Problem while installing opensees on linux cluster

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gourik
Posts: 69
Joined: Wed Dec 31, 2008 10:07 pm
Location: C-DAC,Pune

Problem while installing opensees on linux cluster

Post by gourik »

Hi

I am trying to Install Opensees 2.1.0 on linux cluster with Opensees2.1.0.tar.
My cluster details are
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

After installation it says that
LIBRARIES BUILT ... NOW LINKING OpenSees PROGRAM

But the libBJmisc.a is not created in lib folder of Opensees . Also it throws following error
make[1]: Entering directory `<OpenSees Dir>/SRC/tcl'
make[1]: Nothing to be done for `tcl'.
make[1]: Leaving directory `<OpenSees Dir>/SRC/tcl'
make[1]: Entering directory `<OpenSees Dir>/SRC/modelbuilder/tcl'
Makefile:21: warning: overriding commands for target `tcl'
Makefile:13: warning: ignoring old commands for target `tcl'
Makefile:38: warning: overriding commands for target `tcl'
Makefile:21: warning: ignoring old commands for target `tcl'
Makefile:49: warning: overriding commands for target `tk'
Makefile:29: warning: ignoring old commands for target `tk'
make[2]: Entering directory `<OpenSees Dir>/SRC/tcl'
make[2]: Nothing to be done for `tcl'.
make[2]: Leaving directory `<OpenSees Dir>/SRC/tcl'
echo /usr/local/mpich-1.2.6/bin/mpicxx -rdynamic <OpenSees Dir>/SRC/tcl/tclMain.o <OpenSees Dir>/SRC/tcl/mpiMain.o <OpenSees Dir>/SRC/tcl/commands.o <OpenSees Dir>/SRC/modelbuilder/tcl/myCommands.o <OpenSees Dir>/SRC/actor/channel/MPI_Channel.o <OpenSees Dir>/SRC/actor/machineBroker/MPI_MachineBroker.o <OpenSees Dir>/SRC/domain/subdomain/ActorSubdomain.o <OpenSees Dir>/SRC/domain/subdomain/ShadowSubdomain.o <OpenSees Dir>/SRC/tcl/TclFeViewer.o <OpenSees Dir>/SRC/tcl/TclVideoPlayer.o \
/home/secg/csm/gourik/opensees/lib/libOpenSees.a -L/lib -L/home/secg/csm/gourik/opensees/lib \
-lm /home/secg/csm/gourik/opensees/lib/libArpack.a /home/secg/csm/gourik/opensees/lib/libDistributedSuperLU.a /home/secg/csm/gourik/opensees/lib/libSuperLU.a /home/secg/csm/gourik/opensees/lib/libUmfpack.a /home/secg/csm/gourik/opensees/lib/libLapack.a /home/secg/csm/gourik/opensees/lib/libBlas.a /home/secg/csm/gourik/opensees/lib/libCBlas.a /home/secg/csm/gourik/opensees/lib/libMetis.a <OpenSees Dir>/SRC/system_of_eqn/linearSOE/petsc/PetscSOE.o <OpenSees Dir>/SRC/system_of_eqn/linearSOE/petsc/PetscSolver.o <OpenSees Dir>/SRC/system_of_eqn/linearSOE/petsc/PetscSparseSeqSolver.o <OpenSees Dir>/OTHER/LAPACK/dgebak.o <OpenSees Dir>/OTHER/LAPACK/dgebal.o <OpenSees Dir>/OTHER/LAPACK/dgeev.o <OpenSees Dir>/OTHER/LAPACK/dgehd2.o <OpenSees Dir>/OTHER/LAPACK/dgehrd.o <OpenSees Dir>/OTHER/LAPACK/dhseqr.o <OpenSees Dir>/OTHER/LAPACK/dlahrd.o <OpenSees Dir>/OTHER/LAPACK/dorg2r.o <OpenSees Dir>/OTHER/LAPACK/dorghr.o <OpenSees Dir>/OTHER/LAPACK/dorgqr.o <OpenSees Dir>/OTHER/LAPACK/dpotrf.o <OpenSees Dir>/OTHER/LAPACK/dpotrs.o /home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscsnes.a /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 -lg2c -ldl /home/secg/csm/gourik/tcltk/lib/libtk8.5.so /home/secg/csm/gourik/tcltk/lib/libtcl8.5.so \
-ldl -lieee -lm -lc -lg2c -Wl,-rpath,/usr/lib -lpng -L/usr/local/mpich-1.2.6/lib -lmpich -o /home/secg/csm/gourik/opensees/bin/OpenSees
/usr/local/mpich-1.2.6/bin/mpicxx -rdynamic <OpenSees Dir>/SRC/tcl/tclMain.o <OpenSees Dir>/SRC/tcl/mpiMain.o <OpenSees Dir>/SRC/tcl/commands.o <OpenSees Dir>/SRC/modelbuilder/tcl/myCommands.o <OpenSees Dir>/SRC/actor/channel/MPI_Channel.o <OpenSees Dir>/SRC/actor/machineBroker/MPI_MachineBroker.o <OpenSees Dir>/SRC/domain/subdomain/ActorSubdomain.o <OpenSees Dir>/SRC/domain/subdomain/ShadowSubdomain.o <OpenSees Dir>/SRC/tcl/TclFeViewer.o <OpenSees Dir>/SRC/tcl/TclVideoPlayer.o /home/secg/csm/gourik/opensees/lib/libOpenSees.a -L/lib -L/home/secg/csm/gourik/opensees/lib -lm /home/secg/csm/gourik/opensees/lib/libArpack.a /home/secg/csm/gourik/opensees/lib/libDistributedSuperLU.a /home/secg/csm/gourik/opensees/lib/libSuperLU.a /home/secg/csm/gourik/opensees/lib/libUmfpack.a /home/secg/csm/gourik/opensees/lib/libLapack.a /home/secg/csm/gourik/opensees/lib/libBlas.a /home/secg/csm/gourik/opensees/lib/libCBlas.a /home/secg/csm/gourik/opensees/lib/libMetis.a <OpenSees Dir>/SRC/system_of_eqn/linearSOE/petsc/PetscSOE.o <OpenSees Dir>/SRC/system_of_eqn/linearSOE/petsc/PetscSolver.o <OpenSees Dir>/SRC/system_of_eqn/linearSOE/petsc/PetscSparseSeqSolver.o <OpenSees Dir>/OTHER/LAPACK/dgebak.o <OpenSees Dir>/OTHER/LAPACK/dgebal.o <OpenSees Dir>/OTHER/LAPACK/dgeev.o <OpenSees Dir>/OTHER/LAPACK/dgehd2.o <OpenSees Dir>/OTHER/LAPACK/dgehrd.o <OpenSees Dir>/OTHER/LAPACK/dhseqr.o <OpenSees Dir>/OTHER/LAPACK/dlahrd.o <OpenSees Dir>/OTHER/LAPACK/dorg2r.o <OpenSees Dir>/OTHER/LAPACK/dorghr.o <OpenSees Dir>/OTHER/LAPACK/dorgqr.o <OpenSees Dir>/OTHER/LAPACK/dpotrf.o <OpenSees Dir>/OTHER/LAPACK/dpotrs.o /home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscsnes.a /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 -lg2c -ldl /home/secg/csm/gourik/tcltk/lib/libtk8.5.so /home/secg/csm/gourik/tcltk/lib/libtcl8.5.so -ldl -lieee -lm -lc -lg2c -Wl,-rpath,/usr/lib -lpng -L/usr/local/mpich-1.2.6/lib -lmpich -o /home/secg/csm/gourik/opensees/bin/OpenSees

<OpenSees Dir>/SRC/tcl/tclMain.o(.text+0x145): In function `g3TclMain(int, char**, int (*)(Tcl_Interp*), int, int)':
: undefined reference to `TclFormatInt'
<OpenSees Dir>/SRC/tcl/commands.o(.text+0x26b6): In function `specifySOE(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `DistributedSparseGenColLinSOE::DistributedSparseGenColLinSOE(SparseGenColLinSolver&)'
<OpenSees Dir>/SRC/tcl/commands.o(.text+0x27fc): In function `specifySOE(void*, Tcl_Interp*, int, char const**)':
: undefined reference to `DistributedSuperLU::DistributedSuperLU(int, int)'
/home/secg/csm/gourik/opensees/lib/libOpenSees.a(FEM_ObjectBrokerAllClasses.o)(.text+0x3160): In function `FEM_ObjectBrokerAllClasses::getNewLinearSOE(int, int)':
: undefined reference to `DistributedSuperLU::DistributedSuperLU()'
/home/secg/csm/gourik/opensees/lib/libOpenSees.a(FEM_ObjectBrokerAllClasses.o)(.text+0x3177): In function `FEM_ObjectBrokerAllClasses::getNewLinearSOE(int, int)':
: undefined reference to `DistributedSparseGenColLinSOE::DistributedSparseGenColLinSOE(SparseGenColLinSolver&)'
/home/secg/csm/gourik/opensees/lib/libOpenSees.a(FEM_ObjectBrokerAllClasses.o)(.text+0x340c): In function `FEM_ObjectBrokerAllClasses::getNewLinearSOE(int, int)':
: undefined reference to `DistributedSparseGenColLinSOE::DistributedSparseGenColLinSOE(SparseGenColLinSolver&)'
collect2: ld returned 1 exit status
make[1]: *** [tcl] Error 1
make[1]: Leaving directory `<OpenSees Dir>/SRC/modelbuilder/tcl'
make: *** [all] Error 2

Please guide regarding this
Thanks And Regards,

Gouri
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fmk
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Post by fmk »

if you have tcl85 installed put -D_TCL85 in C__ flags, if 8.4 -D_TCL84
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gourik
Posts: 69
Joined: Wed Dec 31, 2008 10:07 pm
Location: C-DAC,Pune

Post by gourik »

I have changed the CFLAGS as per your suggestion. Still same error is there :(
Thanks And Regards,

Gouri
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fmk
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Post by fmk »

post your Makefile.def for me to have a look at.
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gourik
Posts: 69
Joined: Wed Dec 31, 2008 10:07 pm
Location: C-DAC,Pune

Makefile.def is as mentioned below

Post by gourik »

this make file is copied from MAKES/Makefile.def_LINUX_CLUSTER

############################################################################
#
# 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

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
RELIABILITY = NO_RELIABILITY
GRAPHICS = NONE
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
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/tcltk/lib/libtk8.5.so \
/home/secg/csm/gourik/tcltk/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
FORTRAN = /usr/bin/g77
F90 =
LINKER = /usr/local/mpich-1.2.6/bin/mpicxx

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

CFLAGS = -Wall -D_TCL85 $(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$(BASE)/lib \
-L$(HOME)/lib \




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)\
-lg2c -ldl

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

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


PETSCINC = -I/home/secg/csm/gourik/opensees/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1 -I/home/secg/csm/gourik/opensees/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1/bmake/linux-gnu -I/home/secg/csm/gourik/opensees/OpenSees/SRC/system_of_eqn/linear/petsc/petsc-2.2.1/include \
-I/home/secg/csm/gourik/opensees/petsc-2.2.1/include/mpiuni -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_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 \
/home/secg/csm/gourik/PETSC/petsc-2.2.1/lib/libg/linux-gnu/libpetscsnes.a \
/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/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 $(MPILIB)
endif


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


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

INCLUDES = $(MACHINE_INCLUDES) $(TCL_INCLUDES) $(FE_INCLUDES)
Thanks And Regards,

Gouri
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fmk
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Posts: 5884
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Location: UC Berkeley
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Post by fmk »

you need to add the following to the Makefile.def or else place theem in MACHINE_NUMERICAL_LIBS

PARALLEL_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)
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gourik
Posts: 69
Joined: Wed Dec 31, 2008 10:07 pm
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Post by gourik »

Thanks fmk.. It works :)
Thanks And Regards,

Gouri
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gourik
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Problem while installing opensees on linux cluster

Post by gourik »

Hi ,

I have successfully installed the Opensees with PARLLEL mode.
Now when i changed the mode to
PARALLEL_INTERPRETERS

I got following error. Rest of the make file is same as previous.

/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
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'
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fmk
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Post by fmk »

did you do a 'make wipe; make' in OpenSees
directory? .. if you look i never did the dependencies in the Makefile's and so when you need to change from one app to another the make wipe is required.
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gourik
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Joined: Wed Dec 31, 2008 10:07 pm
Location: C-DAC,Pune

Post by gourik »

After following the same, Now OpenSees executable is getting created in bin folder without display of any error message.
But when I try to run the ./OpenSees command in bin directory I got the following error
./OpenSees: error while loading shared libraries: libpetscsnes.so: cannot open shared object file: No such file or directory

Makefile.def is same as mentioned above. Only change is of Mode its PARALLEL_INTERPRETERS
Thanks And Regards,

Gouri
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fmk
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Post by fmk »

that's a setup problem with petsc .. sit sees the lib in linking but not when running .. suggest you look at your LD_LIBRARY_PATH
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lsantiago
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Post by lsantiago »

Hi, I'm using the same Makefile.def this forum but can not compile it. To compile a PETS follow the following steps:

1. cd /home/Cluster/PETSC
2. export PETSC_DIR=$PWD
3. ./config/configure.py PETSC_ARCH=linux-gnu --with-blas-lapack-dir=/usr/local/lib --with-mpi-dir=/home/Cluster/mpich2
4. make all
5. make test

Once you've compiled and modified from the Makefile.def opens. It is necessary to create the folder linear in OpenSees/SRC/system_of_eqn/ and add the folder to compile PETS?. Or if I got this as well.

The Makefile.def I use is: [url]
http://docs.google.com/Doc?docid=dts9t2 ... hhhf&hl=en[/url]

And the error I get is this:

make[3]: Entering directory `/cluster/opensees/OpenSees/SRC/recorder/response'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/cluster/opensees/OpenSees/SRC/recorder/response'
make[2]: Leaving directory `/cluster/opensees/OpenSees/SRC/damage'
make[2]: Entering directory `/cluster/opensees/OpenSees/SRC/api'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/cluster/opensees/OpenSees/SRC/api'
make[1]: Leaving directory `/cluster/opensees/OpenSees/SRC'
LIBRARIES BUILT ... NOW LINKING OpenSees PROGRAM
make[1]: Entering directory `/cluster/opensees/OpenSees/SRC/tcl'
make[1]: Nothing to be done for `tcl'.
make[1]: Leaving directory `/cluster/opensees/OpenSees/SRC/tcl'
make[1]: Entering directory `/cluster/opensees/OpenSees/SRC/modelbuilder/tcl'
Makefile:21: warning: overriding commands for target `tcl'
Makefile:13: warning: ignoring old commands for target `tcl'
Makefile:38: warning: overriding commands for target `tcl'
Makefile:21: warning: ignoring old commands for target `tcl'
Makefile:49: warning: overriding commands for target `tk'
Makefile:29: warning: ignoring old commands for target `tk'
make[2]: Entering directory `/cluster/opensees/OpenSees/SRC/tcl'
make[2]: Nothing to be done for `tcl'.
make[2]: Leaving directory `/cluster/opensees/OpenSees/SRC/tcl'
echo /cluster/mpich2/bin/mpicxx -rdynamic /cluster/opensees/OpenSees/SRC/tcl/tclMain.o /cluster/opensees/OpenSees/SRC/tcl/mpiMain.o /cluster/opensees/OpenSees/SRC/tcl/commands.o /cluster/opensees/OpenSees/SRC/modelbuilder/tcl/myCommands.o /cluster/opensees/OpenSees/SRC/actor/channel/MPI_Channel.o /cluster/opensees/OpenSees/SRC/actor/machineBroker/MPI_MachineBroker.o /cluster/opensees/OpenSees/SRC/domain/subdomain/ActorSubdomain.o /cluster/opensees/OpenSees/SRC/domain/subdomain/ShadowSubdomain.o /cluster/opensees/OpenSees/SRC/tcl/TclFeViewer.o /cluster/opensees/OpenSees/SRC/tcl/TclVideoPlayer.o \
/cluster/opensees/lib/libOpenSees.a -L/lib -L/cluster/opensees/lib /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSparseGenColLinSOE.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/sparseGEN/SparseGenColLinSOE.o /cluster/opensees/lib/libDistributedSuperLU.a \
-lm /cluster/opensees/lib/libArpack.a /cluster/opensees/lib/libDistributedSuperLU.a /cluster/opensees/lib/libSuperLU.a /cluster/opensees/lib/libUmfpack.a /cluster/opensees/lib/libLapack.a /cluster/opensees/lib/libBlas.a /cluster/opensees/lib/libCBlas.a /cluster/opensees/lib/libMetis.a /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSOE.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSolver.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSparseSeqSolver.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgebak.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgebal.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgeev.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgehd2.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgehrd.o /cluster/opensees/OpenSees/OTHER/LAPACK/dhseqr.o /cluster/opensees/OpenSees/OTHER/LAPACK/dlahrd.o /cluster/opensees/OpenSees/OTHER/LAPACK/dorg2r.o /cluster/opensees/OpenSees/OTHER/LAPACK/dorghr.o /cluster/opensees/OpenSees/OTHER/LAPACK/dorgqr.o /cluster/opensees/OpenSees/OTHER/LAPACK/dpotrf.o /cluster/opensees/OpenSees/OTHER/LAPACK/dpotrs.o /cluster/PETSC/lib/libg/linux-gnu/libpetscsnes.a /cluster/PETSC/lib/libg/linux-gnu/libpetscksp.a /cluster/PETSC/lib/libg/linux-gnu/libpetscdm.a /cluster/PETSC/lib/libg/linux-gnu/libpetscmat.a /cluster/PETSC/lib/libg/linux-gnu/libpetscvec.a /cluster/PETSC/lib/libg/linux-gnu/libpetsc.a \ -lg2c -ldl /cluster/tcltk/lib/libtk8.5.so /cluster/tcltk/lib/libtcl8.5.so \
-ldl -lieee -lm -lc -lg2c -Wl,-rpath,/usr/lib -lpng -L/cluster/mpich2/lib -lmpich -o /cluster/opensees/bin/OpenSees
/cluster/mpich2/bin/mpicxx -rdynamic /cluster/opensees/OpenSees/SRC/tcl/tclMain.o /cluster/opensees/OpenSees/SRC/tcl/mpiMain.o /cluster/opensees/OpenSees/SRC/tcl/commands.o /cluster/opensees/OpenSees/SRC/modelbuilder/tcl/myCommands.o /cluster/opensees/OpenSees/SRC/actor/channel/MPI_Channel.o /cluster/opensees/OpenSees/SRC/actor/machineBroker/MPI_MachineBroker.o /cluster/opensees/OpenSees/SRC/domain/subdomain/ActorSubdomain.o /cluster/opensees/OpenSees/SRC/domain/subdomain/ShadowSubdomain.o /cluster/opensees/OpenSees/SRC/tcl/TclFeViewer.o /cluster/opensees/OpenSees/SRC/tcl/TclVideoPlayer.o /cluster/opensees/lib/libOpenSees.a -L/lib -L/cluster/opensees/lib /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSuperLU.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/sparseGEN/DistributedSparseGenColLinSOE.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/sparseGEN/SparseGenColLinSOE.o /cluster/opensees/lib/libDistributedSuperLU.a -lm /cluster/opensees/lib/libArpack.a /cluster/opensees/lib/libDistributedSuperLU.a /cluster/opensees/lib/libSuperLU.a /cluster/opensees/lib/libUmfpack.a /cluster/opensees/lib/libLapack.a /cluster/opensees/lib/libBlas.a /cluster/opensees/lib/libCBlas.a /cluster/opensees/lib/libMetis.a /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSOE.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSolver.o /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSparseSeqSolver.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgebak.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgebal.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgeev.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgehd2.o /cluster/opensees/OpenSees/OTHER/LAPACK/dgehrd.o /cluster/opensees/OpenSees/OTHER/LAPACK/dhseqr.o /cluster/opensees/OpenSees/OTHER/LAPACK/dlahrd.o /cluster/opensees/OpenSees/OTHER/LAPACK/dorg2r.o /cluster/opensees/OpenSees/OTHER/LAPACK/dorghr.o /cluster/opensees/OpenSees/OTHER/LAPACK/dorgqr.o /cluster/opensees/OpenSees/OTHER/LAPACK/dpotrf.o /cluster/opensees/OpenSees/OTHER/LAPACK/dpotrs.o /cluster/PETSC/lib/libg/linux-gnu/libpetscsnes.a /cluster/PETSC/lib/libg/linux-gnu/libpetscksp.a /cluster/PETSC/lib/libg/linux-gnu/libpetscdm.a /cluster/PETSC/lib/libg/linux-gnu/libpetscmat.a /cluster/PETSC/lib/libg/linux-gnu/libpetscvec.a /cluster/PETSC/lib/libg/linux-gnu/libpetsc.a -lg2c -ldl /cluster/tcltk/lib/libtk8.5.so /cluster/tcltk/lib/libtcl8.5.so -ldl -lieee -lm -lc -lg2c -Wl,-rpath,/usr/lib -lpng -L/cluster/mpich2/lib -lmpich -o /cluster/opensees/bin/OpenSees
c++: /cluster/opensees/lib/libDistributedSuperLU.a: No such file or directory
c++: /cluster/opensees/lib/libDistributedSuperLU.a: No such file or directory
c++: /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSOE.o: No such file or directory
c++: /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSolver.o: No such file or directory
c++: /cluster/opensees/OpenSees/SRC/system_of_eqn/linearSOE/petsc/PetscSparseSeqSolver.o: No such file or directory
c++: : No such file or directory
make[1]: *** [tcl] Error 1
make[1]: Leaving directory `/cluster/opensees/OpenSees/SRC/modelbuilder/tcl'
make: *** [all] Error 2[/url]
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fmk
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Post by fmk »

see this thread:
[url]
http://opensees.berkeley.edu/community/ ... 3158#23158
[/url]
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albertodegama
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Re: Problem while installing opensees on linux cluster

Post by albertodegama »

For the case of direct job subssion, NEES ran 300 OpenSEES jobs for an estimated 2400 hours to analyze the response of a structure called the Self-Centering Steel Plate Shear Wall (SC-SPSW) system.

The OSG User Support team is now helping NEES scale up its workload on OSG by about 2 orders of magnitude. This activity is considered a demo of production computations for NEES. This work is done in support of Andre' Barbosa, a graduate student from UCSD.
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