Re: segmentation fault?

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Nov 05 2008 - 19:14:32 CST

On Wed, 5 Nov 2008, BIN ZHANG wrote:

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

bin,

this error is not weird at all, but if you don't know
what to do about it, you should not do the kind of
hack that you are attempting, and rather let somebody
with at least some experience in programming in a
unix environment handle this.

cheers,
   axel.

BZ>
BZ> ./../unix/tclUnixInit.c
BZ> ./../unix/tclUnixInit.c: In function 'TclpSetVariables':
BZ> ./../unix/tclUnixInit.c:536: error: storage size of 'name' isn't known
BZ> ./../unix/tclUnixInit.c:547: warning: implicit declaration of function
BZ> 'uname'
BZ> ./../unix/tclUnixInit.c:536: warning: unused variable 'name'
BZ> make: *** [tclUnixInit.o] Error 1
BZ>
BZ> Do you know what this is about? Bug of the code, or I'm using
BZ> inappropriate compiler?
BZ> I want to compile it myself because the library provided in that link
BZ> seems to have compatibility issues with the CRAY system I was running
BZ> on.
BZ> Thanks a lot.
BZ>
BZ> Bin
BZ>
BZ>
BZ>
BZ> On Nov 5, 2008, at 3:46 PM, Giacomo Fiorin wrote:
BZ>
BZ> >Hello Bin, for a system of that size the memory usage is of the order
BZ> >of few tens of Mb, certainly too small to explain. Also, most of the
BZ> >times you shouldn't get a segmentation fault (which means that there's
BZ> >an internal error when accessing data), but an operating system error
BZ> >instead.
BZ> >
BZ> >Are you concatenating minimization and dynamics with Tcl? If you have
BZ> >a Tcl library that doesn't behave properly on your Cray's operating
BZ> >system, you may be better off just running separate input files for
BZ> >NAMD that don't use Tcl, and investigate the problem in the meantime.
BZ> >Unless you're using tclForces, results are completely equivalent with
BZ> >and without Tcl. It's just a little less convenient for you to set up
BZ> >separate inputs :-(
BZ> >
BZ> >Giacomo
BZ> >
BZ> >---- -----
BZ> >Giacomo Fiorin
BZ> > Center for Molecular Modeling at
BZ> > University of Pennsylvania
BZ> > 231 S 34th Street, Philadelphia, PA 19104-6323
BZ> >phone: (+1)-215-573-4773
BZ> >fax: (+1)-215-573-6233
BZ> >mobile: (+1)-267-324-7676
BZ> >mail: giacomo.fiorin_<at>_gmail.com
BZ> >web: http://www.cmm.upenn.edu/
BZ> >---- ----
BZ> >
BZ> >
BZ> >
BZ> >On Wed, Nov 5, 2008 at 4:58 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
BZ> > >Hi, there:
BZ> > >
BZ> > > Is there an upper limit of atom number that NAMD can handle?
BZ> > > I was running a simulation with first 1000 step minimization and then
BZ> > >dynamics. But NAMD existed after the minimization with error
BZ> > >
BZ> > >Application 471018 exit signals: Segmentation fault, Killed
BZ> > >
BZ> > > And the error in the output file is:
BZ> > >
BZ> > >APINFO_NIDTERM: compute node initiated termination, possible out of
BZ> > >memory
BZ> > >condition
BZ> > >
BZ> > > Is this a problem of limited compute memory? or, the namd itself(wrong
BZ> > >scripts, et al)? How can I estimate the memory needed for a given atom
BZ> > >number?
BZ> > > BTW, the atom numbers of my system is about 15,000
BZ> > > Thanks a lot.
BZ> > >
BZ> > >Bin
BZ> > >
BZ> > >
BZ> > >
BZ> > >
BZ> > >
BZ> > >
BZ> > >
BZ> > >
BZ> > >
BZ> > >-------------------------------------------------------------
BZ> > >The tree of liberty must be refreshed from time to time with the blood of
BZ> > >patriots and tyrants.
BZ> > >
BZ> > >
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ> -------------------------------------------------------------
BZ> The tree of liberty must be refreshed from time to time with the blood of
BZ> patriots and tyrants.
BZ>

-- 
=======================================================================
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.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:03 CST