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

[Rossen Apostolov]

  Hi,

This bug is now fixed in git release-4-5-patches (commit 0a31a047f429).

Rossen

On 8/6/10 11:33 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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