Linker-fu
Linker-fu
- Subject: Linker-fu
- From: "Mathieu Béliveau" <email@hidden>
- Date: Sun, 17 Feb 2008 18:09:44 -0500
Hi. I'm trying to port a general unix application (multimatlab) to osX
where there is the folliwing error libmpich.dylib is input for the
dynamic linke editor, is not relocatable by the static link editor
again
The application I'm trying to compile uses several librairies, most
from mpich and matlab. Libmpich.dylib is supplied by matlab and file
states it's a ppc bundle.
As the provided makefile didn't took osX in account, I had to
explicitly set the libs path and set the proper architecture.
Concerning the different linker flags, unfortunately, the usual
-bundle -flat_namespace, etc. won't change a thing, I still get the
same error message.
Any help would greatly be appreciated!
Here is the make output showing the full compiler options passed to gcc:
-> mexopts.sh sourced from directory (DIR = $MATLAB/bin)
FILE = /Applications/matlab-new/bin/mexopts.sh
----------------------------------------------------------------
-> MATLAB = /Applications/matlab-new
-> CC = gcc-4.0
-> CC flags:
CFLAGS = -fno-common -no-cpp-precomp -fexceptions
CDEBUGFLAGS = -g
COPTIMFLAGS = -O3 -fno-loop-optimize -DNDEBUG
CLIBS = -L/Applications/matlab-new/bin/mac -lmx
-lmex -lmat -lstdc++
arguments = -DMX_COMPAT_32
-> CXX = g++-4.0
-> CXX flags:
CXXFLAGS = -fno-common -no-cpp-precomp -fexceptions -arch ppc
CXXDEBUGFLAGS = -g
CXXOPTIMFLAGS = -O3 -fno-loop-optimize -DNDEBUG
CXXLIBS = -L/Applications/matlab-new/bin/mac -lmx
-lmex -lmat -lstdc++
arguments = -DMX_COMPAT_32
-> FC = g95
-> FC flags:
FFLAGS = -fexceptions
FDEBUGFLAGS = -g
FOPTIMFLAGS = -O
FLIBS = -L/Applications/matlab-new/bin/mac -lmx
-lmex -lmat -L -lf95
arguments = -DMX_COMPAT_32
-> LD = gcc-4.0
-> Link flags:
LDFLAGS = -bundle -Wl,-flat_namespace -undefined
suppress -Wl,-exported_symbols_list,/Applications/matlab-new/extern/lib/mac/mexFunction.map
LDDEBUGFLAGS = -g
LDOPTIMFLAGS = -O
LDEXTENSION = .mexmac
arguments = -L/usr/local/mpich/lib/ -lmpich -lm
-> LDCXX =
-> Link flags:
LDCXXFLAGS =
LDCXXDEBUGFLAGS =
LDCXXOPTIMFLAGS =
LDCXXEXTENSION =
arguments = -L/usr/local/mpich/lib/ -lmpich -lm
----------------------------------------------------------------
-> gcc-4.0 -c -I/usr/local/mpich -I/usr/local/mpich/include
-I/usr/local/mpich/mpid/ch_p4/p4
-I/usr/local/mpich/mpid/ch_p4/p4/include
-I/Applications/matlab-new/extern/include -DMATLAB_MEX_FILE
-fno-common -no-cpp-precomp -fexceptions -DMX_COMPAT_32 -O3
-fno-loop-optimize -DNDEBUG MMAT.c
MMAT.c:9: warning: initialization makes integer from pointer without a cast
MMAT.c:9: warning: initialization makes integer from pointer without a cast
MMAT.c:9: warning: initialization makes integer from pointer without a cast
MMAT.c:9: warning: initialization makes integer from pointer without a cast
-> gcc-4.0 -c -I/usr/local/mpich -I/usr/local/mpich/include
-I/usr/local/mpich/mpid/ch_p4/p4
-I/usr/local/mpich/mpid/ch_p4/p4/include
-I/Applications/matlab-new/extern/include -DMATLAB_MEX_FILE
-fno-common -no-cpp-precomp -fexceptions -DMX_COMPAT_32 -O3
-fno-loop-optimize -DNDEBUG
/Applications/matlab-new/extern/src/mexversion.c
-> gcc-4.0 -O -bundle -Wl,-flat_namespace -undefined suppress
-Wl,-exported_symbols_list,/Applications/matlab-new/extern/lib/mac/mexFunction.map
-o MMAT.mexmac MMAT.o mexversion.o -L/usr/local/mpich/lib/ -lmpich
-lm -L/Applications/matlab-new/bin/mac -lmx -lmex -lmat -lstdc++
/usr/bin/ld: /usr/local/mpich/lib//libmpich.dylib is input for the
dynamic link editor, is not relocatable by the static link editor
again
collect2: ld returned 1 exit status
mex: link of 'MMAT.mexmac' failed.
make: *** [MMAT.] Error 1
Below, is the content of my make file:
SHELL = /bin/sh
###################################################
#
# NOTE:
#
# Currently MultiMATLAB only works with MATLAB 6.x
#
###################################################
#
# ACMC setup
#
MPI_HOME = /usr/local/mpich
MATLAB_DIR := /Applications/matlab-new
#
# Griffith setup
#
#MPI_HOME = /usr/local/mpich-1.2.7
#MATLAB_DIR := /usr/local/matlab.6.5.1
#
# JCU setup
#
#MPI_HOME := /sw/applications/mpich-1.2.5.2
#MATLAB_DIR := /sw/applications/matlab6.2/
#
# All the needs changing should be above.
# That is, don't touch below here unless
# you know what you are doing.
#
MM_SRC := $(shell pwd)
MM_HOME = $(patsubst %/src,%, $(MM_SRC))
COMM = $(MPI_HOME)/mpid/ch_p4/p4
CC = $(MATLAB_DIR)/bin/mex
CLINKER = $(MATLAB_DIR)/bin/mex
LIB_PATH = -L$(MPI_HOME)/lib/
LIB_LIST = -lmpich
MPILIB = $(MPI_HOME)/lib/libmpich.a
INCLUDE_DIR = -I$(MPI_HOME) -I$(MPI_HOME)/include -I$(COMM) -I$(COMM)/include
MKDIR = mkdir
RM = rm
MV = mv
CP = cp
DOL = "$$"
PLATFORM = $(shell uname -s)
ifeq ($(findstring IRIX, $(PLATFORM)), IRIX)
# ARCH is the matlab mex format. Type help mex in matlab to get the
list of formats.
ARCH = mexsg
CFLAGS = -v -D_BSD_TYPES $(INCLUDE_DIR)
endif
ifeq ($(PLATFORM), Linux)
ARCH = mexglx
CFLAGS = -v -D_XOPEN_SOURCE=600 $(INCLUDE_DIR)
endif
ifeq ($(PLATFORM), SunOS)
ARCH = mexsol
CFLAGS = -v $(INCLUDE_DIR)
endif
CFLAGS = -v $(INCLUDE_DIR)
MMAT_BASE = $(MM_HOME)
SPMD_OBJS = Init.m \
ID.m \
Nproc.m \
Send.m \
Recv.m \
Probe.m \
Coord.m \
Gridsize.m \
Reduce.m \
Allreduce.m \
Barrier.m \
multimatlab.m \
Multimatlab.m \
MultiMATLAB.m \
Graphics.m \
PerformShift.m \
MMgrid.m \
MMwindow.m \
MMresetwindow.m \
MMsum.m \
MMmax.m \
MMmin.m \
MMprod.m \
MMbcast.m
INTERACTIVE_OBJS = Eval.$(ARCH) \
Eval.m \
Quit.m \
Close.m \
Put.m \
Get.m \
pid.$(ARCH) \
Start.m \
Nproc.m \
multimatlab.m \
Multimatlab.m \
MultiMATLAB.m \
Graphics.m \
Init.m \
Max.m\
Min.m \
Window.m \
ResetWindow.m \
Prod.m \
Sum.m \
Grid.m \
Refresh.m \
Bcast.m \
mmchecknodes.m \
Distribute.m \
Shift.m \
DistributeMap.m \
Gather.m \
Collect.m
REMOTE_OBJS = startup.m
ERR_OBJS = Interrupt.m Abort.m
.SUFFIXES: .$(ARCH) .c
all: clean dirs mmat common interactive remote err cshrc
dirs:
mkdir $(MMAT_BASE)/common
chmod 755 $(MMAT_BASE)/common
mkdir $(MMAT_BASE)/interactive
chmod 755 $(MMAT_BASE)/interactive
mkdir $(MMAT_BASE)/remote
chmod 755 $(MMAT_BASE)/remote
mmat: MMAT.$(ARCH)
cp MMAT.$(ARCH) $(MMAT_BASE)/common
cp MMAT.$(ARCH) $(MMAT_BASE)/interactive
chmod 555 $(MMAT_BASE)/common/MMAT.$(ARCH)
chmod 555 $(MMAT_BASE)/interactive/MMAT.$(ARCH)
common: $(SPMD_OBJS)
cp $(SPMD_OBJS) $(MMAT_BASE)/common
chmod a+r $(MMAT_BASE)/common/*
interactive: $(INTERACTIVE_OBJS)
cp $(INTERACTIVE_OBJS) $(MMAT_BASE)/interactive
chmod a+r $(MMAT_BASE)/interactive/*
remote: $(REMOTE_OBJS)
cp $(REMOTE_OBJS) $(MMAT_BASE)/remote
chmod a+r $(MMAT_BASE)/remote/*
err: $(ERR_OBJS)
cp $(ERR_OBJS) $(MMAT_BASE)/interactive
chmod a+r $(MMAT_BASE)/interactive/*
cshrc:
@echo "Creating $(MM_HOME)/cshrc.mm"
@echo "#"
>> $(MM_HOME)/cshrc.mm
@echo "# This file is machine made. Do not edit."
>> $(MM_HOME)/cshrc.mm
@echo "# Users should include this file in their .cshrc"
>> $(MM_HOME)/cshrc.mm
@echo "#"
>> $(MM_HOME)/cshrc.mm
@echo
>> $(MM_HOME)/cshrc.mm
@echo "setenv MPI_HOME $(MPI_HOME)"
>> $(MM_HOME)/cshrc.mm
@echo "if (! "$(DOL)"?LD_LIBRARY_PATH) then"
>> $(MM_HOME)/cshrc.mm
@echo " setenv LD_LIBRARY_PATH" $(DOL)"MPI_HOME/lib"
>> $(MM_HOME)/cshrc.mm
@echo "else"
>> $(MM_HOME)/cshrc.mm
@echo " setenv LD_LIBRARY_PATH
"$(DOL)"{LD_LIBRARY_PATH}:"$(DOL)"MPI_HOME/lib" >> $(MM_HOME)/cshrc.mm
@echo "endif"
>> $(MM_HOME)/cshrc.mm
@echo
>> $(MM_HOME)/cshrc.mm
@echo "setenv MATLAB_DIR $(MATLAB_DIR)"
>> $(MM_HOME)/cshrc.mm
@echo "alias multimatlab "$(DOL)"MATLAB_DIR/bin/matlab -nojvm
-nosplash" >> $(MM_HOME)/cshrc.mm
@echo
>> $(MM_HOME)/cshrc.mm
@echo "setenv MM_HOME $(MM_HOME)"
>> $(MM_HOME)/cshrc.mm
@echo "setenv MATLABPATH
"$(DOL)"MM_HOME/interactive:"$(DOL)"MM_HOME/common:"$(DOL)"MM_HOME/example:"$(DOL)"MM_HOME/example/Demo:"$(DOL)"MM_HOME/example/financial"
>> $(MM_HOME)/cshrc.mm
@echo
>> $(MM_HOME)/cshrc.mm
chmod 644 $(MM_HOME)/cshrc.mm
#patch:
# cp $(MM_HOME)/mpich_patch/*.o .
#.c.o: mm.h $(MPI_HOME)/include/MPI.h $(MPILIB)
#
.c.$(ARCH): mm.h $(MPI_HOME)/include/mpi.h $(MPILIB)
$(CLINKER) $(CFLAGS) $*.c $(LIB_PATH) $(LIB_LIST) -lm
clean:
$(RM) -f $(MMAT_BASE)/cshrc.mm
$(RM) -f *.o *~ PI* *.$(ARCH) $(EXECS)
$(RM) -f $(MMAT_BASE)/common/* $(MMAT_BASE)/interactive/* $(MMAT_BASE)/remote/*
$(RM) -rf $(MMAT_BASE)/common $(MMAT_BASE)/interactive $(MMAT_BASE)/remote
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