symbol lookup error: undefined symbol: _intel_fast_memmove

Charles_S_ · ‎12-20-2016

Hello,

I'm attempting to merge a fortran and a C++ code, a process that has been fraught with errors. The most recent one however has me stumped and I can't figure out what's wrong/how to fix it. I'm including everything I've seen requested for similar errors i've found. let me know if there's any other information that is useful for figuring out what this is.

Makefile:

LDLIBS = -I/share/apps/intel/composer_xe_2011_sp1.10.319/mkl/include \
         -L/share/apps/intel/composer_xe_2011_sp1.10.319/mkl/lib/intel64 \
         -I/share/apps/intel/composer_xe_2011_sp1.10.319/mkl/interfaces/lapack95/source \
         -mkl -openmp -reentrancy hraded

INCLUDE = -I/physics/username/mstl/include \
          -I/physics/username/mstl/include/physics \
          -I/physics/username/mstl/include/math2 \
          -I/physics/username/mstl/include/math2/algebra \
          -I/physics/username/mstl/include/math2/analysis \
          -I/physics/username/mstl/include/math2/data \
          -I/physics/username/mstl/include/math2/geometry \
          -I/physics/username/mstl/include/math2/group \
          -I/physics/username/mstl/include/math2/spline \
          -I/physics/username/mstl/include/math2/probabilityandstatistics

LIBRARY = -L/physics/username/mstl/lib

FC = ifort -c #f compiler
CC = icc -c $c compiler
LK = ifort -v -o ../abXX #linker

CF = -mcmodel=large -i-dynamic -no-ipo -r8 -xW -traceback -fpe0 #f compile flags
OF = $(CF) -O2 #f optimization flags
DF = $(CF) -g -debug -fpstkchk -C -warn interfaces #f debug flags

OPTIONS = -O -loops -lstdc++ -lmstl.icc #c compile flags
LKOPS = -icc -lstdc++ -lmstl.icc -cxxlib -lintlc #c lib linking options

COMP = $(FC) $(OF) # fortran compiler
CMP = $(CC) $(LIBRARY) $(INCLUDE) $(OPTIONS) #c compiler
LINK = $(LK) $(OF)

MODULES = list of all fortran .o files here

COBJS = list of all c++ .o files here

.cpp.o:
         $(CMP) $<

.f.o:
         $(COMP) $<

../abXX: $(MODULES) $(COBJS)
             $(LINK) $(MODULES) $(COBJS) $(LDLIBS) $(LIBRARY) $(INCLUDE) $(LKOPS)

clean:
         rm -v -f *.o *.mod ../abXX

.mybashrc startup file:

echo "I exist in mybashrc"

export PATH=$PATH:/opt/intel/composer_xe_2011_sp1/bin
export PATH=$PATH:/opt/INTEL/bin

source /opt/INTEL/bin/compilervars.sh intel64
export LD_LIBRARY_PATH = $LD_LIBRARY_PATH:/opt/intel/composerxe/mkl/lib/intel64/
export LD_LIBRARY_PATH = /opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/:$LD_LIB_PATH

export INTEL_LICENSE_FILE = /opt/INTEL/licenses/client.lic

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/mkl/lib/intel64

Results of ldd ../abXX:

linux-vdso.so.1 =>  (0x00007fffb51b8000)
libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003171800000)
libintlc.so.5 => /opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libintlc.so.5 (0x00007fc93b678000)
libmkl_intel_lp64.so => /opt/INTEL/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_lp64.so (0x00007fc93ab68000)
libmkl_intel_thread.so => /opt/INTEL/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_thread.so (0x00007fc939238000)
libmkl_core.so => /opt/INTEL/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_core.so (0x00007fc937820000)
libiomp5.so => /opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libiomp5.so (0x00007fc937528000)
libifport.so.5 => /opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libifport.so.5 (0x00007fc9373f0000)
libifcoremt.so.5 => /opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libifcoremt.so.5 (0x00007fc937178000)
libimf.so => /opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libimf.so (0x00007fc936da8000)
libsvml.so => /opt/intel/composer_xe_2011_sp1.10.319/compiler/lib/intel64/libsvml.so (0x00007fc936628000)
libm.so.6 => /lib64/libm.so.6 (0x000000316b000000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003171400000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x000000316b400000)
libdl.so.2 => /lib64/libdl.so.2 (0x000000316b800000)
libc.so.6 => /lib64/libc.so.6 (0x000000316ac00000)
/lib64/ld-linux-x86-64.so.2 (0x000000316a800000)

I'm running with ifort version: 12.1.4 20120410 and icc version: 16.0.3 20160415

When I execute the above makefile, the code compiles and I get my executable, however when I attempt to run the program I get the following error:

./../abXX: symbol lookup error: ./../abXX: undefined symbol: _intel_fast_memmove

The fortran code without the c++ code added in will compile and run just fine. I also used the nm command to look at all undefined symbols and the both the code with and without the c is crawling with _intel_fast_memset and _intel_fast_memcpy as undefined symbols. Only the c code has an instance of _intel_fast_memmove missing.

Any help in resolving this would be greatly appreciated,

CS

Xiaoping_D_Intel · ‎12-21-2016

Can you try to re-build the fortran code with the same version of 16 as the C++ compiler?

Thanks,

Xiaoping Duan

Intel Customer Support

Charles_S_ · ‎12-22-2016

That isn't an option as far as I know. I'm on a university network, and as far as I can tell we only have the v12 ifort and the v16 icc compilers.

Xiaoping_D_Intel · ‎12-22-2016

We recommend using the same major version of icc and ifort in mixed language program. The gap between v12 ifort and v16 icc may cause this issue. Can you append "-Xlinker --cref" to "LINK" setting, re-direct the linkage output to a file and then check the file to see how the missing symbol was resolved during the linkage?

Thanks,

Xiaoping Duan

Intel Customer Support

TimP · ‎12-23-2016

If combining different versions of Intel compilers, you must take care to link against the libraries from the newer one. As pointed out above, you are taking this to extremes, and may be better off using ifort with g++ if you don't have a matching icpc.