[gmx-users] Unary Diez Operator error while compiling gromacs 4.0

Mark Abraham Mark.Abraham at anu.edu.au
Fri Oct 24 03:24:42 CEST 2008

chris.neale at utoronto.ca wrote:
> Hello,
> I am having difficulty compiling gromacs 4.0 on an Itanium2 running HP 
> Linux XC 3.0.
> Gromacs 3.3.1 compiled fine on that machine. I have successfully 
> compiled gromacs 4.0 this way on opterons running HP Linux XC 3.2.1 and 
> HP Linux XC 3.1.
> I have seen a post in the archives showing a slightly different initial 
> error that eventually leads to "Unexpected token: Unary Diez Operator 
> at: Start" for gromacs 3.3.2, but assumed that any such fix would have 
> been incorporated into gromacs 4.0.
> Still, I tried that solution 
> (http://www.gromacs.org/pipermail/gmx-users/2007-October/030212.html) 
> but it did not work, possibly because I am unclear what directory I 
> should execute the command from:

That discussion wasn't ever satisfactorily resolved. On the same machine 
  on which I reported the above, I also failed to compile GROMACS 4.0 
using the Intel 9.1 compilers. The error messages were the same kind as 
before, though I didn't compare in detail.

I succeeded in compiling GROMACS 4.0 on this machine with

module load scsl
module load intel-cc/10.1.018
module load fftw/3.1.1-intel-9.1
../configure --program-suffix=_mpi_c CC=icc CFLAGS="-O3 
-I${FFTWDIR}/include" LIBS="-L${FFTWDIR}/lib -lscs -lmpi" --prefix 
${HOME}/progs --with-external-blas --with-external-lapack 
--with-fft=fftw3 --enable-mpi --without-x
make mdrun

This suggests there's an issue with the Intel 9.1 compilers.

> [cneale at cl31 gromacs-4.0]$ icc -DHAVE_CONFIG_H -I. -I../../../../src 
> -I../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double 
> -I../../../../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" 
> -O0 -w -MT nb_kernel010_ia64_double.lo -MD -MP -MF 
> .deps/nb_kernel010_ia64_double.Tpo -E 
> ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S 
> -fPIC -DPIC -o temp.s
> cpp: 
> ../../../../../src/gmxlib/nonbonded/nb_kernel_ia64_double/nb_kernel010_ia64_double.S: 
> No such file or directory
> cpp: warning: `-x assembler-with-cpp' after last input file has no effect
> cpp: no input files

I see you've copied my icc command from October. I was creating a 
subdirectory under GROMACS 4.0 so that I could maintain separate build 
trees for different compilation options, e.g.

mkdir mpi
cd mpi
../configure --enable-mpi
cd ..
mkdir nonmpi
cd nonmpi
cd ..

etc. This means I don't have to make distclean all the time, and can 
know the state of each subdirectory when I return to it after some time. 
You can also do this while experimenting over a range of compiler 
optimization flags.

You should harvest your own from the make output just before it fails.


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