[CP2K:2496] Test files -H2O

Jörg Saßmannshausen jorg.sassm... at strath.ac.uk
Thu Jan 7 01:06:20 CET 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
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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

Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html



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