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

Szilárd Páll szilard.pall at cbr.su.se
Sun May 8 21:32:50 CEST 2011


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

Not that I know of, I've never had/head about such issues.

I just checked and I couldn't reproduce your issue. Tried with both
autoconf and CMake and with:
Intel Compilers: v12.0.2 20110112.
OS: Ubuntu 10.04.2 x86_64

I ran pdb2gmx on share/tutor/speptide/speptide.pdb located in the
install directory of Gromacs . Is your problem reproducible with all
available force-fields/water models?

I've no clue what could be causing the segfault, but I'd try the following:
- other ff/water model combinations;
- some other pdb inputs;
- binary built with CMake;
- as a last resort you could get a backtrace (build with debug symbols
and run with gdb).


On Sun, May 8, 2011 at 1:12 PM,  <Kalavera at gmx.net> wrote:
> 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.
> For FFTW:
> "./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
> --prefix=/usr/gromacs_4_5_4/install_tests/gromacs_fftw3
> CPPFLAGS="-I/usr/gromacs_4_5_4/install_tests/fftw-3.2.2/fftw_fertig/include"
> LDFLAGS="-L/usr/gromacs_4_5_4/install_tests/fftw-3.2.2/fftw_fertig/lib"
> 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,
> M.Kalavera
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