Hi, > 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). Cheers, -- Szilárd On Sun, May 8, 2011 at 1:12 PM, <[email protected]> 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 > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
