size of short int... 2
checking for int... yes
checking size of int... 4
checking for long int... yes
checking size of long int... 4
checking for float... yes
checking size of float... 4
checking for double... yes
checking size of double... 8
checking for void *... yes
checking size of void *... 4
checking getopt.h usability... yes
checking getopt.h presence... yes
checking for getopt.h... yes
checking whether the compiler implements namespaces... yes
checking whether the compiler has locale... yes
checking whether the compiler has stringstream... yes
checking hash_map usability... no
checking hash_map presence... no
checking for hash_map... no
checking ext/hash_map usability... yes
checking ext/hash_map presence... yes
checking for ext/hash_map... yes
checking hash_set usability... no
checking hash_set presence... no
checking for hash_set... no
checking ext/hash_set usability... yes
checking ext/hash_set presence... yes
checking for ext/hash_set... yes
<<< Configuring library with AMR support >>>
<<< Configuring library with expensive data structures enabled >>>
<<< Configuring library with higher order p-FEM shapes >>>
checking rpc/rpc.h usability... yes
checking rpc/rpc.h presence... yes
checking for rpc/rpc.h... yes
checking for xdrstdio_create... yes
<<< Configuring library with XDR support >>>
<<< Configuring library with real number support >>>
<<< Configuring library with reference counting support >>>
checking for ./contrib/netcdf/lib/i686-pc-linux-gnu/libnetcdf.a... no
checking for ./contrib/netcdf/include/netcdf.h... no
---------------------------------------------
----- Configuring for optional packages -----
---------------------------------------------
checking for /include/petsc.h... no
<<< PETSc disabled. Please set your "$PETSC_ARCH" environment variable
correctly. >>>checking for ./contrib/laspack/lastypes.h... yes
<<< Configuring library with LASPACK version 1.12.3 support >>>
checking for ./contrib/sfcurves/sfcurves.h... yes
<<< Configuring library with SFC support >>>
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for gzopen in -lz... yes
checking for ./contrib/gzstream/gzstream.h... yes
<<< Configuring library with gzstreams support >>>
checking for ./contrib/tecplot/lib/i686-pc-linux-gnu/tecio.a... yes
checking for ./contrib/tecplot/include/TECIO.h... yes
<<< Configuring library with Tecplot API support >>>
checking for ./contrib/metis/Lib/metis.h... yes
<<< Configuring library with Metis support >>>
checking for doxygen... /usr/bin/doxygen
checking for dot... /usr/bin/dot
----------------------------------------------
--- Done configuring for optional packages ---
----------------------------------------------
checking for perl... /usr/bin/perl
configure: creating ./config.status
config.status: creating Make.common
config.status: creating doc/Doxyfile
config.status: creating contrib/bin/libmesh-config
config.status: creating include/base/libmesh_config.h
config.status: include/base/libmesh_config.h is unchanged
---------------------------------------------
--------- Done Configuring libMesh ----------
---------------------------------------------
Make.common:
# $Id: Make.common.in,v 1.37 2004/05/05 15:23:47 spetersen Exp $
#########################################################################=
######## Please note:
## The ./configure script generates Make.common from
## Make.common.in, so if you want to change something,
## then do it in the latter file (here!)and re-run ./configure in the
## top level directory
#########################################################################=
######
#########################################################################=
#######
# The Make.common file defines the build environment for libMesh
# and all its helper applications. If you want to build an application
# that makes use of libMesh it is highly recommended that you include
# this file in your project's Makefile.
#
#########################################################################=
######
#########################################################################=
####### the following lines will be replaced by the output
# of ./configure
hosttype =3D i686-pc-linux-gnu
CXX =3D g++
CC =3D gcc
LDFLAGS =3D
DLFLAGS =3D
LIBS =3D
FLIBS =3D
GXX-VERSION =3D gcc3.3
CXXSHAREDFLAG =3D -shared
CSHAREDFLAG =3D -shared
RPATHFLAG =3D -Wl,-rpath,
# Complex variable support
enable-complex =3D no
ifeq ($(enable-complex),yes)
CXXFLAGS +=3D -DUSE_COMPLEX_NUMBERS
CFLAGS +=3D -DUSE_REAL_NUMBERS
endif
# Petsc iterative solvers for parallel and uniprocessor
# applications
enable-petsc =3D no
petsc-version =3D
petsc-major-minor =3D
PETSC_ARCH =3D
PETSC_DIR =3D
# TetGen tetrahedrization library
enable-tetgen =3D no
# MPI configuration
# (only explicitly defined when PETSc is absent, otherwise snooped from
PETSc)MPI_IMPL =3D
MPI_INCLUDE =3D
MPI_LIB =3D
# Doxygen for generating documentation
doxygen =3D /usr/bin/doxygen
# Perl for making .depend
perl =3D /usr/bin/perl
# Flag for optional packages
enable-optional =3D yes
enable-laspack =3D yes
enable-metis =3D yes
enable-parmetis =3D no
enable-sfcurves =3D yes
enable-gzstream =3D yes
#
# Set the current directory.
libmesh_dir :=3D /usr/local/src/libmesh/libmesh-0.4.3-rc1
#########################################################################=
######
#########################################################################=
#######
# Figure out the compilation mode based on the
# environment variable METHOD.
opt-mode :=3D off
debug-mode :=3D off
prof-mode :=3D off
syn-mode :=3D off
obj-suffix :=3D i686-pc-linux-gnu.o
#
# If the user has no environment variable
# called METHOD, he gets optimized mode.
ifeq (x$(METHOD),x)
METHOD :=3D opt
opt-mode :=3D on
obj-suffix :=3D i686-pc-linux-gnu.o
endif
#
# If METHOD=3Dopt, compile in optimized mode.
ifeq ($(METHOD),opt)
opt-mode :=3D on
obj-suffix :=3D i686-pc-linux-gnu.o
endif
#
# If METHOD=3Ddbg, compile in debug mode.
ifeq ($(METHOD),dbg)
debug-mode :=3D on
obj-suffix :=3D i686-pc-linux-gnu.g.o
endif
#
# If METHOD=3Dpro, compile in profiler mode
ifeq ($(METHOD),pro)
prof-mode :=3D on
obj-suffix :=3D i686-pc-linux-gnu.pg.o
endif
#
# If METHOD=3Dsyn, compile in syntax-checking mode
ifeq ($(METHOD),syn)
syn-mode :=3D on
obj-suffix :=3D i686-pc-linux-gnu.sy.o
endif
#
# Set the option to determine what type of
# library (.so or .a) will be built.
enable-shared :=3D yes
#
# If we are profiling, we CANNOT use shared
# libs. At least I don't think we can ;)
ifeq ($(prof-mode),on)
enable-shared :=3D no
endif
#########################################################################=
######
#########################################################################=
####### Compiler flags, different for optimized, debug, and profiler mode=
s.
ifeq ($(debug-mode),on)
CXXFLAGS +=3D -O2 -felide-constructors -g -ansi -pedantic -W -Wall
-Wunused -Wpointer-arith -Wimplicit -Wformat -Wparentheses
-Wuninitialized -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC -DDEBUG -fPI=
C CFLAGS +=3D -g -DDEBUG -fPIC
endif
ifeq ($(opt-mode),on)
CXXFLAGS +=3D -O2 -felide-constructors -DNDEBUG -fPIC -funroll-loops
-fstrict-aliasing CFLAGS +=3D -O2 -DNDEBUG -fPIC -funroll-loops -fst=
rict-aliasing
endif
ifeq ($(prof-mode),on)
CXXFLAGS +=3D -O2 -felide-constructors -DNDEBUG -g -pg -fPIC
-funroll-loops -fstrict-aliasing CFLAGS +=3D -O2 -DNDEBUG -g -pg -fP=
IC -funroll-loops -fstrict-aliasing
endif
ifeq ($(syn-mode),on)
CXXFLAGS +=3D -fsyntax-only
CFLAGS +=3D -fsyntax-only
endif
ifeq ($(prof-mode),on)
LIBS +=3D -pg
endif
#########################################################################=
######
#########################################################################=
####### The mesh library
#
mesh_library_dir :=3D $(libmesh_dir)/lib/$(hosttype)_$(METHOD)
mesh_library :=3D $(mesh_library_dir)/libmesh.a
ifeq ($(enable-shared),yes)
mesh_library :=3D $(mesh_library_dir)/libmesh.so
DLFLAGS +=3D $(RPATHFLAG)$(mesh_library_dir)
endif
LIBS +=3D $(mesh_library)
#########################################################################=
######
#########################################################################=
####### now configuration for package includes, libraries, etc...
#
# The include directories for libMesh
LIBMESH_INCLUDES =3D -I$(libmesh_dir)/include/base \
-I$(libmesh_dir)/include/enums \
-I$(libmesh_dir)/include/fe \
-I$(libmesh_dir)/include/geom \
-I$(libmesh_dir)/include/mesh \
-I$(libmesh_dir)/include/numerics \
-I$(libmesh_dir)/include/partitioning \
-I$(libmesh_dir)/include/quadrature \
-I$(libmesh_dir)/include/solvers \
-I$(libmesh_dir)/include/utils
INCLUDE +=3D $(LIBMESH_INCLUDES)
#
# Package-specific stuff
#
# Contributed source & libraries
EXTERNAL_LIBDIR :=3D $(libmesh_dir)/contrib/lib/$(hosttype)_$(METHOD)
EXTERNAL_LIBEXT :=3D .a
ifeq ($(enable-shared),yes)
EXTERNAL_LIBEXT :=3D .so
DLFLAGS +=3D $(RPATHFLAG)$(EXTERNAL_LIBDIR)
endif
#
# Optional packages
ifeq ($(enable-optional),yes)
# if Laspack is used we need the header path
# and the lib
LIBS +=3D $(EXTERNAL_LIBDIR)/liblaspack$(EXTERNAL_LIBEXT)
INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/laspack
# if Paretis is used we need the header path
# and the lib
# (Parmetis must precede Metis for static linking)
LIBS +=3D
INCLUDE +=3D
# if Metis is used we need the header path
# and the lib
LIBS +=3D $(EXTERNAL_LIBDIR)/libmetis$(EXTERNAL_LIBEXT)
INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/metis/L=
ib
# if Space filling curves are used we need the
# header path and the lib
LIBS +=3D $(EXTERNAL_LIBDIR)/libsfcurves$(EXTERNAL_LIBEXT)
INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/sfcurve=
s
# if gzstreams are used, we need the
# header path and the lib
LIBS +=3D $(EXTERNAL_LIBDIR)/libgzstream$(EXTERNAL_LIBEXT) -lz
INCLUDE +=3D -I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/gzstrea=
m
#if Tecplot is used, link against tecio.a
LIBS +=3D
/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/tecplot/lib/i686-pc-li=
nux-gnu/tecio.a INCLUDE +=3D
-I/usr/local/src/libmesh/libmesh-0.4.3-rc1/contrib/tecplot/include
#if TetGen is used:
ifeq ($(enable-tetgen),yes)
CXXFLAGS +=3D -DHAVE_TETGEN
CXXFLAGS +=3D
LIBS +=3D
INCLUDE +=3D
endif
#######################################################################=
###### # Petsc
ifeq ($(enable-petsc),yes)
# define BOPT first since it may be used in the packages file
ifeq ($(enable-complex),yes)
CXXFLAGS +=3D -DPETSC_USE_COMPLEX
CFLAGS +=3D -DPETSC_USE_COMPLEX
PETSC_BOPT.g =3D g_complex
PETSC_BOPT.o =3D O_complex
else
PETSC_BOPT.g =3D g
PETSC_BOPT.o =3D O
endif
ifeq ($(debug-mode),on)
BOPT =3D $(PETSC_BOPT.g)
else
BOPT =3D $(PETSC_BOPT.o)
endif
# Depending on petsc version, we include different files
ifeq ($(petsc-version),2.1.0)
include $(PETSC_DIR)/bmake/$(PETSC_ARCH)/base.site # 2.1.0 style
else
C_CLINKER_SLFLAG =3D $(RPATHFLAG)# necessary for PETSc 2.1.6
include $(PETSC_DIR)/bmake/$(PETSC_ARCH)/packages # 2.1.1 or later
style endif
INCLUDE +=3D -I$(PETSC_DIR)/include -I$(PETSC_DIR)/bmake/$(PETSC_ARCH=
) \
$(MPI_INCLUDE) $(BLOCKSOLVE_INCLUDE) $(HYPRE_INCLUDE)
PETSC_LIB =3D $(PETSC_DIR)/lib/lib$(BOPT)/$(PETSC_ARCH)
ifeq ($(enable-shared),yes)
CXXFLAGS +=3D -DPETSC_USE_DYNAMIC_LIBRARIES
CFLAGS +=3D -DPETSC_USE_DYNAMIC_LIBRARIES
DLFLAGS +=3D $(RPATHFLAG)$(PETSC_LIB)
endif
# Depending on petsc version, we link with different libs :-(
ifeq ($(petsc-major-minor),2.2.x) # 2.2.x & newer style
libs-PETSC =3D -L$(PETSC_LIB) \
-lpetscksp \
-lpetscdm \
-lpetscmat \
-lpetscvec \
-lpetsc
else # 2.1.6 & older style
libs-PETSC =3D -L$(PETSC_LIB) \
-lpetscsles \
-lpetscdm \
-lpetscmat \
-lpetscvec \
-lpetsc
endif
LIBS +=3D $(libs-PETSC) $(BLOCKSOLVE_LIB) $(SPOOLES_LIB) \
$(HYPRE_LIB) $(BLASLAPACK_LIB) $(MPI_LIB) \
$(X11_LIB) $(MATLAB_LIB) $(FLIBS)
endif #end ifeq ($(enable-petsc),yes)
# MPI configuration when Petsc is absent
LIBS +=3D $(MPI_LIB)
INCLUDE +=3D $(MPI_INCLUDE)
endif # End of disable-optional test
#if Exodus is used, link against libexoIIv2c.a
LIBS +=3D
INCLUDE +=3D
#if netCDF is used, link against libnetcdf.a
# (note that netCDF is required by exodus if available,
# so we need to link to this _after_ exodus.
LIBS +=3D
INCLUDE +=3D
#
# Finally, Append the linker flags to the libraries
LIBS +=3D $(DLFLAGS) $(LDFLAGS)
#########################################################################=
######
#########################################################################=
####### Build rules
##################################
# C++ rules #
##################################
#
# How to compile optimized C++
#
%.i686-pc-linux-gnu.o : %.C
@echo "Compiling C++ (in optimized mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@
#
# How to compile C++ with debugging flags
#
%.i686-pc-linux-gnu.g.o : %.C
@echo "Compiling C++ (in debug mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@
#
# How to compile C++ with profiling flags
#
%.i686-pc-linux-gnu.pg.o : %.C
@echo "Compiling C++ (in profiler mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@
#
# How to compile C++ with syntax-checking flags
#
%.i686-pc-linux-gnu.sy.o : %.C
@echo "Compiling C++ (in syntax-checker mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $<
$(shell touch $@)
##################################
# C rules #
##################################
# do not show this to the LASPACK Makefile
ifeq (x$(included-from-laspack),x)
#
# How to compile optimized C
#
%.i686-pc-linux-gnu.o : %.c
@echo "Compiling C (in optimized mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
#
# How to compile C with debugging flags
#
%.i686-pc-linux-gnu.g.o : %.c
@echo "Compiling C (in debug mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
#
# How to compile C with profiling flags
#
%.i686-pc-linux-gnu.pg.o : %.c
@echo "Compiling C (in profiler mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
#
# How to compile C with profiling flags
#
%.i686-pc-linux-gnu.sy.o : %.c
@echo "Compiling C (in syntax-checker mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
$(shell touch $@)
else
# only visible for LASPACK Makefile
ifeq ($(enable-complex),yes)
# complex: C++ rules for .c Laspack code
%.i686-pc-linux-gnu.o : %.c
@echo "Compiling C++ (in optimized mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@
%.i686-pc-linux-gnu.g.o : %.c
@echo "Compiling C++ (in debug mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@
%.i686-pc-linux-gnu.pg.o : %.c
@echo "Compiling C++ (in profiler mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $< -o $@
%.i686-pc-linux-gnu.sy.o : %.c
@echo "Compiling C++ (in syntax-checker mode) "$<"..."
@$(CXX) $(CXXFLAGS) $(INCLUDE) -c $<
$(shell touch $@)
else
# real: C rules for .c Laspack code
%.i686-pc-linux-gnu.o : %.c
@echo "Compiling C (in optimized mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
%.i686-pc-linux-gnu.g.o : %.c
@echo "Compiling C (in debug mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
%.i686-pc-linux-gnu.pg.o : %.c
@echo "Compiling C (in profiler mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
%.i686-pc-linux-gnu.sy.o : %.c
@echo "Compiling C (in syntax-checker mode) "$<"..."
@$(CC) $(CFLAGS) $(INCLUDE) -c $< -o $@
$(shell touch $@)
endif
endif
#########################################################################=
######
# Local Variables:
# mode: makefile
# End:
Regards,
Kai
--=20
http://echempp.sourceforge.net
Kai Ludwig
Institut f=FCr Organische Chemie
Auf der Morgenstelle 18
72076 T=FCbingen
Tel.: 07071/29-73049
Mail: kai.ludwig@...
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