[gmx-users] segmentation fault during test set

[Mark Abraham]

Antoine Migeon wrote:
> Hello,
> 
> I freshly installed Gromacs 4.0, but when I run the test set 3.3.3, I
> get "segmentation fault error".

1. 4.0.2 is out, you shouldn't do fresh installs of bugfixed software. 
2. Also don't enable threads - it does nothing for FFTW for GROMACS, but 
won't hurt.
3. Don't compile software as root if you can avoid it. If you do, some 
trivial error in some script can trash your whole system. You should 
reduce your exposure by only doing "make install" (or for GROMACS, "made 
install-mdrun") as root.

> My installation script, no error during the compilation :
> $ pgcc -V
> pgcc 7.2-2 64-bit target on x86-64 Linux -tp k8-64
> Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
> Copyright 2000-2008, STMicroelectronics, Inc.  All Rights Reserved.
> 
> 
> -----------------------------------------
> # tar -zxvf fftw-3.1.3.tar.gz
> # chown -R root.root fftw-3.1.3
> # cd fftw-3.1.3
> 
> # ./configure --prefix=/usr/local/gromacs-4.0.0/fftw-3.1.3
> --enable-float --enable-threads CC="pgcc"
> # make -j 9 2>&1 | tee fftw_single_make.txt
> # make install 2>&1 | tee fftw_single_install.txt
> # make distclean
> 
> # ./configure --prefix=/usr/local/gromacs-4.0.0/fftw-3.1.3
> --enable-threads CC="pgcc"
> # make -j 9 2>&1 | tee fftw_double_make.txt
> # make install 2>&1 | tee fftw_double_install.txt
> # make distclean
> 
> # export CPPFLAGS='-I/usr/local/gromacs-4.0.0/fftw-3.1.3/include'
> # export LDFLAGS='-L/usr/local/gromacs-4.0.0/fftw-3.1.3/lib'
> 
> # tar -zxvf gromacs-4.0.0.tar.gz
> # chown -R root.root gromacs-4.0.0
> # cd gromacs-4.0.0
> 
> # ./configure --prefix=/usr/local/gromacs-4.0.0 --without-x CC="pgcc"
> 2>&1 | tee gromacs_single_configure.txt
> # make -j 9 2>&1 | tee gromacs_single_make.txt
> # make install 2>&1 | tee gromacs_single_install.txt
> # make distclean
> 
> # ./configure --prefix=/usr/local/gromacs-4.0.0 --without-x
> --program-suffix=_d --enable-double CC="pgcc" 2>&1 | tee
> gromacs_double_configure.txt
> # make -j 9 2>&1 | tee gromacs_double_make.txt
> # make install 2>&1 | tee gromacs_double_install.txt
> # make distclean
> 
> # ./configure --prefix=/usr/local/gromacs-par-4.0.0 --without-x
> --program-suffix=_mpi --enable-double --enable-mpi CC="mpicc" 2>&1 | tee
> gromacs_mpi_configure.txt
> # make -j 9 2>&1 | tee gromacs_mpi_make.txt
> # make install 2>&1 | tee gromacs_mpi_install.txt

You've only made MPI-aware gromacs in double precision. That's probably 
not what you want. See the installation guide on the GROMACS website.

> -------------------------------------------
> 
> 
> First I run the test without mpi (/usr/local/gromacs-4.0.0)

I can't really help with this.

Mark