From: vivek.viv.sharma_at_gmail.com
Date: Thu Apr 09 2009 - 22:32:12 CDT
Hello Gengbin,
Thanks for your reply.
Now, NAMD seems to be working fine, all I did was to use the
binary "NAMD_2.7b1_Linux-x86-TCP", . In my upgradation from NAMD2.6 to
NAMD2.7b1, I tried the other binary "NAMD_2.7b1_Linux-x86" but it showed
the same behaviour as the previous one showed (NAMD2.6). I do not know what
exactly are the differences between the two "NAMD_2.7b1_Linux-x86"
AND "NAMD_2.7b1_Linux-x86-TCP". Would you please say few words about the
difference between the two?
thanks again,
Vivek
On Apr 9, 2009 8:52pm, Gengbin Zheng <gzheng_at_illinois.edu> wrote:
> Vivek,
> When NAMD is busy doing communication (sending messages), or doing load
> balancing, it may appear idle, or only one processor shows busy for a
> short period of time. Also check if your job is running close to the
> memory capacity (you can see that from "top"). Operating system may be
> busy swapping your NAMD job to/from disk which also causes idle time.
> Gengbin
> vivek.viv.sharma_at_gmail.com wrote:
> Helllo Axel and all,
> Well, it was my mistake to mention in my previous post that 'job dies'.
> Well, in fact my 'this' statement was based on observing the 'top'
> command on the console. The job is running fine on all the 8 processors.
> Its not dying, but every now and then the 'top' command shows that none
> of the processor is being used by NAMD. Like the NAMD process goes in
> background and comes back running again with all 8 processors in use, as
> observed in the 'top' command. When I check with 'ps -e' all the NAMD
> jobs are there. Can anyone please throw some light on this, that why such
> a behaviour is being observed, that NAMD jobs appear-go in
> background-re-appear in the top command (?)
> Now, am I right in thinking that 'this-way' running of jobs will take
> more time than it should (?). I assume here that when 'top' comamnd does
> not show NAMD running, simulation is not running. (could be wrong though,
> might be something else is being done in this time).
> Axel, thanks for your points, I should have observed more before posting.
> Secondly, I really admire the beauty of this simple NAMD command which
> can be used to run the simulation without much installation work to be
> done.
> thanks and regards,
> Vivek
> On Apr 6, 2009 7:14pm, Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu> wrote:
> > On Mon, 2009-04-06 at 04:45 +0000, vivek.viv.sharma_at_gmail.com wrote:
> >
> > > Hello everyone,
> >
> > >
> >
> > > We have recently bought a machine with the following configuration:
> >
> > >
> >
> > > 2 quad core processors each with 2.33GHz clock rate.
> >
> > > 8 GB RAM
> >
> > > 500GB total hard disk
> >
> > >
> >
> > > I have simply used the "NAMD_2.6_Linux-i686" binaries. And, started
> >
> > > the simulation (membrane protein with membrane, water, ions.). The
> >
> > > simulation starts fine with the command
> >
> > >
> >
> > > ./charmrun ++local +p 8 ./namd2 config.txt > config.log &
> >
> > >
> >
> > > But after 4390 steps the job dies, without giving any error message.
> >
> > > Would you please suggest what is happening? Do I need to install
> >
> >
> >
> > how should anybody know??? does your input run fine elsewhere? have
> >
> > you looked at the trajectory? have you looked at the machine logs?
> >
> > does your os have restrictive limits for interactive use or stack
> >
> > memory? can you run the same job with less processors? how is the
> >
> > CPU temperature? is the crash reproducable? ...
> >
> >
> >
> > this list can go on for much longer. so please keep in mind that
> >
> > the kind of suggestion you can receive from a mailing list is
> >
> > directly proportional to the kind and quality of information
> >
> > you provide. in you case, you just say "it doesn't work". and
> >
> > only for one specific configuration. that is _very_ little.
> >
> >
> >
> > > it(NAMD) from scratch?
> >
> >
> >
> > why? first you have to find out what happens.
> >
> > blind activism never helps!
> >
> >
> >
> > >
> >
> > > NAMD in log file shows clearly:
> >
> > >
> >
> > > >> Info: Running on 8 processors.
> >
> > >
> >
> > > I observed from 'top', indeed simulation runs on all 8 processors,
> >
> > > using more or less efficiently all the processors.
> >
> >
> >
> > there has to be more output, and i am pretty certain that there is
> >
> > some output that indicates what is going wrong.
> >
> >
> >
> > > All your suggestions will be very helpful.
> >
> >
> >
> > well, you got a ton of them already. the most important
> >
> > one is to include more relevant information. there are
> >
> > many, many cases on this mailing list where people ask
> >
> > for help with problems, and you can easily derive from
> >
> > the dialog what information is needed and what _you_
> >
> > can do beforehand to verify and you are seeing a real
> >
> > problem and what information is need to narrow it down.
> >
> >
> >
> > cheers,
> >
> > axel.
> >
> >
> >
> >
> >
> > > thanks and regards,
> >
> > >
> >
> > > Vivek
> >
> > > IMM, India.
> >
> >
> >
> > --
> >
> > =======================================================================
> >
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> >
> > Center for Molecular Modeling -- University of Pennsylvania
> >
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> >
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> >
> > =======================================================================
> >
> > If you make something idiot-proof, the universe creates a better idiot.
> >
> >
> >
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