[email protected] wrote:
Hello,
I have just compiled gromacs 4.0.4 using the intel compiler. While I
believe that gromacs itself doesn't get a huge benefit from icc, fftw
certainly does and it's on the order of a 10% speedup, which is
significant enough for me to dedicate some time to getting this working.
Problem is, invsqrt is defined both in gromacs and in the icc libraries,
as is already known:
http://www.gromacs.org/pipermail/gmx-users/2006-June/022009.html
../../../include/vec.h(152): warning #147: declaration is incompatible
with "double invsqrt(double)" (declared at line 635 of
"/opt/sharcnet/intel/11.0.083/icc/include/math.h")
static inline real invsqrt(real x)
I have solved this problem by the following procedure:
#########################
#!/bin/bash
for i in `find ./gromacs-4.0.4`; do
sed 's/invsqrt/invSAFEsqrt/g' "$i" > tmp;
mv tmp "$i";
done
chmod +x ./gromacs-4.0.4/configure
Using sed -i is a bit more elegant and keeps the permissions, IIRC.
mv ./gromacs-4.0.4/src/gmxlib/cinvsqrtdata.c
./gromacs-4.0.4/src/gmxlib/cinvSAFEsqrtdata.c
#########################
And it now compiles without warning.
I was unable to link an icc-compiled fftw to a PGI or gcc compilation of
gromacs, due to linking problems, although I imagine that that is possible.
First, does anybody see any immediate problems with this?
Looks OK.
Second, is there still a motivation to get rid of this problem?
It seems reasonable to get the GROMACS function out of the standard
namespace, or to test for and use a library function with configure.
Third, does anybody know how I can link an icc-compiled fftw to a PGI or
gcc compilation of gromacs, and if there is any reason that this is a
bad idea?
I would have expected it to just work, however I have had multiple
inexplicable problems with various icc versions on IA64 hardware.
Mark
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