[gmx-users] Fwd: Compiling issue : Compiling gromacs 4.5.4 with intel compiler suite 12.0

Kalavera at gmx.net Kalavera at gmx.net
Sun May 8 13:12:29 CEST 2011

Dear GMX-users,

in a first trial, I successfully managed to compile gromacs 4.5.4 and
fftw 3.2.2 by following the installation instructions on the gromacs
main page. For these compilation, I did not specify the CC CXX or F77
(Compilation was accomplished by GNU compiler 4.5). I was forced to use
--enable-shared for the configuration of FFTW, else the "make" command
of gromacs stopped and showed the described common -fPIC error.
At least, this led me to an compiled and functioning version.

In a second step, I tried to compile FFTW 3.2.2 and Gromacs 4.5.4 with
the intel compiler suite 12.0, which would probably suit my processors
best. Both compilations finished without an error. However, the newly
built pdb2gmx tool quits in the first line with a segmentation fault,
while or after reading the *.pdb file:

"Reading 1OMB.pdb..."

The official gromacs tests showed segmentation faults too.

"./configure --enable-threads --enable-float --enable-shared
--prefix=/usr/gromacs_4_5_4/install_tests/fftw-3.2.2/fftw_fertig/ CC=icc
F77=ifort CXX=icpc
make -j4
make install -j4"

For Gromacs 4.5.4:
"./configure --with-fft=fftw3
CC=icc F77=ifort CXX=icpc

make -j4
make install -j4 "

Is there any common problem for an compilation with the intel compiler
suite 12.0 and FFTW 3.2.2/Gromacs 4.5.4

thanks for all your support,
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