[CPMD-list] still cpmd2cube segmentation fault error occurring

haider abbas haiderabbasphy at yahoo.co.in
Thu Dec 15 10:05:24 CET 2005 

Dear all cpmd user,

I am using cpmd-3.7.2. It was compiled in the mid of
last year with the help of Axel. I was totally new to
this work and he had helped me a lot and when i got
the executable, i saved it in a separate directory and
to learn more i did different experiment with the 
makefile so i am not sure that the below makefile
which i have is the same as was used in compilation
cpmd-3.7.2. It may be or may not be but i have only
this one.
it was compiled using libatlas library from Axel web
page as i remember.
#----------------------------------------------------------------------------
# Makefile for cpmd.x (plane wave electronic
calculation)
# Configuration: PC-IFC
# Creation of Makefile: May 24 2004
# on Linux sarus 2.4.18-14 #1 Wed Sep 4 13:35:50 EDT
2002 i686 i686 i386 GNU/Linux
# Author: haider
#----------------------------------------------------------------------------
#
SHELL = /bin/sh
#
#--------------- Default Configuration for PC-IFC
---------------
SRC  = .
DEST = .
BIN  = .
#QMMM_FLAGS = -D__QMECHCOUPL
#QMMM_LIBS  = -L. -lmm
FFLAGS = -c -r8 -w90 -w95 -O3 -pc64 -axM -ip -tpp7 
LFLAGS = -L. -latlas $(QMMM_LIBS)
CFLAGS = -c -O2 -Wall
CPP = /lib/cpp -P -C -traditional
CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT
-DLINUX_IFC  
NOOPT_FLAG = 
CC = gcc 
FC = ifc 
LD = ifc 
AR = 

and the makefile of cpmd2cube is 

#-----------------------------------------------------------------------------#
# Makefile for cpmd2cube.x
# Configuration: Linux-PC-IFC-P4
# Creation of Makefile: Nov 23 2005
# on Linux robin 2.4.21-15.EL #1 Sun May 16 02:45:06
EDT 2004 i686 athlon i386 GNU/Linux
# Author: haider
#----------------------------------------------------------------------------
#
SHELL = /bin/sh
#
#--------------- Configuration
FC	= ifc
FFLAGS	=  -FR -D__IFC -DFFT_DEFAULT -O -tpp7 -w90 -w95
-pc64
LFLAGS	= -O -tpp7 -w90 -w95 -pc64
LIBS	=  -Vaxlib 
# uncomment and set only if needed
#CC	= cc
#CFLAGS	= 
#--------------- End of Configuration
##############


i am running cpmd2cube and cpmd on the same pc but the
error is still there


Dear Prof. Hutter and Dear Prof. Apsi,

below is the result of what you have suggested me. 

haider at robin:~> cd codes
haider at robin:~/codes> cd cpmd2
haider at robin:~/codes/cpmd2> gdb cpmd2cube.x
GNU gdb Red Hat Linux (6.0post-0.20040223.20rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General
Public License, and you are
welcome to change it and/or distribute copies of it
under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show
warranty" for details.
This GDB was configured as
"i386-redhat-linux-gnu"...(no debugging symbols
found)...Using host libthread_db library
"/lib/tls/libthread_db.so.1".
 
(gdb) run -dens DENSITY
Starting program: /home/haider/codes/cpmd2/cpmd2cube.x
-dens DENSITY
Any sufficiently advanced technology is
indistinguishable from magic.
                -- Arthur C. Clarke
_______________________________________________________________

(no debugging symbols found)...(no debugging symbols
found)...(no debugging symbols found)...(no debugging
symbols found)...[Thread debugging using libthread_db
enabled]
[New Thread -1220262496 (LWP 5561)]
(no debugging symbols found)...(no debugging symbols
found)...
.read input file ... done
I think you stored a density (sum^2 =  0.12582877E-03)
.building g vectors ... done
 
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread -1220262496 (LWP 5561)]
0x08055f58 in cpmd2cube_mp_do_geom_ ()
(gdb)


thanks 
yours sincerely 
Haider Abbas





--- Ari P Seitsonen <ari.p.seitsonen at iki.fi> wrote:

> 
> Dear Haider,
> 
>    Adding to Juerg's comments: Which FFT are you
> using during the 
> compilation (pre-processor flag '-Dxxx')? Is it the
> same as what you used 
> for CPMD? What's the output from 'ulimit -a' (or
> 'limit', if using 
> 'tcsh')? You could also run cpmd2cube.x within a
> debugger (preferrably 
> compiled with debugging, like Juerg suggested) like
> 'gdb' or 'dbx', you 
> call
> 
> # > gdb cpmd2cube.x
> # : run -dens DENSITY
> and when the code crashes
> # : where
> 
> and send us the output. This _might_ help (no
> promises), otherwise we're 
> just guessing.
> 
>      Greetings from Lausanne,
> 
>         apsi
> 
>
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>    Ari P Seitsonen / Ari.P.Seitsonen at iki.fi /
> http://www.iki.fi/~apsi/
>    CNRS & IMPMC, Université Pierre et Marie Curie
>        4 place Jussieu, case 115 / F-75252 Paris
>    Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM:
> +33-6-6736 3820
> 
> On Wed, 14 Dec 2005, Juerg Hutter wrote:
> 
> > Hi
> >
> > maybe you could compile the code with the debug
> flag on,
> > so we would get a meaningful traceback.
> >
> > regards
> >
> > Juerg Hutter
> >
> >
>
----------------------------------------------------------
> > Juerg Hutter                   Phone : ++41 44 635
> 4491
> > Physical Chemistry Institute   FAX   : ++41 44 635
> 6838
> > University of Zurich           E-mail:
> hutter at pci.unizh.ch
> > Winterthurerstrasse 190
> > CH-8057 Zurich, Switzerland
> >
>
----------------------------------------------------------
> >
> >
> > On Wed, 14 Dec 2005, haider abbas wrote:
> >
> >> Dear Axel,
> >> 
> >> I have used the command
> >> 
> >> haider at robin:~/cpmd2cube> ulimit -s unlimited
> >> haider at robin:~/cpmd2cube> cpmd2cube.x -dens
> DENSITY
> >> 
> >> .read input file ... done
> >> I think you stored a density (sum^2 = 
> 0.12582877E-03)
> >> .building g vectors ... done
> >> forrtl: severe (174): SIGSEGV, segmentation fault
> >> occurred
> >> Image              PC        Routine           
> Line
> >>     Source
> >> cpmd2cube.x        08055F58  Unknown
> >> Unknown  Unknown
> >> cpmd2cube.x        0805404E  Unknown
> >> Unknown  Unknown
> >> cpmd2cube.x        0805880F  Unknown
> >> Unknown  Unknown
> >> cpmd2cube.x        0806C9D8  Unknown
> >> Unknown  Unknown
> >> cpmd2cube.x        40099768  Unknown
> >> Unknown  Unknown
> >> cpmd2cube.x        08049CE1  Unknown
> >> Unknown  Unknown
> >> 
> >> but it is still there, i am using intel_fc_80 and
> >> White Box Enterprise Linux release 3.0
> (Liberation
> >> Respin 1)
> >> Kernel 2.4.21-15.EL on an i686
> >> 
> >> now please guide me
> >> Thanks
> >> yours sincerely
> >> Haider Abbas
> >> 
> >> 
> >> 
> >> --- Axel Kohlmeyer <akohlmey at vitae.cmm.upenn.edu>
> >> wrote:
> >> 
> >>> 
> >>> hi,
> >>> 
> >>> this is most likely not a problem of the code.
> >>> please try raising the stacksize using the
> ulimit
> >>> command.
> >>> the newer intel compilers allocate automatic
> arrays
> >>> from
> >>> the stack.
> >>> 
> >>> axel.
> >>> 
> >>> 
> >>
>
=======================================================================
> >>> Axel Kohlmeyer    e-mail:
> akohlmey at cmm.upenn.edu,
> >>> tel: ++1-215-898-1582
> >>>     Center for Molecular Modeling    --
> >>> University of Pennsylvania
> >>> Department of Chemistry, 231 S.34th Street,
> >>> Philadelphia, PA 19104-6323
> >>> 
> >>
>
=======================================================================
> >>> If you make something idiot-proof, the universe
> >>> creates a better idiot.
> >>> 
> >>> On Mon, 12 Dec 2005, haider abbas wrote:
> >>> 
> >>>> Dear all cpmd user,
> >>>> 
> >>>> running cpmd2cube shows the following error
> >>>> 
> >>>> [haider at falcon1 cpmd2cube]$ cpmd2cube.x  -rho
> >>>> -halfmesh ELPOT
> >>>> 
> >>>> .read input file ... done
> >>>> I think you stored a density (sum^2 =
> >>> 0.77965627E-03)
> >>>> .building g vectors ... done
> >>>> forrtl: severe (174): SIGSEGV, segmentation
> fault
> >>>> occurred
> >>>> Image              PC        Routine
> >>> Line
> >>>>     Source
> >>>> cpmd2cube.x        08055F58  Unknown
> >>>> Unknown  Unknown
> >>>> cpmd2cube.x        0805404E  Unknown
> >>>> Unknown  Unknown
> >>>> cpmd2cube.x        0805880F  Unknown
> >>>> Unknown  Unknown
> >>>> cpmd2cube.x        0806C9D8  Unknown
> >>>> Unknown  Unknown
> >>>> cpmd2cube.x        00763E33  Unknown
> >>>> Unknown  Unknown
> >>>> cpmd2cube.x        08049CE1  Unknown
> >>>> Unknown  Unknown
> >>>> 
> >>>> 
> >>>> the makefile of cpmd2cube.x is
> >>>> 
> >>>> 
> >>> 
> >>
>
#-----------------------------------------------------------------------------#
> >>>> # Makefile for cpmd2cube.x
> >>>> # Configuration: Linux-PC-IFC-P4
> >>>> # Creation of Makefile: Nov 23 2005
> >>>> # on Linux robin 2.4.21-15.EL #1 Sun May 16
> >>> 02:45:06
> >>>> EDT 2004 i686 athlon i386 GNU/Linux
> >>>> # Author: haider
> >>>> 
> >>> 
> >>
>
#----------------------------------------------------------------------------
> >>>> #
> >>>> SHELL = /bin/sh
> >>>> #
> >>>> #--------------- Configuration
> >>>> FC	= ifc
> >>>> FFLAGS	=  -FR -D__IFC -DFFT_DEFAULT -O -tpp7
> -w90
> >>> -w95
> >>>> -pc64
> >>>> LFLAGS	= -O -tpp7 -w90 -w95 -pc64
> >>>> LIBS	=  -Vaxlib
> 
=== message truncated ===>
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