Re: segmentation fault?

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed Nov 05 2008 - 18:42:04 CST

> Do you know what this is about? Bug of the code, or I'm using
> inappropriate compiler?

It might help to know which compiler you were using... Beware in any
case, however, that on the Cray you would be dealing with a compiler
modified to match the machine's special architecture.

> 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.

That is possible, but recompiling it yourself is not guaranteed to
work. Can you try to get any support from the staff in this? That's
definitely a more operating system-oriented issue.

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 7:33 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
> 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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