[gmx-users] intel grompp with pathscale mdrun

[chris.neale at utoronto.ca]

Thank you Matthew.

your suggestion for the hanging .o compilation sounds good. I didn't  
try it because in the end the intel compiler produced the fastest  
executables in any event.

For those interested, here are my benchmarking speeds for one of my  
simulation systems (270,000 atoms) on 48 cores of an AMD magny-cours  
cluster at 2.1 GHz. I have no idea why the intel icc compiler  
outperforms the pathscale and pgi compilers on AMD computers, but that  
seems to be the case.

intel icc 12.0.5.220 = 3.733 ns/day
intel icc 12.0.5.220 with -msse3 = 3.765 ns/day
pathscale 4.0.12.1 = 3.467 ns/day
pgi 11.8 = 3.092 ns/day
pgi 11.8 with -tp istanbul -fast = 3.156 ns/day

Again, thank you,
Chris.

-- original message --

As far as compilation hanging...maybe hand-compile that .o with less
aggressive optimization flags, then try "make" again?

MZ

On Tue, Dec 6, 2011 at 2:20 PM, Chris Neale <chris.neale at  
utoronto.ca> wrote:
> Dear users:
>
> can I use a .tpr file created with an intel icc compilation of grompp and
> then do mdrun under a pathscale compilation of mdrun  ? (same version of
> gromacs)
>
> I'm wondering if there would be some strange behaviour. It seems like it
> should be ok, but I wanted to be sure.
>
> I ask because I can only compile mdrun with the pathscale compiler because
> make install hangs while make install-mdrun works fine. make install is
> hanging on making g_rms.o as previously posted:
> http://lists.gromacs.org/pipermail/gmx-users/2011-December/066682.html . I
> tried this again with the 4.0.12.1 version of the compiler and have the same
> result.
>
> Thank you,
> Chris.
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