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

Mark Abraham mark.abraham at anu.edu.au
Tue Aug 10 03:36:52 CEST 2010

----- Original Message -----
From: David.Grocutt at uk.fujitsu.com
Date: Tuesday, August 10, 2010 1:25
Subject: [gmx-users] Double Precision Gromacs 4.5 beta 2 on Intel Xeon "Woodcrest"
To: gmx-users at gromacs.org

> 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

Not really. icc+MKL provides a miniscule improvement over gcc+FFTW3, so if the former gives trouble, use the latter. Search the archive, I probably published some 4.0.7 numbers.

> When compiling the double precision version 4.0.7, I found that 
> I needed to use the configure option --disable-x86-64-sse

That is probably to be expected. If these Woodcrest processors are in some Altix machine, then there's a history of unresolved problems with these nonbonded kernels on such machines. The problem seems not to be with the kernels. Search the archives if relevant.

> 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                                                    

Something's gotten mangled here - the line's incomplete. One needs to take particular care to link correctly to MKL - consult the MKL docs for your system.

> Followed by "make -j 4 && make install"
> Has anyone else tried this yet ? It seems like a quite trivial bug.

icc 11.1 + mkl + double works fine on my Intel Nehalem machine.


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