I recently installed GROMACS on our condor pool. Unsurprisingly code that runs so fast is very dependent on the numerical libraries used during compilation. I therefore chose to use Intel MKL and Intel compiler as they perform very well together. Unfortunately the configure file is not suitable for Intel 10.1 users. I am using GROMACS 3.3.3 (although I hear version 4 should be out imminently), on 32-bit openSUSE 10.3.
First edit your configure file, lines 25897 & 25965:
Alter
LIBS="-lmkl $LIBS"
to
LIBS="-lmkl_intel -lmkl_sequential -lmkl_core $LIBS"
Then run:
./configure CC="icc" CPPFLAGS="-I/opt/intel/mkl/10.0.3.020/include" LDFLAGS="-L/opt/intel/mkl/10.0.3.020/lib/32" --with-fft=mkl
make
make install
You may need to alter the version number or location of your MKL files. I recommend you also download the test set to confirm the compilation. I have 4 fails, but closer inspection revealed they were not show stoppers.
