[gmx-developers] Re: gmx-developers Digest, Vol 50, Issue 5

[Yang Ye]

Hi, Xuji

Please cut of your email from the digest. It confuses people.

Could you test your system with 1, 2, 4, 8, 16, 24 CPUs and get
corresponding speed-up ratios?

Regards,
Yang Ye

xuji wrote:
> gmx-developers-request,您好！
>
> The interconnect is Gigabit Ethernet. The simulation system has 102,136 SPC waters and about 40,000 protein atoms. I use PME to calculate the long-range electrostatic force. And the command line is 
> "mpiexec -machinefile ./mf -n 24 mdrun -v -dd 6 3 1 -npme 6 -dlb -s md1.tpr -o md1.trr -g md1.log  -e md1.edr -x md1.xtc>& md1.job &"
> The machinefile "mf" have all the 24 CPUs of the three nodes. The CVS version I use is "3.3.99_development_200800503".
> Carsten, would you analyse something and help me more? 
>
> Thanks!
>
> ======= 2008-06-21 12:00:00 您在来信中写道：=======
>
>   
>> Message: 2
>> Date: Fri, 20 Jun 2008 20:13:52 +0800
>> From: "xuji"<xuji at home.ipe.ac.cn>
>> Subject: [gmx-developers] problem about Gromacs CVS version
>> 	3.3.99_development_200800503 parallel efficiency
>> To: "gmx-developers" <gmx-developers at gromacs.org>
>> Message-ID: <20080620121421.B083D165 at colibri.its.uu.se>
>> Content-Type: text/plain; charset="gb2312"
>>
>> Hi all
>>
>> I have 3 nodes, and there're 8 CPUs in each node. I run a 24 processes mdrun on the three nodes. And I use MPICH2 environment. But the efficiency of the mdrun program is very low. The occupancy of each CPU is only about 10%. I don't know why. Can some one give me some help?
>>
>> Appricaite any help in advance!
>>
>> Best wishes!
>>
>> Ji Xu
>> xuji at home.ipe.ac.cn
>>
>> 2008-06-20
>> 　　　　　　　　　　　　　　
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 3
>> Date: Fri, 20 Jun 2008 14:22:11 +0200
>> From: Carsten Kutzner <ckutzne at gwdg.de>
>> Subject: Re: [gmx-developers] problem about Gromacs CVS	version
>> 	3.3.99_development_200800503 parallel efficiency
>> To: Discussion list for GROMACS development
>> 	<gmx-developers at gromacs.org>
>> Message-ID: <485BA0F3.8020800 at gwdg.de>
>> Content-Type: text/plain; charset=GB2312
>>
>> xuji wrote:
>>     
>>> Hi all
>>>  
>>> I have 3 nodes, and there're 8 CPUs in each node. I run a 24 processes 
>>> mdrun on the three nodes. And I use MPICH2 environment. But the 
>>> efficiency of the mdrun program is very low. The occupancy of each CPU 
>>> is only about 10%. I don't know why. Can some one give me some help?
>>>       
>> Hi,
>>
>> what kind of interconnect do you have? It should be *at least* Gigabit
>> Ethernet! How big is your system? Are you using PME? Please give more
>> information, also on what was your command line to start the runs and
>> what CVS version (date) you are using.
>>
>> Carsten
>>
>>
>> -- 
>> Dr. Carsten Kutzner
>> Max Planck Institute for Biophysical Chemistry
>> Theoretical and Computational Biophysics Department
>> Am Fassberg 11
>> 37077 Goettingen, Germany
>> Tel. +49-551-2012313, Fax: +49-551-2012302
>> http://www.mpibpc.mpg.de/research/dep/grubmueller/
>> http://www.gwdg.de/~ckutzne
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Fri, 20 Jun 2008 21:04:09 +0800
>> From: Yang Ye <leafyoung at yahoo.com>
>> Subject: Re: [gmx-developers] problem about Gromacs CVS	version
>> 	3.3.99_development_200800503 parallel efficiency
>> To: Discussion list for GROMACS development
>> 	<gmx-developers at gromacs.org>
>> Message-ID: <485BAAC9.9050809 at yahoo.com>
>> Content-Type: text/plain; charset=GB2312
>>
>> Hi,
>>
>> This is related to the type of your network connection.
>>
>> If it is just ethernet, such low CPU utilization is expected. Also, if
>> your system has a small number of atoms, the speed-up through parallel
>> is also small.
>>
>> So, reduce the number of parallel, or wait for Gromacs 4, or change to a
>> better inter-node network (Infiniband, etc), sorted according to
>> required time, IMHO.
>>
>> Regards,
>> Yang Ye
>>
>> xuji wrote:
>>     
>>> Hi all
>>> I have 3 nodes, and there're 8 CPUs in each node. I run a 24 processes
>>> mdrun on the three nodes. And I use MPICH2 environment. But the
>>> efficiency of the mdrun program is very low. The occupancy of each CPU
>>> is only about 10%. I don't know why. Can some one give me some help?
>>> Appricaite any help in advance!
>>> Best wishes!
>>> Ji Xu
>>> xuji at home.ipe.ac.cn <mailto:xuji at home.ipe.ac.cn>
>>>
>>> 2008-06-20
>>> 　　　　　　　　　　　　　　
>>>
>>> 	
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
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>>>       
>>
>>     
>