[gmx-users] pdb2gmx illegal instruction (core dumped)

[David van der Spoel]

On 28/01/16 08:33, Md. Imrul Reza Shishir wrote:
> Hi Everyone.
> I use Lenovo A6-7310 (4 core 2MB cache memory) processor in my laptop. I
> install Gromacs 5.0.7 with latest cmake-3.4.2 and fftw-3.3.4. I use below
> Cmake command to install.
>
> "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON"
>
> I am newbies gromacs user. I am trying to execute the Bevan Lab tutorial
> (Lysozyme in water). my first command is
>
> "gmx pdb2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce"
>
> It execute properly. But when i execute number 15 force
> field(OPLS-AA/L) at the end there is a massage "illegal instruction
> (core dumped)". And in my directory only topology file create. No
> gromacs output file Created "1AKI_processed.gro".
>
Illegal instruction means the program was compiled for another machine 
than what it is run on. Did you really compile the program on the same 
machine you are running on?

In that case you may need to manually set the GMX_SIMD flag when running 
cmake, e.g.
-DGMX_SIMD=SSE4.1


> Any help greatly appreciated.
>
> ​Bst Regards​
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se