46. A VERY rough approach to "benchmarking" gromacs (unscientific) on debian

Here's a comparison between different hardware and binaries which were built as described in http://verahill.blogspot.com/2012/01/debian-testing-64-wheezy-compiling.html

The simulation in question is a 100,000 step 100 ps simulation of a carbonate ion in water. Check back later for more details.

grompp -f carbonate.mdp -c carbonate.pdb -p carbonate.top -o carbonate.tpr

time mdrun -v -deffnm carbonate

Conclusions: 1) Double precision is slower by 25-35 % than single precision. 2) On a single machine there's no gain in using mpi. 3) Sadly, it appears that  intel i5-2400 X4 3.1GHz is more expensive than AMD Phenom II X6 3.1GHz for a reason.

Machines:
Be -- Phenom II X6, 8Gb RAM.
B --   Athlon X3 3.1 GHz 3 core, 4Gb RAM
Ta -- Optiplex 990 (i5 2400 3.1 GHz 4 core, 8Gb RAM). This machine was running a full gnome3/gnome-shell desktop at the same time as the tests were carried out. Take the results with a grain of salt.

Using mdrun (no mpi, single precision)
-------------------------------
Run   Be (6)     Ta (4)   B ( 3)
-------------------------------
1       1m27s    1m1s    1m48s
2       1m28s    1m1s    1m46s
3       1m35s    1m1s    1m47s
4       1m32s    1m1s    1m47s
5       1m33s    1m1s    1m47s


Using mdrun_dd (no mpi, double precision)
-------------------------------
Run   Be (6)     Ta (4)   B ( 3)
-------------------------------
1       1m49s    1m15s    2m25s
2       1m47s    1m15s    2m26s
3       1m51s    1m15s    2m26s
4       1m59s    1m15s    2m24s
5       1m58s    1m15s    2m26s



Using mdrun_mpi (mpi, single precision)

Machine: Be (Phenom II X6, 8Gb RAM).
(5 cores doesn't work)
---------------------------------
Cores/Run:   1            2      
---------------------------------
1                  4m11s   4m13s
2                  2m12s   2m15s
3                  1m46s   1m43s
4                  1m31s   1m31s
5                  ----------------
6                  1m28s   1m35s

Machine: Ta (Optiplex 990 (i5 3.1 GHz 4 core, 8Gb RAM).
---------------------------------
Cores/Run:   1            2           3
--------------------------------
1                  3m20s   3m20s   3m20s
2                  1m39s   1m38s   1m40s
3                  1m12s   1m13s   1m12s
4                  1m01s   1m01s   1m00s


Machine: Athlon X3 3.1 GHz 3 core, 4Gb RAM.
---------------------------------
Cores/Run:   1            2           3
--------------------------------
1                  4m32s   4m33s   4m36s
2                  2m28s   2m28s   2m27s
3                  1m49s   1m50s   1m49s

Using mdrun_ddmpi (mpi, double precision):

Machine: Phenom II X6, 8Gb RAM.
---------------------------------
Cores/Run:   1            2    
---------------------------------
1                  5m23s   5m25s
2                  2m56s   2m54s
3                  2m11s   2m11s
4                  1m56s   1m57s
5                  -----------------
6                  1m51s   1m52s

Machine: Optiplex 990 (i5 3.1 GHz 4 core, 8Gb RAM).
---------------------------------
Cores/Run:   1            2           3
--------------------------------
1                  4m14s   4m13s   4m13s
2                  2m09s   2m09s   2m10s
3                  1m33s   1m33s   1m33s
4                  1m16s   1m16s   1m16s


Machine: Athlon X3 3.1 GHz 3 core, 4Gb RAM.
---------------------------------
Cores/Run:   1            2           3
--------------------------------
1                  5m01s   5m52s   5m50s
2                  3m17s   3m17s   3m18s
3                  2m31s   2m31s   2m31s