[gmx-users] grompp problems

[Christopher Yip]

Taeho

one thing to remember - you didn't OPTIMIZE for the Mac cluster as we 
have discussed before - you simply ran it behind a switch and thus not 
using a cross-over cable.. so it's hardly a fair test esp against a 
properly configured cluster... we need to try this out before we can 
make such global statements w/o qualification

Chris
On Tuesday, March 11, 2003, at 11:13  AM, Taeho Kim wrote:

> Hi,
> It's great to see your useful information.
> For Mac OS X, I am just wondering whether you have better performance 
> - scaling - on multiple Mac machines. I have installed 
> Gromacs3.1.5/LAM-MPI6.5.7/FFTW2.1.3 with the similar configurations to 
> yours. However, I didn't get better performance on two dual CPU 
> machines than one single dual machine.
>
> For your information,
> --------- I have differences from your instructions. I didn't 
> specifically define below ----
> 3C. Export the following environment variables:         ;;( since the 
> lib is in my path, /sw/bin)
> CPPFLAGS = -I/usr/local/lam_mpi/include
> LDFLAGS = -L/usr/local/lam_mpi/lib
> LIBS = -lmpi -llam
> MPICC = cc
> ----
> I'm wondering whether MPICC with cc is different from with "gcc" in 
> performance?  I used "cc=gcc" for configuration.
>
> How can I increase the computing performance on multiple machines of 
> dual 1.0GHz Mac OS X.  I'm willing to try to reinstall software for 
> better scaling.
>
> And what if I add more single CPU Macs machines with lower CPU speeds? 
>  I suspect the lower CPU speed can be the bottle-neck of heterogeneous 
> CPU clusters, even with -shuffle.  Actually, I didn't try this because 
> I didn't get better performance on two machines with the same CPU/OSX 
> over fast Ethernet.
>
> Thank you in advance,
> Taeho
> -----?x:; 8^=CAv-----
> :83= ;g6w: Chng Choon Peng <cpchng at bii.a-star.edu.sg>
> 9^4B ;g6w: gmx-users at gromacs.org <gmx-users at gromacs.org>
> 3/B%: 20033b 3?y 11 at O H-?d at O ?@@| 12:48
> A&8q: Re: [gmx-users] grompp problems
>
>
>> Hi,
>>
>>  Btw, I still maintain a GROMACS how-to-install webpage for Mac OS X
>> (PowerMac G4 and Xserves using LAM/MPI) and IA32/64 Linux using
>> MPICH/MPICH-GM.
>>
>> Please refer to:
>> http://www.bii.a-star.edu.sg/~cpchng/GROMACS_HowTo.html
>>
>> Also, some benchmarks on PIII/4/Athlon/UltraSPARC are also available.
>>
>>
>> Regards,
>> choon peng
>
>
>
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Christopher M. Yip Ph.D., P.Eng
Associate Professor - Canada Research Chair in Molecular Imaging
Departments of Chemical Engineering and Applied Chemistry
Department of Biochemistry
Institute of Biomaterials and Biomedical Engineering
407 - 4 Taddle Creek Rd	
Toronto, Ontario, CANADA M5S 3G9
(416) 978-7853
(416) 978-4317 (fax)
christopher.yip at utoronto.ca
http://bigten.ibme.utoronto.ca
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