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error while compiling opensees source code

https://opensees.berkeley.edu./community/viewtopic.php?t=15250

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error while compiling opensees source code

Posted: Wed Nov 11, 2009 6:51 am
by pankajd
I am getting following error on rhel 5.2 (intel xeon quad core quad socket servers cluster)
Error :

umd2p2.f:(.text+0xcff): undefined reference to `for_write_seq_fmt'
/home/csm/gourik/opensees/OpenSees_sq_intel_3/lib/libLapack.a(dormqr.o): In function `dormqr_':
dormqr.f:(.text+0x257): undefined reference to `for_concat'
dormqr.f:(.text+0x3dc): undefined reference to `for_concat'
/home/csm/gourik/opensees/OpenSees_sq_intel_3/lib/libLapack.a(dormlq.o): In function `dormlq_':
dormlq.f:(.text+0x256): undefined reference to `for_concat'
dormlq.f:(.text+0x3dc): undefined reference to `for_concat'
/home/csm/gourik/opensees/OpenSees_sq_intel_3/lib/libLapack.a(dtrtri.o): In function `dtrtri_':
dtrtri.f:(.text+0x209): undefined reference to `for_concat'
/home/csm/gourik/opensees/OpenSees_sq_intel_3/lib/libLapack.a(ilaenv.o): In function `ilaenv_':
ilaenv.f:(.text+0xd0): undefined reference to `for_cpystr'
make[1]: *** [tcl] Error 1
make[1]: Leaving directory `/home/csm/gourik/opensees/OpenSees_sq_intel_3/OpenSees/SRC/modelbuilder/tcl'
make: *** [all] Error 2


Below is Makefile.def

############################################################################
#
# Program: OpenSees
#
# Purpose: A Top-level Makefile to create the libraries needed
# to use the OpenSees framework.
#
# version created for Redhat 8.0 LINUX distribution
#
# Written: fmk
# Created: 01/2003
#
#
############################################################################

# %---------------------------------%
# | SECTION 1: PROGRAM |
# %---------------------------------%
#
# Specify the location and name of the OpenSees interpreter program
# that will be created (if this all works
#HOME=/home/csm/gourik/opensees/OpenSees_sq_intel_3
OpenSees_PROGRAM = $(HOME)/bin/OpenSees
OpenSees_PROGRAM_MPI = $(HOME)/bin/OpenSeesMPI

# %---------------------------------%
# | SECTION 2: MAKEFILE CONSTANTS |
# %---------------------------------%
#
# Specify the constants the are used as control structure variables in the Makefiles.

OPERATING_SYSTEM = LINUX
#PROGRAMMING_MODE = PARALLEL
PROGRAMMING_MODE = SEQUENTIAL
RELIABILITY = NO_RELIABILITY
#RELIABILITY_FLAG = -D_RELIABILITY
#RELIABILITY_LIBRARY = $(HOME)/lib/libReliability.a
GRAPHICS = NONE
#GRAPHIC_FLAG = -D_GLX
DEBUG_MODE = DEBUG


#PROGRAMMING_MODE = PARALLEL, SEQUENTIAL
#GRAPHICS = NONE, UsingOpenGL
#RELIABILITY = YES_RELIABILITY, NO_RELIABILITY
#DEBUG_MODE = DEBUG, NO_DEBUG


# %---------------------------------%
# | SECTION 3: PATHS |
# %---------------------------------%
#
# Note: if vendor supplied BLAS and LAPACK libraries or if you have
# any of the libraries already leave the directory location blank AND
# remove the directory from DIRS.

BASE = /usr
# PUT YOUR HOME DIRECTOREY HERE
HOME = /home/csm/gourik/opensees/OpenSees_sq_intel_3
FE = $(HOME)/OpenSees/SRC

BLASdir = $(HOME)/OpenSees/OTHER/BLAS
CBLASdir = $(HOME)/OpenSees/OTHER/CBLAS
LAPACKdir = $(HOME)/OpenSees/OTHER/LAPACK
ARPACKdir = $(HOME)/OpenSees/OTHER/ARPACK
UMFPACKdir = $(HOME)/OpenSees/OTHER/UMFPACK
METISdir = $(HOME)/OpenSees/OTHER/METIS
SRCdir = $(HOME)/OpenSees/SRC
SUPERLUdir = $(HOME)/OpenSees/OTHER/SuperLU_3.0/SRCSUPERLU_DISTdir = $(HOME)/OpenSees/OTHER/SuperLU_DIST_2.0/SRC

DIRS = $(BLASdir) \
$(CBLASdir) \
$(SUPERLUdir) \
$(LAPACKdir) \
$(ARPACKdir) \
$(UMFPACKdir) \
$(METISdir) \
$(SUPERLU_DISTdir) \
$(SRCdir)

# %-------------------------------------------------------%
# | SECTION 4: LIBRARIES |
# | |
# | The following section defines the libraries that will |
# | be created and/or linked with when the libraries are |
# | being created or linked with. |
# %-------------------------------------------------------%
#
# Note: if vendor supplied BLAS and LAPACK libraries leave the
# libraries blank. You have to get your own copy of the tcl/tk
# library!!
#
# Note: For libraries that will be created (any in DIRS above)
# make sure the directory exsists where you want the library to go!

FE_LIBRARY = $(HOME)/lib/libOpenSees.a
NDARRAY_LIBRARY = $(HOME)/lib/libndarray.a # BJ_UCD jeremic@ucdavis.edu
MATMOD_LIBRARY = $(HOME)/lib/libmatmod.a # BJ_UCD jeremic@ucdavis.edu
BJMISC_LIBRARY = $(HOME)/lib/libBJmisc.a # BJ_UCD jeremic@ucdavis.edu
LAPACK_LIBRARY = $(HOME)/lib/libLapack.a
BLAS_LIBRARY = $(HOME)/lib/libBlas.a
SUPERLU_LIBRARY = $(HOME)/lib/libSuperLU.a
CBLAS_LIBRARY = $(HOME)/lib/libCBlas.a
ARPACK_LIBRARY = $(HOME)/lib/libArpack.a
UMFPACK_LIBRARY = $(HOME)/lib/libUmfpack.a
METIS_LIBRARY = $(HOME)/lib/libMetis.a
DISTRIBUTED_SUPERLU_LIBRARY = $(HOME)/lib/libDistributedSuperLU.a

#TCL_LIBRARY = /home/csm/gourik/usr/local/lib/libtcl8.5.so \
TCL_LIBRARY = /home/csm/gourik/opensees/OpenSees_sq_intel_3/tkconf/lib/libtcl8.4.so \
/home/csm/gourik/opensees/OpenSees_sq_intel_3/tkconf/lib/libtk8.4.so


GRAPHIC_LIBRARY = -L/usr/X11R6/lib -lGL -lGLU -lXft -lXrender -lXss


ifeq ($(RELIABILITY), YES_RELIABILITY)
RELIABILITY_LIBRARY = $(HOME)/lib/libReliability.a
else
RELIABILITY_LIBRARY =
endif

# WATCH OUT .. These libraries are removed when 'make wipe' is invoked.

WIPE_LIBS = $(FE_LIBRARY) \
$(NDARRAY_LIBRARY) \
$(MATMOD_LIBRARY) \
$(DISTRIBUTED_SUPERLU_LIBRARY) \
$(SUPERLU_LIBRARY) \
$(ARPACK_LIBRARY) \
$(UMFPACK_LIBRARY) \
$(METIS_LIBRARY) \
$(LAPACK_LIBRARY) \
$(BLAS_LIBRARY) \
$(CBLAS_LIBRARY) \
$(RELIABILITY_LIBRARY)# %---------------------------------------------------------%
# | SECTION 5: COMPILERS |
# | |
# | The following macros specify compilers, linker/loaders, |
# | the archiver, and their options. You need to make sure |
# | these are correct for your system. |
# %---------------------------------------------------------%

# ###################################################
# # Compilers
# ###################################################

CC++ = icc
CC = icc
FC = ifort
#FORTRAN = /usr/bin/g77
#F90 =
LINKER = icc

AR = ar
ARFLAGS = cqls
ARCH = ar
ARCHFLAGS = cqls
RANLIB = ranlib
RANLIBFLAGS =

PROGRAMMING_FLAG =

ifeq ($(GRAPHICS), UsinOpenGl)
GRAPHIC_FLAG = -D_GLX
GRAPHIC_LIBRARY =-L/usr/lib -L/usr/X11/R6/lib -lGL -lGLU
else
GRAPHIC_FLAG = -D_NOGRAPHICS
GRAPHIC_LIBRARY =
endif

ifeq ($(RELIABILITY), YES_RELIABILITY)
RELIABILITY_FLAG = -D_RELIABILITY
else
RELIABILITY_FLAG =
endif

ifeq ($(DEBUG_MODE), DEBUG)
DEBUG_FLAG = -D_G3DEBUG
else
DEBUG_FLAG =
endif

ifeq ($(DEBUG_MODE), DEBUG)

C++FLAGS = -Wall -g -pg -D_LINUX -D_UNIX $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG) -D_TCL84
CFLAGS = -Wall -g -pg $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG)
FFLAGS = -Wall
LINKFLAGS = -rdynamic -g -pg

else

C++FLAGS = -Wall -O2 -D_LINUX -D_UNIX -D_TCL84 -Wall $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG) -ffloat-store

CFLAGS = -Wall $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(PROGRAMMING_FLAG)
FFLAGS = -Wall
LINKFLAGS = -rdynamic

endif

# Misc
MAKE = make
CD = cd
ECHO = echo
RM = rm
RMFLAGS = -f
SHELL = /bin/sh

# %---------------------------------------------------------%
# | SECTION 6: COMPILATION |
# | |
# | The following macros specify the macros used in |
# | to compile the source code into object code. |
# %---------------------------------------------------------%

.SUFFIXES:
.SUFFIXES: .C .c .f .f90 .cpp .o .cpp

#
# %------------------%
# | Default command. |
# %------------------%
#
.DEFAULT:
@$(ECHO) "Unknown target $@, try: make help"
#
# %-----------------------------------------------%
# | Command to build .o files from source files. |
# %-----------------------------------------------%
#

.cpp.o:
@$(ECHO) Making $@ from $<
$(CC++) $(C++FLAGS) $(INCLUDES) -c $< -o $@

.C.o:
@$(ECHO) Making $@ from $<
$(CC++) $(C++FLAGS) $(INCLUDES) -c $< -o $@

.c.o:
@$(ECHO) Making $@ from $<
$(CC) $(CFLAGS) -c $<

.f.o:
@$(ECHO) Making $@ from $<
$(FC) $(FFLAGS) -c $< -o $@

.f77.o:
@$(ECHO) Making $@ from $<
$(FC) $(FFLAGS) -c $< -o $@

.f90.o:
@$(ECHO) Making $@ from $<
$(FC90) $(FFLAGS) -c $< -o $@

# %---------------------------------------------------------%
# | SECTION 7: OTHER LIBRARIES |
# | |
# | The following macros specify other libraries that must |
# | be linked with when creating executables. These are |
# | platform specific and typically order does matter!! |
# %---------------------------------------------------------%
MACHINE_LINKLIBS = -L$(BASE)/lib64 \
-L$(HOME)/lib64 \
-L/opt/intel/Compiler/11.0/069/lib/intel64 \

MACHINE_NUMERICAL_LIBS = -lm \
$(ARPACK_LIBRARY) \
$(DISTRIBUTED_SUPERLU_LIBRARY) \
$(SUPERLU_LIBRARY) \
$(UMFPACK_LIBRARY) \
$(LAPACK_LIBRARY) \
$(BLAS_LIBRARY) \
$(CBLAS_LIBRARY) \
$(GRAPHIC_LIBRARY)\
$(METIS_LIBRARY)\
$(RELIABILITY_LIBRARY)\
$(PETSC_LIB)\
-ldl -lgfortran -lpng -lssl
# -lg2c -ldl

#MPICC = /opt/intel/mpi/bin64/mpicc
#MPIINC = -I/opt/intel/mpi/include
#MPILIB = -L/opt/intel/mpi/lib -lmpich

#PETSC_INC = -I/scratch/fmckenna/petsc-2.2.1 \
-I/scratch/fmckenna/petsc-2.2.1/bmake/linux-gnu \
-I/scratch/fmckenna/petsc-2.2.1/include \
-I/scratch/fmckenna/petsc-2.2.1/include/mpiuni \
-DPETSC_USE_BOPT_g -DPETSC_USE_EXTERN_CXX


#PETSCINC = -I/scratch/fmckenna/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1 -I/scratch/fmckenna/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1/bmake/linux-gnu -I/scratch/fmckenna/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1/include \
-I/scratch/fmckenna/petsc-2.2.1/include/mpiuni -DPETSC_USE_BOPT_g -DPETSC_USE_EXTERN_CXX

#PETSCINC = -I/scratch/fmckenna/petsc-2.2.1/include -D_PETSC -I/scratch/fmckenna/petsc-2.2.1/bmake/linux-gnu -DPETSC_USE_BOPT_g -DPETSC_USE_EXTERN_CXX


# $(FE)/system_of_eqn/linearSOE/petsc/PetscSparseSeqSolver.o \


#PETSC_LIB = $(FE)/system_of_eqn/linearSOE/petsc/PetscSOE.o \
$(FE)/system_of_eqn/linearSOE/petsc/PetscSolver.o \
$(FE)/system_of_eqn/linearSOE/petsc/PetscSparseSeqSolver.o \
$(HOME)/OpenSees/OTHER/LAPACK/dgebak.o \
$(HOME)/OpenSees/OTHER/LAPACK/dgebal.o \
$(HOME)/OpenSees/OTHER/LAPACK/dgeev.o \
$(HOME)/OpenSees/OTHER/LAPACK/dgehd2.o \
$(HOME)/OpenSees/OTHER/LAPACK/dgehrd.o \
$(HOME)/OpenSees/OTHER/LAPACK/dhseqr.o \
$(HOME)/OpenSees/OTHER/LAPACK/dlahrd.o \
$(HOME)/OpenSees/OTHER/LAPACK/dorg2r.o \
$(HOME)/OpenSees/OTHER/LAPACK/dorghr.o \
$(HOME)/OpenSees/OTHER/LAPACK/dorgqr.o \
$(HOME)/OpenSees/OTHER/LAPACK/dpotrf.o \
$(HOME)/OpenSees/OTHER/LAPACK/dpotrs.o \
/scratch/fmckenna/petsc-2.2.1/lib/libg/linux-gnu/libpetscsnes.a \
/scratch/fmckenna/petsc-2.2.1/lib/libg/linux-gnu/libpetscksp.a \
/scratch/fmckenna/petsc-2.2.1/lib/libg/linux-gnu/libpetscdm.a \
/scratch/fmckenna/petsc-2.2.1/lib/libg/linux-gnu/libpetscmat.a \
/scratch/fmckenna/petsc-2.2.1/lib/libg/linux-gnu/libpetscvec.a \
/scratch/fmckenna/petsc-2.2.1/lib/libg/linux-gnu/libpetsc.a

# -L/scratch/fmckenna/petsc-2.2.1/lib/libg/linux-gnu/
# -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc

ifeq ($(PROGRAMMING_MODE), THREADS)
MACHINE_SPECIFIC_LIBS = -lpthread
else
MACHINE_SPECIFIC_LIBS = -ldl -lieee -lm -lc -lg2c -Wl,-rpath,/usr/lib -lpng
endif
# %---------------------------------------------------------%
# | SECTION 8: INCLUDE FILES |
# | |
# | The following macros specify include files needed for |
# | compilation. |
# %---------------------------------------------------------%
MACHINE_INCLUDES = -I/usr/include \
-I/usr/bin/mysql/include \
-I$(HOME)/include \
-I${BASE}/include \
-I/usr/include/cxx \
-I$(HOME)/blitz \
-I$(UMFPACKdir) \
-I$(SUPERLUdir) \
-I/home/csm/gourik/opensees/OpenSees_sq_intel_3/OpenSees/OpenSees/OTHER/SuperLU_3.0/SRC \
-I${HOME}/OpenSees/OTHER/SuperLU_3.0/SRC/util.h \
-I${HOME}/OpenSees/OTHER/SuperLU/util.h \
-I${HOME}/OTHER/SuperLU_3.0/SRC/util.h \
-I${HOME}/OTHER/SuperLU_DIST_2.0/SRC/util.h \
-I${HOME}/OTHER/SuperLU/util.h \
-I${HOME}/OpenSees/SRC/modelbuilder\
-I${HOME}/OpenSees/SRC/modelbuilder/tcl \
-I${HOME}/OpenSees/SRC/tcl/include \
-I/opt/intel/mpi/include64 \
-I/opt/intel/Compiler/11.0/069/include

#MACHINE_INCLUDES = $(MPIINC) \
-I/usr/local/BerkeleyDB.4.0/include \
-I/usr/include/mysql \
-I$(HOME)/include \
-I$(UMFPACKdir) \
-I$(SUPERLU_DISTdir) \
-I$(SUPERLUdir) \
-I$(PETSCINC)


# this file contains all the OpenSees/SRC includes
include $(FE)/Makefile.incl

#TCL_INCLUDES = -I/home/fmk/tcl8.3.3/generic

#INCLUDES = $(MACHINE_INCLUDES) $(TCL_INCLUDES) $(FE_INCLUDES)
#TCL_INCLUDES = -I/home/csm/gourik/usr/local/include -I/home/csm/gourik/usr/local/tk/include
TCL_INCLUDES = -I/home/csm/gourik/opensees/OpenSees_sq_intel_3/tclconf/include -I/home/csm/gourik/opensees/OpenSees_sq_intel_3/tkconf/include

INCLUDES = $(TCL_INCLUDES) $(FE_INCLUDES) $(MACHINE_INCLUDES)

Posted: Thu Nov 12, 2009 3:32 pm
by fmk
you are missing the intel fortran routines, try -lifcore .. i could be others but you have to root around the intel fortran lib files.

Posted: Sat Jan 02, 2010 12:26 pm
by pankajd
thanks..but where should i pur -lifcore.i mean in which line?can u pl tell

Posted: Fri Jan 08, 2010 11:51 am
by fmk
MACHINE_SPECIFIC_LIBS
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