[gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"

[Roland Schulz]

Hi,

I can reproduce it. Probably won't have time till Monday to look at the
reason.

Roland

On Fri, Aug 6, 2010 at 5:33 AM, <David.Grocutt at uk.fujitsu.com> wrote:

> Hi, this is the first time I have messaged this group, so please bear with
> me.
>
> I have had little trouble with previous versions (4.0.7 for example),
> however with this version the pdb2gmx program gives a segmentation fault
> error if run stand-alone, even with no input. When compiled with debug, idb
> claims it is a "strlen" problem in glibc. Running either grompp or mdrun or
> any other of the executables without any input files merely yields the help
> screen (as expected).
>
> The single precision version works fine with Intel Compiler and MKL !
> The double precision version works with GNU compiler and MKL, but I need it
> to work with Intel
>
> When compiling the double precision version 4.0.7, I found that I needed to
> use the configure option --disable-x86-64-sse
>
>
> For 4.5b2, I have downloaded both the current version from Git (05Aug -
> 1500 BST), as well as the tar.gz versions and got the same problem.
>
> I compiled with icc 10.1 and am using mkl 10.2 on very standard Linux
> distribution.
>
> Here is my configure line
>
> ./configure CC=icc CPPFLAGS="-I$MKL_ROOT/include"
> LDFLAGS="-L$MKL_ROOT/lib/" --with-fft=mkl
> --prefix=$HOME/gromacs-4.5b2/icc/double --enable-double
> --program-suffix=""LD=icc
>
> Followed by "make -j 4 && make install"
>
> Has anyone else tried this yet ? It seems like a quite trivial bug.
>
> Thanks
>
> David
>
> David Grocutt
> Environment & Health Research Division
> Fujitsu Laboratories of Europe
> Phone: +44 (0) 208 606 4533
> Fax: +44 (0) 208 606 4539
> Email David.Grocutt at uk.fujitsu.com
>
>
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