[gmx-users] Illegal instruction flag raised in GMX 5.0.4

[Mark Abraham]

... and see
http://www.gromacs.org/Documentation/Installation_Instructions#portability-aspects

Mark

On Tue, Dec 23, 2014 at 7:25 PM, Carsten Kutzner <ckutzne at gwdg.de> wrote:

> Hi there,
>
> On 23 Dec 2014, at 08:59, Harry Mark Greenblatt <
> harry.greenblatt at weizmann.ac.il> wrote:
>
> > BS"D
> >
> > Gromacs is telling you that the -h option you supplied is not valid for
> this command.
> No, that is not true, the -h option works for all Gromacs commands.
> It is exactly this option that lists the valid command line arguments :)
>
> One reason why you could get an illegal instruction at that point is
> that your executable was compiled with an instruction set that the CPU you
> are running on is not supporting.
>
> E.g. if you run Gromacs cmake on an Intel Ivy Bridge it will compile
> in AVX_256 vector instructions. Running mdrun -h on a machine that
> has only SSE4.1 will then result in an illegal instruction.
>
> In that case, either compile on the machine you are running on, or use
> -DGMX_SIMD=SSE2 for the tools for maximum compatibility.
>
> Carsten
>
>
> >  You can see all the valid arguments for each
> > command here
> >
> > http://manual.gromacs.org/online.html
> >
> > Harry M. Greenblatt
> > Associate Staff Scientist
> > Dept of Structural Biology           harry.greenblatt at weizmann.ac.il
> > Weizmann Institute of Science        Phone:  972-8-934-3625
> > 234 Herzl St.                        Facsimile:   972-8-934-4159
> > Rehovot, 76100
> > Israel
> >
> > ________________________________________
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Jayant
> James [jayant.james at gmail.com]
> > Sent: Tuesday, December 23, 2014 9:42 AM
> > To: Discussion list for GROMACS users
> > Subject: [gmx-users] Illegal instruction flag raised in GMX 5.0.4
> >
> > Hi!
> > In the process of trying to simulate phosphorylated serines I installed
> > gromacs 5.0.4 because I was running into problems with pdb2gmx command
> not
> > able to merge files. After installation I ran a test command and got the
> > error below.  I am kinda lost as to what could be happening!!
> > I would appreciate any suggestions
> > Thank you
> > Jayant James
> >
> > ERROR MESSAGE
> > --------------------------
> >
> > GROMACS:      gmx editconf, VERSION 5.0.4
> > Executable:   /share/apps/gromacs/5.0.4/bin/gmx
> > Library dir:  /share/apps/gromacs/5.0.4/share/gromacs/top
> > Command line:
> >  editconf -h
> >
> > Illegal instruction
> > --
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>
> --
> Dr. Carsten Kutzner
> Max Planck Institute for Biophysical Chemistry
> Theoretical and Computational Biophysics
> Am Fassberg 11, 37077 Goettingen, Germany
> Tel. +49-551-2012313, Fax: +49-551-2012302
> http://www.mpibpc.mpg.de/grubmueller/kutzner
> http://www.mpibpc.mpg.de/grubmueller/sppexa
>
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