[gmx-users] 3.3.1 installation on True64 Unix system

Lei Zhou zhoumadison at gmail.com
Thu Apr 27 15:41:43 CEST 2006


Hi, actually I am in close contact with the system administrator. They are
also puzzled by the installatiom of 3.3.1. I was told there was always a
floating point problem. I am wondering whether you have any suggestions
about the floating point error, doule precision and True64 Unix system.
Thank you.

On 4/27/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Lei Zhou wrote:
> > Dear GMX-users,
> >
> > Here are the script I used to install the GROMACS-3.3.1 double precision
> > on a True64 Unix system.
> > I installed fftw-3.0.1 first and it was successful.
> >
> > ./configure --enable-float --enable-type-prefix; make; make install
> > ./configure --enable-type-prefix; make; make install
> >
> > Then I started the gromacs installation:
> > ./configure --enable-double --program-suffix=_d; make
> >
> > I got the following message on the screen:
> > mkdir .libs
> > rm -fr .libs/libgmx_d.lax
> > mkdir .libs/libgmx_d.lax
> > rm -fr .libs/libgmx_d.lax/libnonbonded.a
> > mkdir .libs/libgmx_d.lax/libnonbonded.a
> > (cd .libs/libgmx_d.lax/libnonbonded.a && ar x
> > /usr/users/5/lzhou2/gmx/gromacs-3.3.1
> /src/gmxlib/nonbonded/.libs/libnonbonded.a)
> > rm -fr .libs/libgmx_d.lax/libblas.a
> > mkdir .libs/libgmx_d.lax/libblas.a
> > (cd .libs/libgmx_d.lax/libblas.a && ar x
> > /usr/users/5/lzhou2/gmx/gromacs-3.3.1
> /src/gmxlib/gmx_blas/.libs/libblas.a)
> > rm -fr .libs/libgmx_d.lax/liblapack.a
> > mkdir .libs/libgmx_d.lax/liblapack.a
> > sh: 210705 Memory fault - core dumped
> > *** Exit 139
>
> this looks like a compiler bug. contact your sysadmin and/or computer
> vendor
>
>
> >
> > In the config.log file, I got another error message:
> >
> > #define PACKAGE "gromacs"
> > #define PACKAGE_BUGREPORT "gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>"
> > #define PACKAGE_NAME "GROMACS"
> > #define PACKAGE_STRING "GROMACS 3.3.1"
> > #define PACKAGE_TARNAME "gromacs"
> > #define PACKAGE_VERSION "3.3.1"
> > #define RETSIGTYPE void
> > #define SIZEOF_INT 4
> > #define SIZEOF_LONG_INT 8
> > #define SIZEOF_LONG_LONG_INT 8
> > #define STDC_HEADERS 1
> > #define VERSION "3.3.1"
> > #define inline __inline
> > #endif
> > #endif
> > #ifdef __cplusplus
> > #ifndef __cplusplus
> > extern "C" void std::exit (int) throw (); using std::exit;
> >
> > configure: exit 0
> >
> >
> > I am wondering the connection between these two error messages and how
> > to correct them.
> >
> > Thank you in advance for the help.
> >
> > Lei Zhou
> > Columbia University
> >
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
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>
>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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