Re: [ccp4bb] sleeping refmac

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: sleeping refmac
From: "Harry M {- dot -} Greenblatt" harry {- dot -} greenblatt {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2007-07-18

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From: m zhang mzhang_75 {- at -} HOTMAIL {- dot -} COM
Date: 2007-07-18

Subject: Re: sleeping refmac
From: Ronan Keegan r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-07-18

Hi Harry,

Might not be the problem but does this machine have its ccp4 scratch
space ($CCP4_SCR) mounted from another machine by nfs across a network?
Refmac writes a lot of temporary files to CCP4_SCR and if this is across
a busy network it can really slow Refmac's progress.

Ronan

Harry M. Greenblatt wrote:
> BS"D
>
> Dear All,
>
> One our our linux boxes (kernel 2.4.20) has begun recently to run
> refmac at worse than snail's pace. This is a 3.2 GHz Xeon dual CPU
> Dell machine from 4 years ago. All other things seem fine, including
> other CCP programs. But refmac jobs (for various proteins) that take
> a minute or two on other machines can sit for many tens of minutes
> making very slow progress (but yes, they are getting somewhere).
> Using top, one can see that the machine is completely idle, and the
> refmac job has used up a few seconds of CPU time, even after ten
> minutes, although its priority is normal. In top, under the status
> column, it has a status of "D", which, according to the documentation,
> is "uninterruptible sleep". Running refmac on another computer, I see
> that is does enter the "D" state a few times during the run, but never
> stays that way very long. Any ideas?
>
>
> Thanks
>
> Harry
>
> -------------------------------------------------------------------------
>
> Harry M. Greenblatt
>
> Staff Scientist
>
> Dept of Structural Biology harry.greenblatt@weizmann.ac.il
>
>
> Weizmann Institute of Science Phone: 972-8-934-3625
>
> Rehovot, 76100 Facsimile: 972-8-934-4159
>
> Israel
>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: sleeping refmac
From: "Harry M {- dot -} Greenblatt" harry {- dot -} greenblatt {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2007-07-18

Next message:
Subject: questions about CNS
From: m zhang mzhang_75 {- at -} HOTMAIL {- dot -} COM
Date: 2007-07-18