Build Errors in CentOS 6.2 64bit, Need help

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ysp8293
Posts: 1
Joined: Mon Sep 27, 2010 10:06 pm
Location: CSUFT

Build Errors in CentOS 6.2 64bit, Need help

Post by ysp8293 » Tue May 10, 2016 4:32 am

I have download the OpenSees by svn co svn://peera.berkeley.edu/usr/local/svn/OpenSees/trunk OpenSees, when i build it, the errors as follow appears:
Could you help with the compiliation problem?
Thanks,

/home/ysp8293/lib/libSuperLU.a(dgstrs.o): In function `dgstrs':
dgstrs.c:(.text+0x846): undefined reference to `_intel_fast_memcpy'
dgstrs.c:(.text+0xacc): undefined reference to `_intel_fast_memcpy'
dgstrs.c:(.text+0xbfa): undefined reference to `_intel_fast_memcpy'
dgstrs.c:(.text+0xd8a): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(dsnode_dfs.o): In function `dsnode_dfs':
dsnode_dfs.c:(.text+0x27d): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(dcolumn_dfs.o):dcolumn_dfs.c:(.text+0x232): more undefined references to `_intel_fast_memcpy' follow
/home/ysp8293/lib/libSuperLU.a(dmemory.o): In function `doubleCalloc':
dmemory.c:(.text+0x126d): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(dmemory.o): In function `dexpand..2':
dmemory.c:(.text+0x1833): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(dmemory.o): In function `dexpand..3':
dmemory.c:(.text+0x1b01): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(dutil.o): In function `dCopy_CompCol_Matrix':
dutil.c:(.text+0x1e1): undefined reference to `_intel_fast_memcpy'
dutil.c:(.text+0x222): undefined reference to `_intel_fast_memcpy'
dutil.c:(.text+0x271): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(dutil.o):dutil.c:(.text+0x4fc): more undefined references to `_intel_fast_memcpy' follow
/home/ysp8293/lib/libSuperLU.a(memory.o): In function `intCalloc':
memory.c:(.text+0x2bd): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(get_perm_c.o): In function `get_colamd':
get_perm_c.c:(.text+0xd1): undefined reference to `_intel_fast_memcpy'
get_perm_c.c:(.text+0x11e): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(get_perm_c.o): In function `getata':
get_perm_c.c:(.text+0x3fb): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(get_perm_c.o): In function `at_plus_a':
get_perm_c.c:(.text+0xaa1): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(get_perm_c.o): In function `get_perm_c':
get_perm_c.c:(.text+0x1177): undefined reference to `_intel_fast_memset'
get_perm_c.c:(.text+0x16a4): undefined reference to `_intel_fast_memcpy'
get_perm_c.c:(.text+0x16f9): undefined reference to `_intel_fast_memcpy'
get_perm_c.c:(.text+0x1890): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(sp_preorder.o): In function `sp_preorder':
sp_preorder.c:(.text+0x2b0): undefined reference to `_intel_fast_memcpy'
sp_preorder.c:(.text+0x34c): undefined reference to `_intel_fast_memcpy'
sp_preorder.c:(.text+0x3e8): undefined reference to `_intel_fast_memcpy'
sp_preorder.c:(.text+0x480): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(sp_preorder.o): In function `check_perm':
sp_preorder.c:(.text+0x6e8): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(relax_snode.o): In function `relax_snode':
relax_snode.c:(.text+0x43): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(heap_relax_snode.o): In function `heap_relax_snode':
heap_relax_snode.c:(.text+0x1ba): undefined reference to `_intel_fast_memcpy'
heap_relax_snode.c:(.text+0x1f1): undefined reference to `_intel_fast_memset'
heap_relax_snode.c:(.text+0x528): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(colamd.o): In function `symamd':
colamd.c:(.text+0x3af): undefined reference to `_intel_fast_memcpy'
colamd.c:(.text+0x713): undefined reference to `_intel_fast_memcpy'
/home/ysp8293/lib/libSuperLU.a(dsp_blas2.o): In function `sp_dtrsv':
dsp_blas2.c:(.text+0x4a): undefined reference to `__intel_sse2_strncmp'
dsp_blas2.c:(.text+0x60): undefined reference to `__intel_sse2_strncmp'
dsp_blas2.c:(.text+0x86): undefined reference to `__intel_sse2_strncmp'
dsp_blas2.c:(.text+0x9c): undefined reference to `__intel_sse2_strncmp'
dsp_blas2.c:(.text+0xb2): undefined reference to `__intel_sse2_strncmp'
/home/ysp8293/lib/libSuperLU.a(dsp_blas2.o):dsp_blas2.c:(.text+0xd5): more undefined references to `__intel_sse2_strncmp' follow
/home/ysp8293/lib/libSuperLU.a(dsp_blas2.o): In function `sp_dgemv':
dsp_blas2.c:(.text+0x1336): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(sp_coletree.o): In function `sp_coletree':
sp_coletree.c:(.text+0x75): undefined reference to `_intel_fast_memset'
sp_coletree.c:(.text+0xa9): undefined reference to `_intel_fast_memset'
sp_coletree.c:(.text+0xe7): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(sp_coletree.o): In function `TreePostorder':
sp_coletree.c:(.text+0x4ac): undefined reference to `_intel_fast_memset'
/home/ysp8293/lib/libSuperLU.a(sp_coletree.o):sp_coletree.c:(.text+0x4e6): more undefined references to `_intel_fast_memset' follow
collect2: ld returned 1 exit status
make[1]: *** [tcl] Error 1
make[1]: Leaving directory `/home/ysp8293/OpenSees/SRC/modelbuilder/tcl'
make: *** [all] Error 2


########################################################################
Content of Makefile.def
########################################################################
############################################################################
#
# Program: OpenSees
#
# Purpose: A Top-level Makefile to create the libraries needed
# to use the OpenSees framework. Works on Linux version 6.1
# and below.
#
# Written: fmk
# Created: 10/99
#
# Send bug reports, comments or suggestions to fmckenna@ce.berkeley.edu
#
############################################################################

## ssh to machine from your own:
# chmod 'go+rwx' XXX.pem
# (right click running instance, click connect, click connect with standalone ssh client to get command:
# ssh -i XXX.pem root@YYY.amazonaws.com

# Following are commands to build OpenSees
# on EC2 FEDORA 64 bit machine (ami-7d0c6314) once logged in

# sudo yum install gcc.x86_64
# sudo yum install gcc-c++.x86_64
# sudo yum install gcc-gfortran.x86_64
# sudo yum install tcl.x86_64
# sudo yum install tcl-devel.x86_64
# sudo yum install svn
# sudo yum install emacs
# mkdir bin
# mkdir lib
# svn co svn://opensees.berkeley.edu:/usr/local/svn/OpenSees/trunk OpenSees
# cd OpenSees
# cp ./MAKES/Makefile.def.EC2-REDHAT-ENTERPRISE ./Makefile.def
# make

# END of commands to build OpenSees.


# %---------------------------------%
# | 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

OPERATING_SYSTEM = LINUX
GRAPHICS = NONE
GRAPHIC_FLAG = -D_NOGRAPHICS
PROGRAMMING_MODE = SEQUENTIAL
DEBUG_MODE = NO_DEBUG
RELIABILITY = NO_RELIABILITY


# %---------------------------------%
# | SECTION 2: 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 = /home/ysp8293
FE = $(HOME)/OpenSees/SRC

AMDdir = $(HOME)/OpenSees/OTHER/AMD
BLASdir = $(HOME)/OpenSees/OTHER/BLAS
CBLASdir = $(HOME)/OpenSees/OTHER/CBLAS
LAPACKdir = $(HOME)/OpenSees/OTHER/LAPACK
SUPERLUdir = $(HOME)/OpenSees/OTHER/SuperLU_5.2.0/SRC
ARPACKdir = $(HOME)/OpenSees/OTHER/ARPACK
UMFPACKdir = $(HOME)/OpenSees/OTHER/UMFPACK
METISdir = $(HOME)/OpenSees/OTHER/METIS
CSPARSEdir = $(HOME)/OpenSees/OTHER/CSPARSE
SRCdir = $(HOME)/OpenSees/SRC
CSPARSEdir = $(HOME)/OpenSees/OTHER/CSPARSE

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

# %-------------------------------------------------------%
# | SECTION 3: 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
CSPARSE_LIBRARY = $(HOME)/lib/libCBlas.a
ARPACK_LIBRARY = $(HOME)/lib/libArpack.a
AMD_LIBRARY = $(HOME)/lib/libAMD.a
UMFPACK_LIBRARY = $(HOME)/lib/libUmfpack.a
METIS_LIBRARY = $(HOME)/lib/libMetis.a
TCL_LIBRARY = /usr/lib64/libtcl8.5.so
BLITZ_LIBRARY = $(HOME)/blitz/lib/libblitz.a
GRAPHIC_LIBRARY =
CSPARSE_LIBRARY = $(HOME)/lib/libCSparse.a

# WATCH OUT .. These libraries are removed when 'make wipe' is invoked.
WIPE_LIBS = $(FE_LIBRARY) \
$(LAPACK_LIBRARY) \
$(BLAS_LIBRARY) \
$(CBLAS_LIBRARY) \
$(SUPERLU_LIBRARY) \
$(ARPACK_LIBRARY) \
$(UMFPACK_LIBRARY) \
$(METIS_LIBRARY)

# %---------------------------------------------------------%
# | SECTION 4: 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/gfortran

AR = ar
ARFLAGS = cqls
RANLIB = ranlib
RANLIBFLAGS =

# Compiler Flags
#
# NOTES:
# C++ FLAGS TAKE need _UNIX or _WIN32 for preprocessor dircetives
# - the _WIN32 for the Windows95/98 or NT operating system.
# C FLAGS used -DUSE_VENDOR_BLAS (needed in SuperLU) if UNIX in C++ FLAGS
#

# modified as optimizaton currently causing problems with Steeln01 code
ifeq ($(DEBUG_MODE), DEBUG)

C++FLAGS = -Wall -D_LINUX -D_UNIX -D_TCL85 \
$(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG) \
-g -pg


CFLAGS = -Wall -pg $(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) $(PROGRAMMING_FLAG)
FFLAGS = -Wall

# Linker
LINKER = $(CC++)
LINKFLAGS = -g -pg

else

C++FLAGS = -Wall -D_LINUX -D_UNIX -D_TCL85 \
$(GRAPHIC_FLAG) $(RELIABILITY_FLAG) $(DEBUG_FLAG) \
$(PROGRAMMING_FLAG) -O3 -ffloat-store
CFLAGS = -Wall -O2
FFLAGS = -Wall -O

# Linker
LINKER = $(CC++)
LINKFLAGS = -rdynamic -Wl

endif


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

# %---------------------------------------------------------%
# | SECTION 5: 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 .f 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 $< -o $@
.f.o:
@$(ECHO) Making $@ from $<
$(FC) $(FFLAGS) -c $< -o $@

# %---------------------------------------------------------%
# | SECTION 6: 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) \
$(SUPERLU_LIBRARY) \
$(UMFPACK_LIBRARY) \
$(LAPACK_LIBRARY) $(BLAS_LIBRARY) $(CBLAS_LIBRARY) $(CSPARSE_LIBRARY) \
$(AMD_LIBRARY) $(GRAPHIC_LIBRARY)\
-ldl -lgfortran

MACHINE_SPECIFIC_LIBS =



# %---------------------------------------------------------%
# | SECTION 7: INCLUDE FILES |
# | |
# | The following macros specify include files needed for |
# | compilation. |
# %---------------------------------------------------------%
MACHINE_INCLUDES = -I/usr/include \
-I$(BASE)/include \
-I/usr/include/cxx \
-I$(HOME)/include -I$(HOME)/blitz

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

TCL_INCLUDES = -I/usr/includes/tcl-private/generic

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

fmk
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Posts: 5866
Joined: Fri Jun 11, 2004 2:33 pm
Location: UC Berkeley
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Re: Build Errors in CentOS 6.2 64bit, Need help

Post by fmk » Wed May 11, 2016 4:25 pm

those missing symbols are not from a gcc compiler .. looks like intel .. figure out what compiler you are using and see if i have a similar Makefile.def

if that fails try googling the missing symbols to see waht libraries you need .. alternativeily go find compiler lib directory, search files for missing symbols and add to LIBS

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