segmentation fault

Nikita vakul... at gmail.com
Fri Jul 22 13:01:06 UTC 2011
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Hi Peter!

Thank you very much for the ARCH file! Yes, I'm trying to build it on
SKIF Chebyshev. But using your arch file I got warning:

********************
ifort: command line warning #10156: ignoring option '-static'; no
argument required
make[1]: warning:  Clock skew detected.  Your build may be incomplete.
make[1]: Leaving directory `/home/vakula/CP2K_NEW/cp2k/obj/
skif_chebyshev/popt'
make: warning:  Clock skew detected.  Your build may be incomplete.
********************

Nevertheless, I had tried to run my calculation with obtained
(chebyshev arch) executable and I got the same problem:

********************
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line
Source
cp2k.popt          00000000011ADFE0  Unknown               Unknown
Unknown
cp2k.popt          00000000010637CB  Unknown               Unknown
Unknown
cp2k.popt          00000000004EA0F1  Unknown               Unknown
Unknown
cp2k.popt          000000000042FAE1  Unknown               Unknown
Unknown
cp2k.popt          000000000042AB6E  Unknown               Unknown
Unknown
cp2k.popt          0000000000429B3C  Unknown               Unknown
Unknown
libc.so.6          00007FF4AAB0FCF4  Unknown               Unknown
Unknown
cp2k.popt          0000000000429A49  Unknown               Unknown
Unknown
********************

plus a new one

*******************
[55:node-62-01] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 55
[61:node-41-05] unexpected disconnect completion event from
[7:node-41-03]
[62:node-41-05] unexpected disconnect completion event from
[7:node-41-03]
[57:node-41-05] unexpected disconnect completion eventrank 4 in job 1
t60-2.parallel.ru_42663   caused collective abort of all ranks
  exit status of rank 4: killed by signal 9
 from [7:node-41-03]
[58:node-41-05] unexpected disconnect completion event from
[7:node-41-03]
[56:node-41-05] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 56
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 57
[60:node-41-05] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
[63:node-41-05] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 63
[51:node-62-01] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 51
[52:node-62-01] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 58
[59:node-41-05] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 59
internal ABORT - process 60
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 61
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 62
[50:node-62-01] unexpected disconnect completion event from
[7:node-41-03]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 50
[1:node-41-03] unexpected disconnect completion event from
[33:node-62-07]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 1
[0:node-41-03] unexpected disconnect completion event from
[33:node-62-07]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 0
[2:node-41-03] unexpected disconnect completion event from
[33:node-62-07]
[3:node-41-03] unexpected disconnect completion event from
[33:node-62-07]
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 3
Assertion failed in file ../../dapl_module_util.c at line 1593: 0
internal ABORT - process 2
rank 1 in job 1  t60-2.parallel.ru_42663   caused collective abort of
all ranks
  exit status of rank 1: killed by signal 9
rank 0 in job 1  t60-2.parallel.ru_42663   caused collective abort of
all ranks
  exit status of rank 0: killed by signal 9
******************************
Any suggestions? And do you use CP2K on SKIF? Does it work without any
problem?

Thank you in advance,
Nikita

On Jul 22, 3:37 pm, Peter Mamonov <pmam... at gmail.com> wrote:
> Hi Nikita!
>
> Correct me if I'm wrong, but as i can see you are trying to build CP2K
> for SKIF `Chebyshev`. If so, you can try this (working) arch file for
> Chebyshev (see below). Also be sure to switch to intel's compiler
> using command:
>
> mpi-selector --set intel_mpi_intel64-4.0.0.025
>
> and run your task with `-as intel` option:
>
> mpirun -as intel -blah -blah blah
>
> Best regards,
> Peter
> --
>
> # Chebyshev ARCH file
>
> MKL_ROOT  = /opt/intel/mkl/10.2.4.032
> MKL_LIB = $(MKL_ROOT)/lib/em64t
> MKL_INCLUDE = $(MKL_ROOT)/include
>
> CC       = cc
> CPP      =
> FC       = mpif90
> LD       = mpif90
> AR       = ar -r
>
> DFLAGS   = -D__INTEL -D__FFTSG -D__FFTMKL -D__parallel -D__BLACS
> -D__SCALAPACK -D__HAS_NO_ISO_C_BINDING
>
> CPPFLAGS = -traditional -C $(DFLAGS) -I$(MKL_INCLUDE)/include
>
> FCFLAGS  = -fc=ifort $(DFLAGS) -I$(MKL_INCLUDE) -O2 -xHost
> -heap-arrays 64 -fpp -free
>
> LDFLAGS  = $(FCFLAGS) -L$(MKL_LIB)
>
> LIBS     = -Wl,--start-group \
> $(MKL_LIB)/libmkl_scalapack_lp64.a \
> $(MKL_LIB)/libmkl_blacs_intelmpi_lp64.a \
> $(MKL_LIB)/libmkl_intel_lp64.a \
> $(MKL_LIB)/libmkl_sequential.a \
> $(MKL_LIB)/libmkl_core.a \
> -static-mpi \
> -Wl,--end-group
>
> OBJECTS_ARCHITECTURE = machine_intel.o
>
> # End of Chebyshev ARCH file
>
> On Fri, Jul 22, 2011 at 2:56 PM, Jörg Saßmannshausen
>
>
>
>
>
>
>
> <j.sassma... at ucl.ac.uk> wrote:
> > Dear Nikita,
>
> > did you use that before you started a run as well?
>
> > Unfortunately, it is some time that I have compiled cp2k so I don't know on
> > top of my head. The limit of the stack-size is usually the culprit here.
>
> > All the best from a sunny London
>
> > Jörg
>
> > On Friday 22 July 2011 11:06:51 Nikita wrote:
> >> Hi Jörg,
>
> >> thanks for your suggestion! But I had already tried this before
> >> compilation, but the error occured all the same.
> >> Maybe there are some other tricks to overcome this obstacle?
>
> >> Thank you in advance,
> >> Nikita
>
> >> On Jul 22, 1:36 pm, Jörg Saßmannshausen <j.sassma... at ucl.ac.uk>
>
> >> wrote:
> >> > Hi Nikita,
>
> >> > the intel compiler is notorious for doing segfaults.
>
> >> > Have you tried:
>
> >> > $ ulimit -s unlimited
>
> >> > That might cure the problem.
>
> >> > Regards
>
> >> > Jörg
>
> >> > On Friday 22 July 2011 10:13:53 Nikita wrote:
> >> > > Dear CP2K users and developers,
>
> >> > > I have recently compiled CP2K on our university cluster. But the
> >> > > calculation failed with the following message:
> >> > > ********************************************
> >> > > --------------------------
> >> > >  OPTIMIZATION STEP:      2
> >> > >  --------------------------
> >> > > forrtl: severe (174): SIGSEGV, segmentation fault occurred
> >> > > Image              PC                Routine            Line
> >> > > Source
> >> > > cp2k.popt          0000000001195583  Unknown               Unknown
> >> > > Unknown
> >> > > cp2k.popt          000000000104A51A  Unknown               Unknown
> >> > > Unknown
> >> > > cp2k.popt          00000000004CEDA1  Unknown               Unknown
> >> > > Unknown
> >> > > cp2k.popt          000000000040E631  Unknown               Unknown
> >> > > Unknown
> >> > > cp2k.popt          00000000004096BE  Unknown               Unknown
> >> > > Unknown
> >> > > cp2k.popt          000000000040868C  Unknown               Unknown
> >> > > Unknown
> >> > > libc.so.6          00007FED46734CF4  Unknown               Unknown
> >> > > Unknown
> >> > > cp2k.popt          0000000000408599  Unknown               Unknown
> >> > > Unknown
> >> > > ************************************************
>
> >> > > Could you suggest any solutions to my problem? By the way, here is my
> >> > > arch file:
>
> >> > > **********************************
> >> > > INTEL_MKL = /opt/intel/mkl/10.2.4.032
> >> > > INTEL_INC = $(INTEL_MKL)/include/fftw
> >> > > INTEL_LIB = $(INTEL_MKL)/lib/em64t
>
> >> > > CC       = mpicc
> >> > > CPP      =
> >> > > FC =  mpif90
> >> > > LD = mpif90
> >> > > AR       = /usr/bin/ar -r
> >> > > DFLAGS   = -D__INTEL -D__FFTSG -D__parallel -D__SCALAPACK -D__BLACS -
> >> > > D__FFTW3 -D__LIBINT  -D__HAS_NO_ISO_C_BINDING
> >> > > CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
> >> > > FCFLAGS  = $(DFLAGS) -I$(INTEL_INC) \
> >> > >            -O2 -xW -funroll-loops -fpp -free -heap-arrays 64
> >> > > LDFLAGS  = $(FCFLAGS) -I$(INTEL_INC) -i-static
> >> > > LIBS     = -L$(INTEL_LIB) -lmkl_scalapack_lp64 -
> >> > > lmkl_blacs_intelmpi_lp64 \
> >> > >            -lmkl_intel_lp64 -lmkl_sequential -lmkl_core \
> >> > >            /home/vakula/CP2K_NEW/fftw3_compiled/lib/libfftw3.a \
> >> > >            /home/vakula/CP2K_NEW/cp2k/tools/hfx_tools/libint_tools/
> >> > > libint_cpp_wrapper.o \
> >> > >            /home/vakula/CP2K_NEW/libint_compiled/lib/libderiv.a \
> >> > >            /home/vakula/CP2K_NEW/libint_compiled/lib/libint.a \
> >> > >            -lstdc++
>
> >> > > OBJECTS_ARCHITECTURE = machine_intel.o
> >> > > ******************************
>
> >> > > Thank you in advance,
> >> > > Nikita Vakula
> >> > > PhD student, Moscow State University
>
> >> > --
> >> > *************************************************************
> >> > Jörg Saßmannshausen
> >> > University College London
> >> > Department of Chemistry
> >> > Gordon Street
> >> > London
> >> > WC1H 0AJ
>
> >> > email: j.sassma... at ucl.ac.uk
> >> > web:http://sassy.formativ.net
>
> >> > Please avoid sending me Word or PowerPoint attachments.
> >> > Seehttp://www.gnu.org/philosophy/no-word-attachments.html
>
> > --
> > *************************************************************
> > Jörg Saßmannshausen
> > University College London
> > Department of Chemistry
> > Gordon Street
> > London
> > WC1H 0AJ
>
> > email: j.sassma... at ucl.ac.uk
> > web:http://sassy.formativ.net
>
> > Please avoid sending me Word or PowerPoint attachments.
> > Seehttp://www.gnu.org/philosophy/no-word-attachments.html
>
> > --
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