Re: Memory keep increasing.

From: Ming (ebullience_at_emails.bjut.edu.cn)
Date: Sun Nov 15 2009 - 04:14:10 CST

Hi Dow,
Thanks! As you said, I can run the "sync" command when the NAMD job is runing and this can help me decrease the cached memeory. Am I right? Again, how often should I run this command? Many thanks!

Ming

>>From: Mindspring <Dow.Hurst_at_mindspring.com>
>>Reply-To:
>>To: Ming <ebullience_at_emails.bjut.edu.cn>
>>Subject: Re: namd-l: Memory keep increasing.
>>Date:Sun, 15 Nov 2009 03:12:43 -0500
>>
>>XFS is the file system used on an SGI. It caches data heavily in
>>RAM. Sync will flush the data to disk.
>>
>>Sincerely,
>>Dow Hurst
>>
>>On Nov 14, 2009, at 9:28 PM, "Ming"
>
>>wrote:
>>
>>> Hi Dow,
>>> Thanks for your reply. I'm sorry I don't understand what you said.
>>> I'm very poor on runing a on a SGI station. Could you please tell me
>>> what XFS mean? I didn'y run sync. Again, I don't know why you ask me
>>> to run sync. Do you mean I shold tell the system save some data into
>>> hard drive but not buffer?
>>>
>>>
>>> I ran the "free" command and i didn't find out any decrease in
>>> cached filesystem data. Any suggestions? Thanks in advance!
>>>
>>>
>>>
>>>
>>>> From: Dow_Hurst
>
>>>> Reply-To: Dow_Hurst
>
>>>> To: Ming
>
>>>> Subject: Re: namd-l: Memory keep increasing.
>>>> Date:Sat, 14 Nov 2009 02:10:51 -0500 (EST)
>>>>
>>>> I remember that XFS loves to cache data. Have you run sync on the
>>>> workstation during the run? And, measured any decrease in cached
>>>> filesystem data?
>>>> Dow
>>>>
>>>> -----Original Message-----
>>>>> From: Ming
>>>
>>>>> Sent: Nov 13, 2009 12:51 AM
>>>>> To: akohlmey_at_gmail.com
>>>>> Cc: namd-l_at_ks.uiuc.edu
>>>>> Subject: Re: namd-l: Memory keep increasing.
>>>>>
>>>>> Hi Axel,
>>>>> Thanks for your reply. I've been keeping moitering the memory
>>>>> changes. I found the memory still kept increasing while the job is
>>>>> runing. Below is the output of the "free -m -s 30". I'm sure
>>>>> nobody else uses this SGI Altix station. Is this increase in
>>>>> memory normal? Thanks!
>>>>>
>>>>> P.S.By the way, I found the used memory increased by 6G within 12
>>>>> hours.
>>>>>
>>>>> total used free shared buffers
>>>>> cached
>>>>> Mem: 61521 11543 49978 0
>>>>> 0 166
>>>>> -/+ buffers/cache: 11377 50144
>>>>> Swap: 9999 0 9999
>>>>>
>>>>> total used free shared buffers
>>>>> cached
>>>>> Mem: 61521 11553 49968 0
>>>>> 0 171
>>>>> -/+ buffers/cache: 11382 50139
>>>>> Swap: 9999 0 9999
>>>>>
>>>>> total used free shared buffers
>>>>> cached
>>>>> Mem: 61521 11555 49965 0
>>>>> 0 171
>>>>> -/+ buffers/cache: 11384 50137
>>>>> Swap: 9999 0 9999
>>>>>
>>>>> total us
>>

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