[CPMD-list] how to speed up on amd64 machines
Bin Pan
binpan at MIT.EDU
Tue Apr 17 16:10:18 CEST 2007
Hi Prof. Hutter and Dr. Kohlmeyer:
Thank you very much for replying.
I did some further observations (which may not totally reflect what
you suggested) as below.
1. On Dual Core AMD Opteron(tm) Processor 870 connected by myrinet,
the output looks like:
NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES
0 4375 48825 24 214 1062 33 1
1 4369 48782 24 213 1061 33 1
2 4363 48827 24 214 1062 33 1
3 4365 48823 24 214 1062 33 1
4 4367 48819 24 214 1062 33 1
5 4368 48822 24 212 1060 33 1
G=0 COMPONENT ON PROCESSOR : 1
while on 4 CPU's on a Intel(R) Xeon(TM) CPU 3.00GHz connected by ethernet
NCPU NGW NHG PLANES GXRAYS HXRAYS ORBITALS Z-PLANES
0 6553 73223 36 322 1594 49 1
1 6550 73185 36 319 1591 50 1
2 6550 73246 36 320 1592 49 1
3 6554 73244 36 320 1592 50 1
G=0 COMPONENT ON PROCESSOR : 1
2. For every MD cycle:
On Dual Core AMD Opteron(tm) Processor 870 connected by myrinet,
710 0.07737 290.2 -408.64335 -408.54915
-408.47177 0.153E+01 91.77
711 0.07742 289.8 -408.64330 -408.54920
-408.47177 0.154E+01 76.60
712 0.07748 289.4 -408.64325 -408.54925
-408.47177 0.154E+01 132.64
713 0.07753 289.0 -408.64320 -408.54930
-408.47178 0.154E+01 74.70
The TCPU varies a lot.
while on 4 CPU's on a Intel(R) Xeon(TM) CPU 3.00GHz connected by ethernet
122 0.03874 335.5 -408.65297 -408.56072
-408.52198 0.144E+00 64.90
123 0.03842 333.9 -408.65206 -408.56040
-408.52198 0.146E+00 65.10
124 0.03808 332.2 -408.65113 -408.56006
-408.52198 0.148E+00 65.03
125 0.03774 330.5 -408.65020 -408.55972
-408.52198 0.151E+00 64.90
The TCPU almost stayed as a constant.
3. I do not currently have the timing info for exactly the same MD
steps. However,
On Dual Core AMD Opteron(tm) Processor 870 connected by myrinet for
980 MD steps,
TOTAL TIME 80248.07 89842.31
****************************************************************
CPU TIME : 22 HOURS 38 MINUTES 41.85 SECONDS
ELAPSED TIME : 25 HOURS 20 MINUTES 49.45 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS 65772/ 218376 kBYTES ***
while on 4 CPU's on a Intel(R) Xeon(TM) CPU 3.00GHz connected by
ethernet for 1000 MD steps.
TOTAL TIME 68513.29 68799.50
****************************************************************
CPU TIME : 19 HOURS 39 MINUTES 1.36 SECONDS
ELAPSED TIME : 20 HOURS 7 MINUTES 12.96 SECONDS
*** CPMD| SIZE OF THE PROGRAM IS 78444/ 250344 kBYTES ***
I am going to try to recompile as what Dr. Kohlmeyer suggested for
the flags. Also do some additional benchmarking.
BTW, one thing I guess that I did not mention is that on intel
cluster, I used IFC to compile, while on AMD I used PGI.
I am wondering whether IFC can be used on AMD machines so that I have
one more option to try out.
Thanks a lot and I do appreciate!
Best regards,
Bin.
At 12:27 4/16/2007, Juerg Hutter wrote:
>Hi
>
>your additional information indicates that there is a
>problem. However, we still need more information to
>locate the problem.
>In addition to Axel's advice and request,
>please send the timing information from an output with
>a full run.
>In addition it would be helpfull if you could run your
>example with the serial code and with the parallel code
>for 1, 2, 4, 8 cpus.
>
>regards
>
>Juerg Hutter
>
>
>----------------------------------------------------------
>Juerg Hutter Phone : ++41 44 635 4491
>Physical Chemistry Institute FAX : ++41 44 635 6838
>University of Zurich E-mail: hutter at pci.unizh.ch
>Winterthurerstrasse 190
>CH-8057 Zurich, Switzerland
>----------------------------------------------------------
>
>
>On Mon, 16 Apr 2007, Bin Pan wrote:
>
>>Hi Prof. Hutter,
>>
>>I said that it is very slow because I used 6 CPU's on a Dual Core AMD
>>Opteron(tm) Processor 870 connected by myrinet and compared the
>>time required to finish one MD cycle with that done by 4 CPU's on a
>>Intel(R) Xeon(TM) CPU 3.00GHz connected by ethernet for the same system.
>>The first needs ~90 seconds, however the second only needs ~60.
>>I expected the first one has faster CPU and better network connection.
>>
>>Are these enough info for you to give me some advice in how to
>>improve the speed?
>>Thanks a lot!
>>
>>Best regards,
>>Bin.
>>
>>At 02:57 4/16/2007, Juerg Hutter wrote:
>>>Hi
>>>
>>>you have to give us more precise information.
>>>What exactly do you mean by 'it is very slow'.
>>>Do you mean slow in general, e.g. compared to
>>>another plane wave code or slow because
>>>of bad speedups in parallel compared to the
>>>serial runs?
>>>You should also give us some information on your
>>>computer. What is the exact version of your CPUs
>>>and what is the type of your network?
>>>At the end of each run CPMD prints timing information.
>>>Please attach at least one such timing information
>>>block for a run that you consider too slow.
>>>
>>>regards
>>>
>>>Juerg Hutter
>>>
>>>----------------------------------------------------------
>>>Juerg Hutter Phone : ++41 44 635 4491
>>>Physical Chemistry Institute FAX : ++41 44 635 6838
>>>University of Zurich E-mail: hutter at pci.unizh.ch
>>>Winterthurerstrasse 190
>>>CH-8057 Zurich, Switzerland
>>>----------------------------------------------------------
>>>
>>>
>>>On Sun, 15 Apr 2007, Bin Pan wrote:
>>>
>>>>Hi CPMD users,
>>>>
>>>>I am wondering how to speed up CPMD runs on amd64 cluster using MPI
>>>>parallelization.
>>>>Previously I compiled CPMD using pgi compiler with acml. However, I
>>>>found it is very slow.
>>>>The flags I used are:
>>>>
>>>>CPPFLAGS = -P -C -traditional -D__Linux -D__PGI -DFFT_DEFAULT
>>>>-DPOINTER8 -D__pgf90 -DPARALLEL -DMYRINET
>>>>CC = gcc -O2 -Wall -m64
>>>>FC = pgf90 -c -fastsse -tp k8-64
>>>>LD = pgf90 -fastsse -tp k8-64
>>>>
>>>>Can you please let me know how to improve the performance?
>>>>Thanks a lot!
>>>>
>>>>Best regards,
>>>>Bin.
>>>>
>>>>_______________________________________________
>>>>CPMD-list mailing list
>>>>CPMD-list at cpmd.org
>>>>http://cpmd.org/mailman/listinfo/cpmd-list
>>
>>
>>
>>---------------------------------------------------------------------
>>Bin Pan
>>Ph.D. Candidate
>>Department of Chemical Engineering
>>Massachusetts Institute of Technology
>>Tel: 617-253-6675
>>E-mail: binpan at mit.edu
>>Room E19-528, 77 Mass. Ave. Cambridge, MA
>>----------------------------------------------------------------------
>>
>>_______________________________________________
>>CPMD-list mailing list
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