Dear all,
I have recently purchased an NVIDIA GTX680 Graphiics card and installed it on my desktop
OS is OpenSuse 12.1. I have installed the NVIDIA ToolsKit 5 as well as the driver for the new graphics card.
I set the environment to point to /usr/local/cuda for CUDA_HOME,
$CUDA_HOME/bin for the binaries and $CUDA_HOME/lib & lib64 for CUDA libraries
I use Intel fortran and cc compilers v13
Basically AMBER12 serial and parallel installations went OK and passed the tests..
I configured AMBER12 CUDA as follows
./configure -cuda intel
everything seems to be OK in the config.h file.
NVCC=$(CUDA_HOME)/bin/nvcc -use_fast_math -O3 -gencode arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20
PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
PMEMD_CU_LIBS=-L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib -lcurand -lcufft -lcudart ./cuda/cuda.a
PMEMD_CU_DEFINES=-DCUDA
#PMEMD Specific build flags
PMEMD_F90=ifort -DMKL -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
PMEMD_FOPTFLAGS=-ip -O3 -no-prec-div -xHost
PMEMD_CC=icc
PMEMD_COPTFLAGS=-ip -O3 -no-prec-div -xHost -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
PMEMD_FLIBSF=-Wl,--start-group /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_sequential.a /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread
PMEMD_LD= ifort
LDOUT= -o
However, I seem to have a problem with pmemd.CUDA installation.
I get the following error message after I type make install
-L/usr/local/cuda-5.0/lib64 -L/usr/local/cuda-5.0/lib -lcurand -lcufft -lcudart ./cuda/cuda.a -L/usr/local/amber12/lib -L/usr/local/amber12/lib -lnetcdf -shared-intel -Wl,--start-group /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_intel_lp64.a /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_sequential.a /opt/intel/composer_xe_2013.3.163/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -lpthread
ld: ./cuda/cuda.a(kNLRadixSort.o): undefined reference to symbol '__cxa_pure_virtual..CXXABI_1.3'
ld: note: '__cxa_pure_virtual..CXXABI_1.3' is defined in DSO /usr/lib64/libstdc++.so.6 so try adding it to the linker command line
/usr/lib64/libstdc++.so.6: could not read symbols: Invalid operation
make[3]: *** [pmemd.cuda] Error 1
make[3]: Leaving directory `/usr/local/amber12/src/pmemd/src'
make[2]: *** [cuda] Error 2
make[2]: Leaving directory `/usr/local/amber12/src/pmemd'
make[1]: *** [cuda] Error 2
make[1]: Leaving directory `/usr/local/amber12/src'
make: *** [install] Error 2
I guess the error is related to "/usr/lib64/libstdc++.so.6: could not read symbols: Invalid operation"
Does anyone have a clue what might be going wrong with the installation?
Best regards,
Cenk Andac, M.S., Ph.D.
Asst. Professor of Medical Pharmacology
Department of Medical Pharmacology
School of Medicine, Mevlana University, Konya
Turkiye 42003
Cell: +90-(536)-4813012
E-Mail:cenk_andac.yahoo.com
Web : http://med.mevlana.edu.tr/personel.asp?ID=1
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Received on Wed May 15 2013 - 10:00:02 PDT
