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

David.Grocutt at uk.fujitsu.com David.Grocutt at uk.fujitsu.com
Fri Aug 6 11:33:03 CEST 2010

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.



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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