Test files -H2O

Amit Patel amita... at gmail.com
Fri Jan 8 06:17:09 CET 2010


I have the same issue. any help ??

-Amit

On Jan 7, 4:52 pm, Sandeep Kumar Reddy <kuma... at gmail.com> wrote:
> Hello,
>         i tried with this arch and it compiled successfully. But when i ran
> the test jobs, it got stopped during the SCF cycle.( It hasn't done a single
> SCF step but it is runnning without any output) .
> The arch. file that i used to compile the serial version is
>
> Make file "Linux-x86-64-intel-jnc.sopt"
>
> CC       = cc
> CPP      =
> FC       = ifort
> LD       = ifort
>
> AR       = ar -r
> DFLAGS   = -D__INTEL -D__FFTSG -D_FFTW3
> # -D__FFTACML
> # -D_FFTSG
> INTEL_INC = -I/sfs1/intel_122009/Compiler/11.1/059/mkl/include
> -I/sfs3/home/amit/compilledpackages/fftw-3.2.2/installed/include
> INTEL_LIB = /sfs1/intel_122009/Compiler/11.1/059/mkl/lib/em64t
> MKLPATH  = /sfs1/intel_122009/Compiler/11.1/059/mkl/lib/em64t
> FFTW3_LIB = /sfs3/home/amit/compilledpackages/fftw-3.2.2/installed/lib
>
> CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
> FCFLAGS  = $(DFLAGS) -I$(INTEL_INC) -O2 -xW -heap-arrays 64 -fpp -free
> FCFLAGS2 = $(DFLAGS) -I$(INTEL_INC) -O1 -xW -heap-arrays 64 -fpp -free
>
> LDFLAGS  = $(FCFLAGS)
> LIBS     =  $(MKLPATH)/libmkl_solver_lp64.a -Wl,--start-group
>  $(MKLPATH)/libmkl_intel_lp64.a $(MKLPATH)/libmkl_sequential.a
> $(MKLPATH)/libmkl_core.a -Wl,--end-group -lpthread -lguide
> $(FFTW3_LIB)/libfftw3.a
>
> Any help?
>
> Thank you,
>
> Regards,
> Sandeep kumar reddy
>
> On Thu, Jan 7, 2010 at 5:36 AM, Jörg Saßmannshausen <
>
> jorg.sassm... at strath.ac.uk> wrote:
> > Dear Sandeep
>
> > how does your arch file look like?
>
> > Reading this:
>
> >http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/cp2k/INSTALL?view=mark...
>
> > I am wondering whether you might have forgotten to swap the -D__FFTW3 with
> > the -D__FFTACML (as you are using the ACML FFT) flag.
>
> > Just a guess of course ;-)
>
> > All the best
>
> > Jörg
>
> > On Mittwoch 06 Januar 2010 Sandeep Kumar Reddy wrote:
> > > Hello sir,
> > >               When i try to compile with popt, I got these error.
>
> > > mkl_sequential.a
> > > /sfs1/intel_122009/Compiler/11.1/059/mkl/lib/em64t/libmkl_core.a
> > > -Wl,--end-group -lpthread -lguide
>
> > /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
> > (.text+0xadf): In function `fftacml3d_':
> > > : undefined reference to `zfft3dx_'
>
> > /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
> > (.text+0xb47): In function `fftacml3d_':
> > > : undefined reference to `zfft3dx_'
>
> > /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
> > (.text+0xdb0): In function `fftacml1dm_':
> > > : undefined reference to `zfft1mx_'
>
> > /sfs3/home/amit/compilledpackages/CP2K/cp2k/makefiles/../lib/Linux-x86-64-intel-jnc/sopt/libcp2k_fft_lib.a(fftacml_lib.o)
> > (.text+0xe2b): In function `fftacml1dm_':
> > > : undefined reference to `zfft1mx_'
>
> > >    I don't know what this error means. Could you help me ?
>
> > >  Regards,
> > > Sandeep kumar reddy
>
> > > On Wed, Jan 6, 2010 at 1:56 PM, Teodoro Laino
> > > <teodor... at gmail.com<mailto:teodor... at gmail.com>> wrote: Hello,
>
> > > If I would be you I would first try to check if a popt works! If it is
> > > working (with same compiler/libraries setup) then I would go for trying
> > the
> > > psmp.
>
> > > Teo
>
> > > Sandeep Kumar Reddy wrote:
> > > Hello,
>
> > >       Thank you for your quick reply. Following are the details about
> > > compilers, arch etc.
>
> > > Intel Compiler(ifort) Version : 10.1
>
> > > My Arch File : "Linux-x86-64-intel.psmp"
>
> > > # by default some intel compilers put temporaries on the stack
> > > # this might lead to segmentation faults is the stack limit is set to low
> > > # stack limits can be increased by sysadmins or e.g with ulimit -s 256000
> > > # furthermore new ifort (10.0?) compilers support the option
> > > # -heap-arrays 64
> > > # add this to the compilation flags is the other options do not work
> > > # The following settings worked for:
> > > # - AMD64 Opteron
> > > # - SUSE Linux Enterprise Server 10.0 (x86_64)
> > > # - Intel(R) Fortran Compiler for Intel(R) EM64T-based applications,
> > > Version 10.0 # - AMD acml library version 3.6.0
> > > # - MPICH2-1.0.5p4
> > > # - FFTW 3.1.2
> > > #
> > > CC       = cc
> > > CPP      =
> > > FC       = ifort -openmp -FR -O0
> > > LD       = ifort -openmp -FR -O0
> > > AR       = ar -r
> > > DFLAGS   = -D__INTEL -D__FFTSG -D__FFTW3
> > > CPPFLAGS = -C -traditional $(DFLAGS) -I$(INTEL_INC)
> > > INTEL_INC= -I/sfs1/intel_012008/mkl/10.0.011/include
> > > -I/sfs1/intel_012008/mkl/10.0.011/include/fftw INTEL_LIB=
> > > /sfs1/intel_012008/mkl/10.0.011/lib/em64t
> > > FCFLAGS  = $(DFLAGS) $(INTEL_INC) -heap-arrays 64
> > > FCFLAGS2 = $(DFLAGS) $(INTEL_INC) -heap-arrays 64
> > > LDFLAGS  = $(FCFLAGS) -i-static
> > > MKLPATH  = /sfs1/intel_012008/mkl/10.0.011/lib/em64t/
> > > LIBS     = -L$(MKLPATH) -lfftw3xf_intel $(MKLPATH)/libmkl_solver_lp64.a
> > > -Wl,--start-group $(MKLPATH)/libmkl_intel_lp64.a
> > > $(MKLPATH)/libmkl_intel_thread.a $(M KLPATH)/libmkl_core.a
> > -Wl,--end-group
> > > -openmp -lpthread
>
> > > # $(INTEL_LIB)/libmkl_scalapack_lp64.a \
>
> > > #           $(INTEL_LIB)/libmkl_core.a \
>
> > > #           $(INTEL_LIB)/libfftw3.a
>
> > > OBJECTS_ARCHITECTURE = machine_intel.o
>
> > > graphcon.o: graphcon.F
> > >      $(FC) -c $(FCFLAGS2) $<
> > > Linux-jnc.psmp (END)
>
> > > Regards,
> > > Sandeep kumar reddy
>
> > > On Wed, Jan 6, 2010 at 12:27 PM, Laino Teodoro
> > > <teodor... at gmail.com<mailto:teodor... at gmail.com>
> > > <mailto:teodor... at gmail.com<mailto:teodor... at gmail.com>>> wrote:
>
> > >    Hello Sandeep,
>
> > >    your executable is giving almost random numbers:
>
> > >        1 P_Mix/Diag. 0.40E+00    0.3     1.96524988
> >  -17.0390500821
> > > -1.70E+01 2 P_Mix/Diag. 0.40E+00    0.4     1.17914993
> > > -13.5426292836  3.50E+00 3 P_Mix/Diag. 0.40E+00    0.4     0.70748996
> > >     -9.9067192962  3.64E+00 4 P_Mix/Diag. 0.40E+00    0.4     0.42449397
> > >        -7.1955092465  2.71E+00 5 P_Mix/Diag. 0.40E+00    0.4
> > 0.25469638
> > >           -5.3903907002  1.81E+00
>
> > >    while a correct executable should give more reasonable numbers:
>
> > >        1 P_Mix/Diag. 0.40E+00    0.7     0.94986401
> >  -17.0390500821
> > > -1.70E+01 2 P_Mix/Diag. 0.40E+00    0.7     0.55704339
> > > -17.1017974052 -6.27E-02 3 P_Mix/Diag. 0.40E+00    0.8     0.33374888
> > >    -17.1395184934 -3.77E-02 4 P_Mix/Diag. 0.40E+00    0.8     0.19743634
> > >       -17.1616212665 -2.21E-02 5 P_Mix/Diag. 0.40E+00    0.9
> > 0.11691752
> > >          -17.1746976329 -1.31E-02
>
> > >    (Please check the 6th column)
>
> > >     You need to provide your arch file, compiler, version, libraries
> > >    and first of all look through all the past messages to see if
> > >    somebody experienced the same problem you have (very probably you
> > >    have a bugged compiler version or wrong libraries).
>
> > >    Teo
>
> > >    On 6 Jan 2010, at 07:47, Sandeep Kumar Reddy wrote:
>
> > >        Hello,
> > >                 Please help a new user of CP2K.  I am trying to learn
> > >        CP2K. When i try to execute H2O.inp  given in tests directory
> > >        of cp2k, the output file terminated after reading the contents
> > >        of the input file. I am using a serial executable. Following
> > >        is the input file.
>
> > >        &FORCE_EVAL
> > >         METHOD Quickstep
> > >         &DFT
> > >           &MGRID
> > >             CUTOFF 280
> > >           &END MGRID
> > >           &QS
> > >             EPS_DEFAULT 1.0E-12
> > >           &END QS
> > >           &SCF
> > >             SCF_GUESS ATOMIC
> > >             EPS_SCF 3.0E-7
> > >             MAX_SCF 50
> > >             &DIAGONALIZATION
> > >                ALGORITHM STANDARD
> > >             &END DIAGONALIZATION
> > >           &END SCF
> > >           &XC
> > >             &XC_FUNCTIONAL BLYP
> > >             &END XC_FUNCTIONAL
> > >           &END XC
> > >         &END DFT
> > >         &SUBSYS
> > >           &CELL
> > >             ABC 5.0 5.0 5.0
> > >           &END CELL
> > >           &COORD
> > >           O   0.000000    0.000000   -0.065587
> > >           H   0.000000   -0.757136    0.520545
> > >           H   0.000000    0.757136    0.520545
> > >           &END COORD
> > >           &KIND H
> > >             BASIS_SET DZVP-GTH-BLYP
> > >             POTENTIAL GTH-BLYP-q1
> > >           &END KIND
> > >           &KIND O
> > >             BASIS_SET DZVP-GTH-BLYP
> > >             POTENTIAL GTH-BLYP-q6
> > >           &END KIND
> > >         &END SUBSYS
> > >        &END FORCE_EVAL
> > >        &GLOBAL
> > >         PROJECT H2O
> > >         RUN_TYPE ENERGY_FORCE
> > >         PRINT_LEVEL MEDIUM
> > >        &END GLOBAL
>
> > >        The  output file is
> > >        ----------------------------
>
> > >         SCF PARAMETERS         Density guess:
> > >             ATOMIC
> > --------------------------------------------------------
> > > max_scf:                                                     50
> > > max_scf_history:                                              0 max_diis:
> > >                                                   4
> > > -------------------------------------------------------- eps_scf:
> > >                                     3.00E-07 eps_scf_history:
> > >                         0.00E+00 eps_diis:
> > >             1.00E-01 eps_eigval:
> > > 1.00E-05 --------------------------------------------------------
> > > level_shift [a.u.]:                                        0.00
> > > -------------------------------------------------------- Mixing method:
> > >                              DIRECT_P_MIXING
> > > -------------------------------------------------------- No outer SCF
>
> > >         PW_GRID: Information for grid number
> > >                  1 PW_GRID: Cutoff [a.u.]
> > >                         140.0 PW_GRID: spherical cutoff:
> > >                                       NO PW_GRID:   Bounds   1
> > > -27      26                       Points:          54 PW_GRID:   Bounds
> > 2
> > >            -27      26                       Points:          54 PW_GRID:
> > > Bounds   3          
>
> ...
>
> read more »



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