Sigsegv error during cell optimization

Peter pmam... at gmail.com
Fri May 8 14:41:50 CEST 2009


> the administrators have already checked for the stack size

Sorry, I've overlooked this. Disregard my previous advice.

Peter

On May 8, 4:21 pm, Peter Mamonov <pmam... at gmail.com> wrote:
> Hello there!
>
> Try adding "-heap-arrays 64" to FCFLAGS.
>
> Peter
>
> On Wed, May 6, 2009 at 11:48 AM,  <Maricarme... at cemes.fr> wrote:
>
> > Hello everyone,
>
> > I'm running a DFT cell optimization for Mx-V4O11 crystals (M = Ag and
> > Cu). My cells are approximately 14x7x7 and about 260 atoms. Below is a
> > copy of one of my input files. The problem is I keep getting a SIGSEGV
> > (11) error, usually when starting the SCF cycles for the second cell
> > opt step (an extract from the output file is also below).
> > I'm running parallel on a calculus center (http://www.cines.fr/
> > spip.php?rubrique186), and the administrators have already checked for
> > the stack size (which according to them is set to unlimited). Below is
> > also a copy of the job submission's file, and of the arch file.
> > I even tried to run a cell opt test for a smaller cell (14*3*3, about
> > 68 atoms), which I had already ran in a different calculus center
> > without any issues, and I will still get the segmentation fault error.
> > This clearly indicates me that the problem is associated to a
> > configuration of the machines, to the way CP2K was installed, or to
> > the job submission's characteristics (or to something else??). I must
> > say I always get the exact same error during cell opt's second step,
> > no matter what the system is (small or big cell, Ag or Cu).
> > I tried running an Energy test on the smaller cell and it worked fine.
>
> > I would really appreciate if any of you can throw some light at this,
> > for I'm pretty stuck on it right now.
>
> > Cheers,
>
> > Maricarmen.
>
> > Arch file:
>
> > # by default some intel compilers put temporaries on the stack
> > # this might lead to segmentation faults if the stack limit is set to
> > low
> > # stack limits can be increased by sysadmins or e.g with ulimit -s
> > 256000
> > # Tested on a HPC non-Itanium clusters @ UDS (France)
> > # Note: -O2 produces an executable which is slightly faster than -O3
> > # and the compilation time was also much shorter.
> > CC       = icc -diag-disable remark
> > CPP      =
> > FC       = ifort -diag-disable remark -openmp
> > LD       = ifort -diag-disable remark -openmp
> > AR       = ar -r
>
> > #Better with mkl (intel lapack/blas) only
> > #DFLAGS   = -D__INTEL -D__FFTSG -D__parallel
> > #If you want to use BLACS and SCALAPACK use the flags below
> > DFLAGS   = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK -
> > D__FFTW3
> > CPPFLAGS =
> > FCFLAGS  = $(DFLAGS) -fpp -free -O3 -xS -I/opt/software/SGI/intel/mkl/
> > 10.0.3.020/include -I/opt/software/SGI/intel/mkl/10.0.3.020/include/
> > fftw
> > LDFLAGS  =  -L/opt/software/SGI/intel/mkl/10.0.3.020/lib/em64t
> > #LIBS     = -lmkl -lm -lpthread -lguide -openmp
> > #If you want to use BLACS and SCALAPACK use the libraries below
> > LIBS     = -Wl,--allow-multiple-definition -lmkl_scalapack_lp64 /
> > scratch/grisolia/blacsF77init_MPI-LINUX-0.a /scratch/grisolia/
> > blacs_MPI-LINUX-0.a -lmpi -lmkl -lfftw3xf_intel -lmkl_blacs_lp64
>
> > OBJECTS_ARCHITECTURE = machine_intel.o
>
> > -------
>
> > Job submission's file (getting the sigsegv error):
>
> > #PBS -N cp2k
> > #PBS -l walltime=24:00:00
> > #PBS -S /bin/bash
> > #PBS -l select=8:ncpus=8:mpiprocs=8:ompthreads=1
> > #PBS -j oe
> > #PBS -M  gris... at cemes.fr -m abe
>
> > PBS_O_WORKDIR=/scratch/grisolia/CuVO/Fixed/
>
> > cd $PBS_O_WORKDIR
>
> > export OMP_NUM_THREADS=1
> > export MKL_NUM_THREADS=1
> > export MPI_GROUP_MAX=512
>
> > /usr/pbs/bin/mpiexec /scratch/grisolia/cp2k/exe/Linux-x86-64-jade/
> > cp2k.psmp CuV4O11-CellOpt.inp
>
> > --------------
>
> > Input file:
>
> > &GLOBAL
> >  PROJECT     CuV4O11-CellOpt
> >  RUN_TYPE    CELL_OPT
> >  PRINT_LEVEL MEDIUM
> >  WALLTIME  86000
> > &END GLOBAL
> > &FORCE_EVAL
> >  METHOD Quickstep
> >  &DFT
> >    BASIS_SET_FILE_NAME /scratch/grisolia/cp2k/tests/QS/BASIS_MOLOPT
> >    POTENTIAL_FILE_NAME /scratch/grisolia/cp2k/tests/QS/GTH_POTENTIALS
> >    LSD
> >    &MGRID
> >      CUTOFF 280
> >      NGRIDS 5
> >    &END MGRID
> >    &QS
> >      EPS_DEFAULT   1.0E-10
> >      EXTRAPOLATION PS
> >      EXTRAPOLATION_ORDER 1
> >    &END QS
> >    &SCF
> >      SCF_GUESS RESTART
> >      EPS_SCF 2.0E-7
> >      MAX_SCF 30
> >      &OUTER_SCF
> >         EPS_SCF 2.0E-7
> >         MAX_SCF 15
> >      &END
> >      &OT
> >        MINIMIZER CG
> >        PRECONDITIONER FULL_SINGLE_INVERSE
> >        ENERGY_GAP 0.05
> >      &END
> >      &PRINT
> >         &RESTART
> >            FILENAME = CuV4O11-CellOpt.wfn
> >         &END
> >      &END
> >    &END SCF
> >    &XC
> >      &XC_FUNCTIONAL PBE
> >      &END XC_FUNCTIONAL
> >    &END XC
> >     &PRINT
> >       &MO_CUBES
> >          WRITE_CUBE F
> >          NLUMO      20
> >          NHOMO      20
> >       &END
> >     &END
> >  &END DFT
> >  &SUBSYS
> >    &CELL
> >      @INCLUDE CuV4O11-GeoOpt.cell
> >    &END CELL
> >    &COORD
> >      @INCLUDE CuV4O11-GeoOpt.coord
> >    &END COORD
> >    &END COORD
> >    &KIND Cu
> >      BASIS_SET DZVP-MOLOPT-SR-GTH
> >      POTENTIAL GTH-PBE-q11
> >    &END KIND
> >    &KIND O
> >      BASIS_SET DZVP-MOLOPT-SR-GTH
> >      POTENTIAL GTH-PBE-q6
> >    &END KIND
> >    &KIND V
> >      BASIS_SET DZVP-MOLOPT-SR-GTH
> >      POTENTIAL GTH-PBE-q13
> >    &END KIND
> >  &END SUBSYS
> >  STRESS_TENSOR ANALYTICAL
> > &END FORCE_EVAL
> > &MOTION
> >  &MD
> >      TIMESTEP [fs] 0.5
> >      STEPS         10000
> >      TEMPERATURE   500
> >      ENSEMBLE      NVE
> >  &END
> >  &CELL_OPT
> >    TYPE GEO_OPT
> >    OPTIMIZER CG
> >    MAX_ITER 20
> >    EXTERNAL_PRESSURE [bar] 0.0
> >    MAX_DR 0.02
> >    RMS_DR 0.01
> >    MAX_FORCE 0.002
> >    RMS_FORCE 0.001
> >    KEEP_ANGLES T
> >    &CG
> >      &LINE_SEARCH
> >        TYPE 2PNT
> >        &2PNT
> >        &END
> >      &END
> >    &END
> >  &END
> >  &GEO_OPT
> >    MAX_ITER 300
> >    MINIMIZER LBFGS
> >  &END
> > &END
>
> > -------
>
> > Extract from the output file ( sigsegv error):
>
> > MPI: On host r17i2n5, Program /scratch/cem6039/grisolia/cp2k/exe/Linux-
> > x86-64-jade/cp2k.psmp, Rank 0, Process 4568 received signal SIGSEGV
> > (11)
>
> > MPI: --------stack traceback-------
> > MPI: On host r17i3n12, Program /scratch/cem6039/grisolia/cp2k/exe/
> > Linux-x86-64-jade/cp2k.psmp, Rank 57, Process 29665 received signal
> > SIGSEGV(11)
>
> > MPI: --------stack traceback-------
> > MPI: On host r17i3n0, Program /scratch/cem6039/grisolia/cp2k/exe/Linux-
> > x86-64-jade/cp2k.psmp, Rank 25, Process 542 received signal SIGSEGV
> > (11)
>
> > MPI: --------stack traceback-------
> > MPI: On host r17i3n1, Program /scratch/cem6039/grisolia/cp2k/exe/Linux-
> > x86-64-jade/cp2k.psmp, Rank 32, Process 5057 received signal SIGSEGV
> > (11)
>
> > MPI: --------stack traceback-------
> > MPI: GNU gdb 6.6
> > MPI: Copyright (C) 2006 Free Software Foundation, Inc.
> > MPI: GDB is free software, covered by the GNU General Public License,
> > and you are
> > MPI: welcome to change it and/or distribute copies of it under certain
> > conditions.
> > MPI: Type "show copying" to see the conditions.
> > MPI: There is absolutely no warranty for GDB.  Type "show warranty"
> > for details.
> > MPI: This GDB was configured as "x86_64-suse-linux"...
> > MPI: Using host libthread_db library "/lib64/libthread_db.so.1".
> > MPI: Attaching to program: /proc/4568/exe, process 4568
> > MPI: [Thread debugging using libthread_db enabled]
> > MPI: [New Thread 46912551614368 (LWP 4568)]
> > MPI: [New Thread 1073809728 (LWP 4588)]
> > MPI: 0x00002aaaad94073f in waitpid () from /lib64/libpthread.so.0
> > MPI: (gdb) #0  0x00002aaaad94073f in waitpid () from /lib64/
> > libpthread.so.0
> > MPI: #1  0x00002aaaaadb5133 in MPI_SGI_stacktraceback () from /usr/
> > lib64/libmpi.so
> > MPI: #2  0x00002aaaaadb5773 in slave_sig_handler () from /usr/lib64/
> > libmpi.so
> > MPI: #3  <signal handler called>
> > MPI: #4  0x00000000017f7ad0 in fftw_destroy_plan ()
> > MPI: #5  0x00000000017f794d in dfftw_destroy_plan_ ()
> > MPI: #6  0x000000000169332a in fftw3_destroy_plan_ ()
> > MPI: #7  0x000000000169199e in fft_destroy_plan_ ()
> > MPI: #8  0x000000000044229e in
> > fft_tools_mp_deallocate_fft_scratch_type_ ()
> > MPI: #9  0x00000000004678ae in fft_tools_mp_resize_fft_scratch_pool_
> > ()
> > MPI: #10 0x00000000004556c8 in fft_tools_mp_get_fft_scratch_ ()
> > MPI: #11 0x000000000046ca53 in fft_tools_mp_fft3d_ps_ ()
> > MPI: #12 0x00000000007360c9 in pw_methods_mp_fft_wrap_pw1pw2_ ()
> > MPI: #13 0x0000000000732a01 in pw_methods_mp_pw_transfer_ ()
> > MPI: #14 0x0000000000778bcd in qs_collocate_density_mp_density_rs2pw_
> > ()
> > MPI: #15 0x0000000000777ba3 in
> > qs_collocate_density_mp_calculate_rho_elec_ ()
> > MPI: #16 0x00000000008fdda2 in qs_rho_methods_mp_qs_rho_update_rho_ ()
> > MPI: #17 0x00000000009647e0 in
> > qs_wf_history_methods_mp_wfi_extrapolate_ ()
> > MPI: #18 0x0000000000916d5b in qs_scf_mp_scf_env_initial_rho_setup_ ()
> > MPI: #19 0x00000000009147fc in qs_scf_mp_init_scf_run_ ()
> > MPI: #20 0x0000000000902413 in qs_scf_mp_scf_ ()
> > MPI: #21 0x000000000078b347 in qs_energy_mp_qs_energies_scf_ ()
> > MPI: #22 0x000000000078a20d in qs_energy_mp_qs_energies_ ()
> > MPI: #23 0x0000000000799e54 in qs_force_mp_qs_forces_ ()
> > MPI: #24 0x000000000049403c in
> > force_env_methods_mp_force_env_calc_energy_force_ ()
> > MPI: #25 0x00000000004ba72f in cp_eval_at_ ()
> > MPI: #26 0x0000000000ef4986 in
> > cp_lbfgs_optimizer_gopt_mp_cp_opt_gopt_step_ ()
> > MPI: #27 0x0000000000eee975 in
> > cp_lbfgs_optimizer_gopt_mp_cp_opt_gopt_next_ ()
> > MPI: #28 0x0000000000eee653 in cp_lbfgs_geo_mp_geoopt_lbfgs_ ()
> > MPI: #29 0x00000000004b3539 in geo_opt_mp_cp_geo_opt_low_ ()
> > MPI: #30 0x00000000004b376d in geo_opt_mp_cp_geo_opt_ ()
> > MPI: #31 0x00000000004b977e in cp_eval_at_ ()
> > MPI: #32 0x0000000000e23d5c in cg_utils_mp_linmin_2pnt_ ()
> > MPI: #33 0x0000000000e22e5b in
>
> ...
>
> read more »


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