Re: segmentation fault?

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Nov 05 2008 - 18:33:29 CST

Hi, Giacomo:
     Thanks for your suggestion. I will try that.
      In the mean time, while I was trying to compile the
tcl8.3.3_hacked from(http://www.ks.uiuc.edu/Research/namd/libraries/),
I got the following weird error:

        ./../unix/tclUnixInit.c
./../unix/tclUnixInit.c: In function 'TclpSetVariables':
./../unix/tclUnixInit.c:536: error: storage size of 'name' isn't known
./../unix/tclUnixInit.c:547: warning: implicit declaration of function
'uname'
./../unix/tclUnixInit.c:536: warning: unused variable 'name'
make: *** [tclUnixInit.o] Error 1

      Do you know what this is about? Bug of the code, or I'm using
inappropriate compiler?
      I want to compile it myself because the library provided in that
link seems to have compatibility issues with the CRAY system I was
running on.
      Thanks a lot.

Bin

On Nov 5, 2008, at 3:46 PM, Giacomo Fiorin wrote:

> Hello Bin, for a system of that size the memory usage is of the order
> of few tens of Mb, certainly too small to explain. Also, most of the
> times you shouldn't get a segmentation fault (which means that there's
> an internal error when accessing data), but an operating system error
> instead.
>
> Are you concatenating minimization and dynamics with Tcl? If you have
> a Tcl library that doesn't behave properly on your Cray's operating
> system, you may be better off just running separate input files for
> NAMD that don't use Tcl, and investigate the problem in the meantime.
> Unless you're using tclForces, results are completely equivalent with
> and without Tcl. It's just a little less convenient for you to set up
> separate inputs :-(
>
> Giacomo
>
> ---- -----
> Giacomo Fiorin
> Center for Molecular Modeling at
> University of Pennsylvania
> 231 S 34th Street, Philadelphia, PA 19104-6323
> phone: (+1)-215-573-4773
> fax: (+1)-215-573-6233
> mobile: (+1)-267-324-7676
> mail: giacomo.fiorin_<at>_gmail.com
> web: http://www.cmm.upenn.edu/
> ---- ----
>
>
>
> On Wed, Nov 5, 2008 at 4:58 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
>> Hi, there:
>>
>> Is there an upper limit of atom number that NAMD can handle?
>> I was running a simulation with first 1000 step minimization and
>> then
>> dynamics. But NAMD existed after the minimization with error
>>
>> Application 471018 exit signals: Segmentation fault, Killed
>>
>> And the error in the output file is:
>>
>> APINFO_NIDTERM: compute node initiated termination, possible out
>> of memory
>> condition
>>
>> Is this a problem of limited compute memory? or, the namd
>> itself(wrong
>> scripts, et al)? How can I estimate the memory needed for a given
>> atom
>> number?
>> BTW, the atom numbers of my system is about 15,000
>> Thanks a lot.
>>
>> Bin
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> -------------------------------------------------------------
>> The tree of liberty must be refreshed from time to time with the
>> blood of
>> patriots and tyrants.
>>
>>

-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.

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