segmentation fault on a water example
Axel
akoh... at gmail.com
Mon Mar 9 19:19:33 UTC 2009
On Mar 9, 1:10 pm, "Santo K. P." <sant... at gmail.com> wrote:
> Hi
>
> Have you checked whether your program requires RAM more than available on
> your computer?
regtest inputs are miniscule by design. so memory is
not an issue.
for the record. it works fine for me using
intel 10.1 with these settings.
DFLAGS = -D__INTEL -D__FFTSGL -D__FFTSG -D__FFTW3 -D__LIBINT #-
DCODATA_VERSION=1998
CPPFLAGS = -traditional -C $(DFLAGS) -P
FCFLAGS = $(DFLAGS) -O2 -unroll -march=pentium3 -mtune=core2 -pc64 -
fpp -heap-arrays 64
LDFLAGS = -i-static $(FCFLAGS) -L/opt/intel/mkl/10.0.1.014/lib/em64t -
L$(HOME)/libint/lib
LIBS = -Wl,-Bstatic,--start-group,-lmkl_intel_lp64,-
lmkl_sequential,-lmkl_core,--end-group,-lfftw3,-lfftw3f,-Bdynamic \
../../../libint_tools/libint_cpp_wrapper.o -lderiv -lint -lstdc
++
cheers,
axel.
>
> Santo
>
>
>
> On Mon, Mar 9, 2009 at 11:03 AM, Fawzi Mohamed <fa... at gmx.ch> wrote:
>
> > If you have problems with a regtest that the web shows should work,
> > http://cp2k.berlios.de/regtest.html
> > that is normally a good indication that you miscompiled something.
> > The problem is probably your compiler, or your libraries.
>
> > Fawzi
>
> > On 9-mar-09, at 17:58, Marius Retegan wrote:
>
> > > I've forgot to say that the older version worked, even though I've got
> > > some strange results :-).
>
> > > On Mon, Mar 9, 2009 at 5:48 PM, Marius Retegan
> > > <marius.s... at gmail.com> wrote:
> > >> Hello,
>
> > >> I'm having some trouble running the cp2k/tests/QMMM/SE/regtest/
> > >> water_3.inp test.
> > >> With a version compiled this afternoon from CVS i get the following
> > >> output (I posted only the beginning and the error message)
>
> > >> ==============================================================
> > >> mretegan at fougeron has created process
> > >> number 0 27382
>
> > >> **** **** ****** ** PROGRAM STARTED AT Mon Mar 9
> > >> 17:41:14 2009
> > >> ***** ** *** *** ** PROGRAM STARTED
> > >> ON fougeron
> > >> ** **** ****** PROGRAM STARTED
> > >> BY mretegan
> > >> ***** ** ** ** ** PROGRAM PROCESS
> > >> ID 27382
> > >> **** ** ******* ** PROGRAM STARTED IN /fougeron/home/mretegan/
> > >> software/cp2k
> > >> /tests/QMMM/SE/regtest
>
> > >> CP2K| version string: CP2K version 2.0.1
> > >> (Development Version)
> > >> CP2K| is freely available from
> >http://cp2k.berlios.de/
> > >> CP2K| Program compiled at Mon Mar 9
> > >> 15:25:57 CET 2009
> > >> CP2K| Program compiled
> > >> on fougeron
> > >> CP2K| Program compiled for
> > >> Linux-ia64-intel
> > >> CP2K| Last CVS
> > >> entry /lib//
> > >> CP2K| Input file
> > >> name water_3.inp
> > >> .
> > >> .
> > >> .
> > >> ********************** begin of velocity initialization
> > >> ***********************
> > >> Initial
> > >> Temperature
> > >> 298.00 K
> > >> COM velocity: 0.000000000000 0.000000000000
> > >> 0.000000000000
> > >> *********************** end of velocity initialization
> > >> ************************
>
> > >> Translating the system in order to center the QM fragment in the
> > >> QM box.
> > >> QMMM| Information on the QM/MM Electrostatic Potential:
>
> > >> DISTRIBUTION OF THE NEIGHBOR LISTS
>
> > >> Total number of particle pairs: 6
> > >> Total number of matrix elements: 27
> > >> Average number of particle pairs: 6
> > >> Maximum number of particle pairs: 6
> > >> Average number of matrix element: 27
> > >> Maximum number of matrix elements: 27
>
> > >> DISTRIBUTION OF THE OVERLAP
>
> > >> Number of non-zero blocks: 6
> > >> Percentage non-zero blocks: 100.00
> > >> Average number of blocks per CPU: 6
> > >> Maximum number of blocks per CPU: 6
> > >> Average number of matrix elements per CPU: 27
> > >> Maximum number of matrix elements per CPU: 27
> > >> QMMM| No QM/MM Electrostatic coupling. Just Mechanical Coupling!
> > >> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> > >> Image PC Routine Line
> > >> Source
> > >> cp2k.sopt 400000000268CF50 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 4000000002687C50 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 40000000000B7BF0 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 4000000000065F50 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 40000000005A1CC0 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 400000000059F980 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 40000000021EB680 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 4000000001890170 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 400000000010C3C0 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 40000000000FD220 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 400000000010BCE0 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 4000000000401B40 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 4000000000400220 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 400000000000FD70 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 400000000000D390 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 4000000000008200 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 40000000000072C0 Unknown Unknown
> > >> Unknown
> > >> libc.so.6.1 2000000000555C50 Unknown Unknown
> > >> Unknown
> > >> cp2k.sopt 4000000000007000 Unknown Unknown
> > >> Unknown
> > >> ==============================================================
>
> > >> My first guess was that the program was miscompiled, and I've tried
> > >> an
> > >> older version compiled also from CVS on the 4 Feb 2009.
> > >> ==============================================================
> > >> mretegan at fougeron has created process
> > >> number 0 27441
>
> > >> **** **** ****** ** PROGRAM STARTED AT Mon Mar 9
> > >> 17:47:02 2009
> > >> ***** ** *** *** ** PROGRAM STARTED
> > >> ON fougeron
> > >> ** **** ****** PROGRAM STARTED
> > >> BY mretegan
> > >> ***** ** ** ** ** PROGRAM PROCESS
> > >> ID 27441
> > >> **** ** ******* ** PROGRAM STARTED IN /fougeron/home/mretegan/
> > >> software/cp2k
> > >> /tests/QMMM/SE/regtest
>
> > >> CP2K| version string: CP2K version 2.0.1
> > >> (Development Version)
> > >> CP2K| is freely available from
> >http://cp2k.berlios.de/
> > >> CP2K| Program compiled at Mon Mar 9
> > >> 17:07:32 CET 2009
> > >> CP2K| Program compiled
> > >> on fougeron
> > >> CP2K| Program compiled for
> > >> Linux-ia64-intel
> > >> CP2K| Last CVS entry xray_diffraction.F/1.25/Wed Feb 4
> > >> 08:44:19 2009
> > >> CP2K| Input file
> > >> name water_3.inp
> > >> ==============================================================
> > >> The same flags where used to compile both versions.
>
> > >> Does anybody have an idea on how to solve this?
>
> > >> Thanks,
> > >> Marius
>
> --
>
> Dr. K. P. Santo
> Post doctoral fellow
> Department of Mechanical Engineering and
> National Institute of Nano Technology
> University of Alberta
> Edmonton, Canadahttp://www.cein.ualberta.ca/research/nint/theory-modeling-group/peopl...
More information about the CP2K-user
mailing list