Re: segmentation fault?

From: Joachim Hein (joachim_at_epcc.ed.ac.uk)
Date: Thu Nov 06 2008 - 12:18:50 CST

Hi,

The TCL supplied on the NAMD wiki worked fine under catamount, however not
on a system running what used to be called CNL.

We build NAMD using gcc (So far I didn't get round to study what the
DEISA people are using). Concerning the tcl, get the 8.4.19 tarball
and the sequence

   module unload PrgEnv-pgi
   module load PrgEnv-gnu

   ./configure --enable-shared=no --prefix=install_directory

   make
   make install

so far worked for us. Obviously, in the above, you need to replace the
"install_directory" with the path where you want everything installed.

For a full NAMD build, we also need a charm++ and an fftw2.1.5
libary which are compiled with gcc (the above module unload and load
sequenze).

But may I also ask which XT service are you using? Most services have it
installed. Ask their helpdesk whether they have it and what you need to
do to get access.

Best wishes
   Joachim

On Wed, 5 Nov 2008, Giacomo Fiorin wrote:

>> 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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