Regarding opensees installation on linux

[gourik]

Hi. I am installing Opensees 2.2.1 on Linux cluster with petsc-2.2.1, tcl/tk-8.5.4 and facing following issues .

My machine configuration is
Linux xn00.npsf.cdac.ernet.in 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:30:39 EST 2005 i686 i686 i386 GNU/Linux

errors :

/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x8c9): In function `wipeAnalysis(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x928): In function `wipeModel(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x9cb): In function `resetModel(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0xa14): In function `initializeAnalysis(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0xa34): In function `initializeAnalysis(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0xa5e): more undefined references to `theDomain' follow
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x2add): In function `specifySOE(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `PetscSolver::PetscSolver(char*, char*, double, double, double, int)'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x2af5): In function `specifySOE(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `PetscSOE::PetscSOE(PetscSolver&, int)'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x2b73): In function `specifySOE(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `PetscSparseSeqSolver::PetscSparseSeqSolver(char*, char*, double, double, double, int)'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x3959): In function `specifyAlgorithm(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x4993): In function `specifyCTest(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x4d8a): In function `specifyIntegrator(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x5105): In function `specifyIntegrator(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x89c7): In function `addRecorder(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `theDomain'
/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/tcl/commands.o(.text+0x89f9): more undefined references to `theDomain' follow
/home/secg/csm/gourik/opensees_parallel/lib/libOpenSees.a(FEM_ObjectBrokerAllClasses.o)(.text+0x304f): In function `FEM_ObjectBrokerAllClasses::getNewLinearSOE(int, int)':
: undefined reference to `PetscSolver::PetscSolver()'
/home/secg/csm/gourik/opensees_parallel/lib/libOpenSees.a(FEM_ObjectBrokerAllClasses.o)(.text+0x3069): In function `FEM_ObjectBrokerAllClasses::getNewLinearSOE(int, int)':
: undefined reference to `PetscSOE::PetscSOE(PetscSolver&, int)'
collect2: ld returned 1 exit status
make[1]: *** [tcl] Error 1
make[1]: Leaving directory `/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/modelbuilder/tcl'
make: *** [all] Error 2


I am trying this sonce so many days and stuck at this point only. Please help me regarding this. My make file is as follows

# %---------------------------------%
# | SECTION 1: PROGRAM |
# %---------------------------------%
#
# Specify the location and name of the OpenSees interpreter program
# that will be created (if this all works

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_INTERPRETERS
#PROGRAMMING_MODE = PARALLEL
RELIABILITY = NO_RELIABILITY
GRAPHICS = NONE
#DEBUG_MODE = DEBUG
DEBUG_MODE = NO_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 =
# PUT YOUR HOME DIRECTOREY HERE
HOME = /home/secg/csm/gourik/opensees_parallel
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/SRC
SUPERLU_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/secg/csm/gourik/usr/local//lib/libtk8.5.so \
/home/secg/csm/gourik/usr/local//lib/libtcl8.5.so


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++ = /usr/bin/g++
CC = /usr/bin/gcc
FC = /usr/bin/g77
#CC++ = /usr/local/mpich-1.2.6/bin/mpicxx
#CC = /usr/local/mpich-1.2.6/bin/mpicc
#FC = /usr/local/mpich-1.2.6/bin/mpif90
FORTRAN = /usr/local/mpich-1.2.6/bin/mpif90
F90 =
LINKER = /usr/local/mpich-1.2.6/bin/mpicxx
#LINKER = /usr/bin/g++

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

PROGRAMMING_FLAG =

ifeq ($(GRAPHICS), UsinOpenGl)
GRAPHIC_FLAG = -D_GLX
#GRAPHIC_LIBRARY = -L/usr/X11/R6/lib -lGL -lGLU
GRAPHIC_LIBRARY = -L/usr/X11R6/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 -O2 -D_LINUX -D_UNIX $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG) -D_PARALLEL_PROCESSING -D_TCL85 -D_PETSC

CFLAGS = -Wall -g -pg -D_TCL85 $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG) -D_PETSC

FFLAGS = -Wall
LINKFLAGS = -rdynamic -g -pg

else

C++FLAGS = -Wall -O2 -D_LINUX -D_UNIX -D_TCL85 -Wall $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG) -D_PARALLEL_PROCESSING -ffloat-store -D_PETSC

CFLAGS = -Wall -O2 -D_TCL85 $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(PROGRAMMING_FLAG) -D_PETSC
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$(BASE)/lib \
-L$(HOME)/lib \

# ------ added fmk

#PRALLEL_LIB = $(FE)/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.o \
$(FE)/system_of_eqn/linearSOE/sparseGEN/DistributedSparseGenColLinSOE.o \
$(FE)/system_of_eqn/linearSOE/sparseGEN/SparseGenColLinSOE.o \
$(DISTRIBUTED_SUPERLU_LIBRARY)

PARALLEL_LIB = $(FE)/system_of_eqn/linearSOE/diagonal/DistributedDiagonalSOE.o \
$(FE)/system_of_eqn/linearSOE/diagonal/DistributedDiagonalSolver.o \
$(FE)/system_of_eqn/linearSOE/sparseGEN/DistributedSparseGenColLinSOE.o \
$(FE)/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.o \
$(FE)/system_of_eqn/linearSOE/sparseGEN/SparseGenColLinSOE.o \
$(DISTRIBUTED_SUPERLU_LIBRARY)
# -----------------------------------------------------------


MPICC = mpicc
#MPICC = -I/usr/local/mpich-1.2.6/bin/mpicc
MPIINC = -I/usr/local/mpich-1.2.6/include
MPILIB = -L/usr/local/mpich-1.2.6/lib -lmpich -lpmpich

PETSC_INC = -I/home/secg/csm/gourik/PETSC/petsc-2.2.1 \
-I/home/secg/csm/gourik/PETSC/petsc-2.2.1/bmake/linux-gnu \
-I/home/secg/csm/gourik/PETSC/petsc-2.2.1/include \
-I/home/secg/csm/gourik/PETSC/petsc-2.2.1/include/mpiuni \
-DPETSC_USE_BOPT_g -DPETSC_USE_EXTERN_CXX

#PETSC = -I$(FE)/system_of_eqn/linearSOE/petsc

PETSCINC = -I/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1 -I/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1/bmake/linux-gnu -I/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1/include -I/home/secg/csm/gourik/opensees_parallel/OpenSees/SRC/system_of_eqn/linearSOE/sparseGEN -I/home/secg/csm/gourik/opensees_parallel/petsc-2.2.1/include/mpiuni \
-I/home/secg/csm/gourik/PETSC/petsc-2.2.1/include -D_PETSC -I/home/secg/csm/gourik/PETSC/petsc-2.2.1/bmake/linux-gnu -DPETSC_USE_BOPT_g -DPETSC_USE_EXTERN_CXX

PETSCINC = -I/home/secg/csm/gourik/PETSC/petsc-2.2.1/include -D_PETSC -I/home/secg/csm/gourik/PETSC/petsc-2.2.1/bmake/linux-gnu -DPETSC_USE_BOPT_g -DPETSC_USE_EXTERN_CXX


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

PETSC_DIR = /home/secg/csm/gourik/PETSC/petsc-2.2.1
#PETSC_ARCH = /home/secg/csm/gourik/PETSC/petsc-2.2.1/bin/petscarch
PETSC_ARCH = linux-gnu
# -L/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/ \

#PETSC_LIB = -L$(PETSC_DIR)/lib/libg/$(PETSC_ARCH) \
#PETSC_LIB = -L$(PETSC_DIR)/lib/libg/linux-gnu \
# -lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc \
PETSC_LIB =$(FE)/system_of_eqn/linearSOE/petsc/PetscSOE.o \
$(FE)/system_of_eqn/linearSOE/petsc/PetscSolver.o \
$(FE)/system_of_eqn/linearSOE/sparseGEN/SparseGenRowLinSOE.o \
$(FE)/system_of_eqn/linearSOE/sparseGEN/SparseGenRowLinSolver.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/dorghr.o \
$(HOME)/OpenSees/OTHER/LAPACK/dpotrf.o \
$(HOME)/OpenSees/OTHER/LAPACK/dpotrs.o \
$(HOME)/OpenSees/OTHER/LAPACK/dpotrs.o \
/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscsnes.so \
/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscksp.a \
/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscdm.a \
/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscmat.a \
/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscvec.a \
/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetsc.a \
-L$(PETSC_DIR)/lib/libg/linux-gnu \
-L$(PETSC_DIR)/bmake/linux-gnu \
-lpetscsnes -lpetscksp -lpetscdm -lpetscmat -lpetscvec -lpetsc


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


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)\
$(PRALLEL_LIB)\
$(TCL_LIBRARY)\
-lg2c -ldl


ifeq ($(PROGRAMMING_MODE), THREADS)
MACHINE_SPECIFIC_LIBS = -lpthread
#MACHINE_SPECIFIC_LIBS = -ldl -lieee -lm -lc -lg2c -Wl,-rpath,/usr/lib -lpng $(MPILIB)
else
MACHINE_SPECIFIC_LIBS = -ldl -lieee -lm -lc -lg2c -Wl,-rpath,/usr/lib -lpng $(MPILIB)
endif

# %---------------------------------------------------------%
# | SECTION 8: INCLUDE FILES |
# | |
# | The following macros specify include files needed for |
# | compilation. |
# %---------------------------------------------------------%


MACHINE_INCLUDES = $(MPIINC) \
-I/usr/local/BerkeleyDB.4.0/include \
-I/usr/local/mpich-1.2.6/include \
-I/usr/include/mysql \
-I$(HOME)/include \
-I$(UMFPACKdir) \
-I$(SUPERLUdir) \
-I$(SUPERLU_DISTdir) \
$(PETSC_INC) $(PETSCINC)


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

#TCL_INCLUDES = -I/home/secg/csm/gourik/tcltk/tcl8.5.6/generic/generic
TCL_INCLUDES = -I/home/secg/csm/gourik/usr/local/include

INCLUDES = $(MACHINE_INCLUDES) $(TCL_INCLUDES) $(FE_INCLUDES) -I/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/ -I${PETSC_DIR}/bmake/${PETSC_ARCH}

[lsquinones]

Check this variable TCL_LIBRARY, I think it should be

TCL_LIBRARY = /home/secg/csm/gourik/usr/local/lib/libtk8.5.so \
/home/secg/csm/gourik/usr/local/lib/libtcl8.5.so

and not


TCL_LIBRARY = /home/secg/csm/gourik/usr/local//lib/libtk8.5.so \
/home/secg/csm/gourik/usr/local//lib/libtcl8.5.so

[gourik]

hey ..

i have changed the path ..
still same error

[lsquinones]

What is the Makefile.de that OpenSees Parallel compile?