[CP2K:2495] Test files -H2O
Sandeep Kumar Reddy
kuma... at gmail.com
Wed Jan 6 15:29:23 UTC 2010
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>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>> 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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>
>
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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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