[CP2K:2496] Test files -H2O
Jörg Saßmannshausen
jorg.sassm... at strath.ac.uk
Thu Jan 7 00:06:20 UTC 2010
Dear Sandeep
how does your arch file look like?
Reading this:
http://cvs.berlios.de/cgi-bin/viewcvs.cgi/cp2k/cp2k/INSTALL?view=markup&content-type=text%2Fvnd.viewcvs-markup&revision=HEAD
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
Jï¿œrg
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 -27 26 Points: 54
> PW_GRID: Volume element (a.u.^3) 0.5357E-02 Volume
> (a.u.^3) 843.5418
> PW_GRID: Grid span
> FULLSPACE
>
> PW_GRID: Information for grid number
> 2 PW_GRID: Cutoff [a.u.]
> 46.7 PW_GRID: spherical cutoff:
> NO PW_GRID: Bounds 1
> -15 14 Points: 30 PW_GRID: Bounds 2
> -15 14 Points: 30 PW_GRID:
> Bounds 3 -15 14 Points: 30
> PW_GRID: Volume element (a.u.^3) 0.3124E-01 Volume
> (a.u.^3) 843.5418
> PW_GRID: Grid span
> FULLSPACE
>
> PW_GRID: Information for grid number
> 3 PW_GRID: Cutoff [a.u.]
> 15.6 PW_GRID: spherical cutoff:
> NO PW_GRID: Bounds 1
> -9 8 Points: 18 PW_GRID: Bounds 2
> -9 8 Points: 18 PW_GRID:
> Bounds 3 -9 8 Points: 18
> PW_GRID: Volume element (a.u.^3) 0.1446 Volume
> (a.u.^3) 843.5418
> PW_GRID: Grid span
> FULLSPACE
>
> PW_GRID: Information for grid number
> 4 PW_GRID: Cutoff [a.u.]
> 5.2 PW_GRID: spherical cutoff:
> NO PW_GRID: Bounds 1
> -4 4 Points: 9 PW_GRID: Bounds 2
> -4 4 Points: 9 PW_GRID:
> Bounds 3 -4 4 Points: 9
> PW_GRID: Volume element (a.u.^3) 1.157 Volume
> (a.u.^3) 843.5418
> PW_GRID: Grid span
> FULLSPACE
>
> RS_GRID: Information for grid number
> 1 RS_GRID: Bounds 1 -27 26
> Points: 54 RS_GRID: Bounds 2 -27 26
> Points: 54 RS_GRID: Bounds 3
> -27 26 Points: 54
>
> RS_GRID: Information for grid number
> 2 RS_GRID: Bounds 1 -15 14
> Points: 30 RS_GRID: Bounds 2 -15 14
> Points: 30 RS_GRID: Bounds 3
> -15 14 Points: 30
>
> RS_GRID: Information for grid number
> 3 RS_GRID: Bounds 1 -9 8
> Points: 18 RS_GRID: Bounds 2 -9 8
> Points: 18 RS_GRID: Bounds 3
> -9 8 Points: 18
>
> RS_GRID: Information for grid number
> 4 RS_GRID: Bounds 1 -4 4
> Points: 9 RS_GRID: Bounds 2 -4 4
> Points: 9 RS_GRID: Bounds 3
> -4 4 Points: 9
>
> 2D_CM| distribution_2d cost model info
> 2D_CM| molecular_distribution
> NO 2D_CM| account for symmetry
> YES 2D_CM| cost model
> BLOCK SURFACE
>
> 2D_MC| Monte Carlo annealing to optimize the distribution_2d
> 2D_MC| Number of moves
> 400000 2D_MC| Number of annealing cycles
> 10 2D_MC| Number of reduction steps per cycle
> 5 2D_MC| Reduction factor per step
> 0.8000000000 2D_MC| Termination
> tolerance 0.0200000000 2D_MC|
> Maximum temperature
> 0.5000000000 2D_MC| Swap probability
> 0.9000000000 2D_MC| Number of processor rows
> 1 2D_MC| Number of processor cols
> 1 2D_MC| Number of elements
> 3 2D_MC| What do we
> minimize SMALLEST MAXIMUM 2D_MC|
> Cost of optimal distribution
> 374 2D_MC| Cost of found distribution
> 374 2D_MC| Difference in percent
> 0
>
>
> DISTRIBUTION OF THE PARTICLES (ROWS)
>
> Process row Number of particles Number of matrix rows
>
> 0 3 -1
>
> Sum 3 -1
>
>
> DISTRIBUTION OF THE PARTICLES (COLUMNS)
>
> Process col Number of particles Number of matrix columns
>
> 0 3 -1
>
> Sum 3 -1
>
> DISTRIBUTION OF THE NEIGHBOR LISTS
>
> Total number of particle pairs: 155
> Total number of matrix elements: 9763
> Average number of particle pairs: 155
> Maximum number of particle pairs: 155
> Average number of matrix element: 9763
> Maximum number of matrix elements: 9763
>
>
> DISTRIBUTION OF THE OVERLAP MATRIX
>
> 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: 374
> Maximum number of matrix elements per CPU: 374
>
> Number of electrons:
> 8 Number of occupied orbitals:
> 4 Number of molecular orbitals:
> 4
>
> Number of orbital functions:
> 23 Number of independent orbital functions:
> 23
>
> Extrapolation method: initial_guess
>
> Atomic guess: The first density matrix is obtained in terms
> of atomic orbitals
> and electronic configurations assigned to each
> atomic kind
>
> Guess for atomic kind: O
>
> Electronic structure
> Total number of core electrons
> 2.00 Total number of valence electrons
> 6.00 Total number of electrons
> 8.00 Multiplicity
> not specified S [ 2.00] 2.00
> P 4.00
>
>
>
> ***************************************************************************
>**** Iteration Convergence Energy [au]
> ***************************************************************************
>**** 1 1.66618 -14.807077685535 2
> 2.18144 -14.856922221361 3 0.941861E-01
> -15.651433198989 4 0.311542E-02
> -15.652878316096 5 0.129713E-02
> -15.652879617314 6 0.810331E-03
> -15.652879783588 7 0.223809E-04
> -15.652879889876 8 0.143180E-06
> -15.652879889960
>
> Energy components [Hartree] Total Energy ::
> -15.652879889960 Band Energy :: -2.992123709411 Kinetic
> Energy :: 11.832933160969 Core Energy ::
> -26.139880136201 XC Energy :: -3.155492704318 Coulomb
> Energy :: 13.642492950559 Total Pseudopotential Energy ::
> -38.007855496846 Local Pseudopotential Energy ::
> -39.320898599300 Nonlocal Pseudopotential Energy ::
> 1.313043102454 Confinement :: 0.350421996757
>
> Orbital energies State L Occupation Energy[a.u.]
> Energy[eV]
>
> 1 0 2.000 -0.861204
> -23.434552 2 0 0.000 0.744977
> 20.271849
>
> 1 1 4.000 -0.317429
> -8.637681 2 1 0.000 0.561513
> 15.279549
>
>
> Guess for atomic kind: H
>
> Electronic structure
> Total number of core electrons
> 0.00 Total number of valence electrons
> 1.00 Total number of electrons
> 1.00 Multiplicity
> not specified S 1.00
>
>
>
> ***************************************************************************
>**** Iteration Convergence Energy [au]
> ***************************************************************************
>**** 1 0.316896E-02 -0.422453501026 2
> 0.328845E-03 -0.422462494147 3 0.113312E-06
> -0.422462591984
>
> Energy components [Hartree] Total Energy ::
> -0.422462591984 Band Energy :: -0.193030813655 Kinetic
> Energy :: 0.475635387250 Core Energy ::
> -0.478998252516 XC Energy :: -0.248263936733 Coulomb
> Energy :: 0.304799597265 Total Pseudopotential Energy ::
> -0.972153085242 Local Pseudopotential Energy ::
> -0.972153085242 Nonlocal Pseudopotential Energy ::
> 0.000000000000 Confinement :: 0.175194454757
>
> Orbital energies State L Occupation Energy[a.u.]
> Energy[eV]
>
> 1 0 1.000 -0.193031
> -5.252636 2 0 0.000 0.807984
> 21.986353
>
> Re-scaling the density matrix to get the right number of
> electrons
> # Electrons Trace(P)
> Scaling factor 8 8.002
> 1.000
>
>
> SCF WAVEFUNCTION OPTIMIZATION
>
> Step Update method Time Convergence Total
> energy Change
>
> ---------------------------------------------------------------------------
>---
>
> Total electronic density (r-space): -7.9999999948
> 0.0000000052 Total core charge density (r-space):
> 8.0000000000 0.0000000000 Total charge density (r-space):
> 0.0000000052 Total charge density
> (g-space): 0.0000000052 1
> P_Mix/Diag. 0.40E+00 0.3 1.96524988 -17.0390500821
> -1.70E+01
>
> Total electronic density (r-space): -4.7999999969
> 3.2000000031 Total core charge density (r-space):
> 8.0000000000 0.0000000000 Total charge density (r-space):
> 3.2000000032 Total charge density
> (g-space): 3.2000000032 2
> P_Mix/Diag. 0.40E+00 0.4 1.17914993 -13.5426292836
> 3.50E+00
>
> Total electronic density (r-space): -2.8799999981
> 5.1200000019 Total core charge density (r-space):
> 8.0000000000 0.0000000000 Total charge density (r-space):
> 5.1200000019 Total charge density
> (g-space): 5.1200000019 3
> P_Mix/Diag. 0.40E+00 0.4 0.70748996 -9.9067192962
> 3.64E+00
>
> Total electronic density (r-space): -1.7279999989
> 6.2720000011 Total core charge density (r-space):
> 8.0000000000 0.0000000000 Total charge density (r-space):
> 6.2720000011 Total charge density
> (g-space): 6.2720000011 4
> P_Mix/Diag. 0.40E+00 0.4 0.42449397 -7.1955092465
> 2.71E+00
>
> Total electronic density (r-space): -1.0367999993
> 6.9632000007 Total core charge density (r-space):
> 8.0000000000 0.0000000000 Total charge density (r-space):
> 6.9632000007 Total charge density
> (g-space): 6.9632000007 5
> P_Mix/Diag. 0.40E+00 0.4 0.25469638 -5.3903907002
> 1.81E+00
>
> Total electronic density (r-space): -0.6220799996
> 7.3779200004 Total core charge density (r-space):
> 8.0000000000 0.0000000000 Total charge density (r-space):
> 7.3779200004 Total charge density
> (g-space): 7.3779200004 Aborted
>
>
> Could anyone help me please ?
>
> Thank you,
> Regards,
> Sandeep kumar reddy
> Molecular simulations lab,
> JNCASR
>
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> --
>
> Sandeep Kumar Reddy
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit JNCASR
> Bangalore-560064
> Ph: 080 22082809
> ---------------------------------------------------------
> Sometimes our ambitions get flop,
> Sometimes our assumtions go wrong,
> But our goal is still wating for us,
> Let us be positive and be active,
> Our life is simply what our thoughts makes it,
> Why not we think good, positive
> and big and make our life
> a Grand celebration.
> Have a wonderful day.
>
>
>
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> --
>
> Sandeep Kumar Reddy
> Molecular Simulations Lab
> Chemistry and Physics of Materials Unit JNCASR
> Bangalore-560064
> Ph: 080 22082809
> ---------------------------------------------------------
> Sometimes our ambitions get flop,
> Sometimes our assumtions go wrong,
> But our goal is still wating for us,
> Let us be positive and be active,
> Our life is simply what our thoughts makes it,
> Why not we think good, positive
> and big and make our life
> a Grand celebration.
> Have a wonderful day.
--
*************************************************************
Jï¿œrg Saï¿œmannshausen
Research Fellow
University of Strathclyde
Department of Pure and Applied Chemistry
295 Cathedral St.
Glasgow
G1 1XL
email: jorg.sassm... at strath.ac.uk
web: http://sassy.formativ.net
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