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 <div class="gmail_quote">On Wed, Jan 6, 2010 at 1:56 PM, Teodoro Laino <<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>> wrote: <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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: <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> Hello,<div><div></div><div class="h5"> 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 </div></div><div><div></div><div class="h5"> On Wed, Jan 6, 2010 at 12:27 PM, Laino Teodoro <<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a> <mailto:<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>>> 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 -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> </div></div> <mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>>.<div class="im"> To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a> </div> <mailto:<a href="mailto:unsub...@googlegroups.com" target="_blank">unsub...@googlegroups.com</a>>.<div class="im"> For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a> </div> <mailto:<a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>>.<div class="im"> To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a> </div> <mailto:<a href="mailto:cp2k%252Bu...@googlegroups.com" target="_blank">cp2k%2Bun...@googlegroups.com</a>>.<div class="im"> For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. -- 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. </div> ------------------------------------------------------------------------<div class="im"> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank">cp2k+uns...@googlegroups.com</a>. For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. </div></blockquote> -- You received this message because you are subscribed to the Google Groups "cp2k" group. To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>. To unsubscribe from this group, send email to <a href="mailto:cp2k%2Bun...@googlegroups.com">cp2k+uns...@googlegroups.com</a>. For more options, visit this group at <a href="http://groups.google.com/group/cp2k?hl=en" target="_blank">http://groups.google.com/group/cp2k?hl=en</a>. </blockquote></div> -- 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.