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楼主要跑分子动力学?
放弃GNU编译器,改用Intel编译器吧。
另外gromacs不用CMake也能编译。
export CC=icc
export CXX=icpc
export F77=ifort
export MPICC=mpicc
export CFLAGS=-O2
export CXXFLAGS=-O2
export FFLAGS=-O2
export CPPFLAGS=-I$HOME/lib/fftw-3.3.4-sp/include
export LDFLAGS=-L/$HOME/lib/fftw-3.3.4-sp/lib
# with multi-thread support
./configure --prefix=$HOME/workspace/abc/gromacs-4.5.4-mt \
--enable-shared=no --enable-fortran \
--enable-mpi \
--with-fft=fftw3 \
--with-external-blas="-Wl,--start-group $HOME/lib/mkl-mkl-13.0.080/libmkl_intel_lp64.a \
$HOME/lib/mkl-mkl-13.0.080/libmkl_sequential.a \
$HOME/lib/mkl-mkl-13.0.080/libmkl_core.a -Wl,--end-group" \
--with-external-lapack="-Wl,--start-group $HOME/lib/mkl-mkl-13.0.080/libmkl_intel_lp64.a \
$HOME/lib/mkl-mkl-13.0.080/libmkl_sequential.a \
$HOME/lib/mkl-mkl-13.0.080/libmkl_core.a -Wl,--end-group"