Swati, This kind of error - multiple processes executed independently in the serial mode - is usually related to inconsistent MPI use. Make sure you use the proper mpirun: which mpirun command should show you the same directory you installed mpich in. ldd /path/to/siesta should also show you the same path for the libmpich library.
Cheers, Bartek On Sun, 2014-01-19 at 07:53 -0800, Arun Kumar wrote: > You should check whether mpif90 or sililar pachage (like openmpi) is > installed or not > > > Arun Kumar > Research Scholar > Deptt of Physics > Himachal Pradesh University > Shimla-5 > Himachal Pradesh > India > > > On Saturday, 18 January 2014, 13:18, Swati Khatta > <[email protected]> wrote: > > I add MPI_LIBS= -L/home/sprakash/mpich2-install/lib > > in LIBS line. this install siesta without any error but when I run > the test programme to see is it install successfully in parallel I > get the following error > > PSiesta Version: siesta-3.1 > Architecture : x86_64-unknown-linux-gnu--unknown > Compiler flags: /home/sprakash/mpich2-install/bin/mpif90 -g -O2 > PARALLEL version > > * Running in serial mode > >> Start of run: 18-JAN-2014 12:26:15 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > ************************** End of input data file > ***************************** > > reinit: > ----------------------------------------------------------------------- > reinit: System Name: > reinit: > ----------------------------------------------------------------------- > reinit: System Label: > siesta > reinit: > ----------------------------------------------------------------------- > > initatom: Reading input for the pseudopotentials and atomic orbitals > ---------- > No species found!!! > ERROR STOP from Node: 0 > Siesta Version: siesta-3.1 > Architecture : x86_64-unknown-linux-gnu--unknown > Compiler flags: /home/sprakash/mpich2-install/bin/mpif90 -g -O2 > PARALLEL version > > * Running in serial mode > >> Start of run: 18-JAN-2014 12:26:15 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > ************************** End of input data file > ***************************** > > reinit: > ----------------------------------------------------------------------- > reinit: System Name: > reinit: > ----------------------------------------------------------------------- > reinit: System Label: > siesta > reinit: > ----------------------------------------------------------------------- > > initatom: Reading input for the pseudopotentials and atomic orbitals > ---------- > No species found!!! > ERROR STOP from Node: 0 > Siesta Version: siesta-3.1 > Architecture : x86_64-unknown-linux-gnu--unknown > Compiler flags: /home/sprakash/mpich2-install/bin/mpif90 -g -O2 > PARALLEL version > > * Running in serial mode > >> Start of run: 18-JAN-2014 12:26:15 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > ************************** End of input data file > ***************************** > > reinit: > ----------------------------------------------------------------------- > reinit: System Name: > reinit: > ----------------------------------------------------------------------- > reinit: System Label: > siesta > reinit: > ----------------------------------------------------------------------- > > initatom: Reading input for the pseudopotentials and atomic orbitals > ---------- > No species found!!! > ERROR STOP from Node: 0 > Siesta Version: siesta-3.1 > Architecture : x86_64-unknown-linux-gnu--unknown > Compiler flags: /home/sprakash/mpich2-install/bin/mpif90 -g -O2 > PARALLEL version > > * Running in serial mode > >> Start of run: 18-JAN-2014 12:26:15 > > *********************** > * WELCOME TO SIESTA * > *********************** > > reinit: Reading from standard input > ************************** Dump of input data file > **************************** > SystemName Water molecule > SystemLabel h2o > NumberOfAtoms 3 > NumberOfSpecies 2 > %block ChemicalSpeciesLabel > 1 8 O # Species index, atomic number, species label > 2 1 H > %endblock ChemicalSpeciesLabel > AtomicCoordinatesFormat Ang > %block AtomicCoordinatesAndAtomicSpecies > 0.000 0.000 0.000 1 > 0.757 0.586 0.000 2 > -0.757 0.586 0.000 2 > %endblock AtomicCoordinatesAndAtomicSpecies > ************************** End of input data file > ***************************** > > reinit: > ----------------------------------------------------------------------- > reinit: System Name: Water molecule > reinit: > ----------------------------------------------------------------------- > reinit: System Label: > h2o > reinit: > ----------------------------------------------------------------------- > > initatom: Reading input for the pseudopotentials and atomic orbitals > ---------- > Species number: 1 Label: O Atomic number: 8 > Species number: 2 Label: H Atomic number: 1 > Ground state valence configuration: 2s02 2p04 > Reading pseudopotential information in formatted form from O.psf > > Valence configuration for pseudopotential generation: > 2s( 2.00) rc: 1.14 > 2p( 4.00) rc: 1.14 > 3d( 0.00) rc: 1.14 > 4f( 0.00) rc: 1.14 > Ground state valence configuration: 1s01 > Reading pseudopotential information in formatted form from H.psf > > Valence configuration for pseudopotential generation: > 1s( 1.00) rc: 1.25 > 2p( 0.00) rc: 1.25 > 3d( 0.00) rc: 1.25 > 4f( 0.00) rc: 1.25 > For O, standard SIESTA heuristics set lmxkb to 3 > (one more than the basis l, including polarization orbitals). > Use PS.lmax or PS.KBprojectors blocks to override. > For H, standard SIESTA heuristics set lmxkb to 2 > (one more than the basis l, including polarization orbitals). > Use PS.lmax or PS.KBprojectors blocks to override. > > <basis_specs> > =============================================================================== > O Z= 8 Mass= 16.000 Charge= 0.17977 > +309 > Lmxo=1 Lmxkb= 3 BasisType=split Semic=F > L=0 Nsemic=0 Cnfigmx=2 > n=1 nzeta=2 polorb=0 > splnorm: 0.15000 > vcte: 0.0000 > rinn: 0.0000 > rcs: 0.0000 0.0000 > lambdas: 1.0000 1.0000 > L=1 Nsemic=0 Cnfigmx=2 > n=1 nzeta=2 polorb=1 > splnorm: 0.15000 > vcte: 0.0000 > rinn: 0.0000 > rcs: 0.0000 0.0000 > lambdas: 1.0000 1.0000 > ------------------------------------------------------------------------------- > L=0 Nkbl=1 erefs: 0.17977+309 > L=1 Nkbl=1 erefs: 0.17977+309 > L=2 Nkbl=1 erefs: 0.17977+309 > L=3 Nkbl=1 erefs: 0.17977+309 > =============================================================================== > </basis_specs> > > atom: Called for O (Z = 8) > > read_vps: Pseudopotential generation method: > read_vps: ATM3 Troullier-Martins > Total valence charge: 6.00000 > > xc_check: Exchange-correlation functional: > xc_check: Ceperley-Alder > V l=0 = -2*Zval/r beyond r= 1.1278 > V l=1 = -2*Zval/r beyond r= 1.1278 > V l=2 = -2*Zval/r beyond r= 1.1278 > V l=3 = -2*Zval/r beyond r= 1.1138 > All V_l potentials equal beyond r= 1.1278 > This should be close to max(r_c) in ps generation > All pots = -2*Zval/r beyond r= 1.1278 > > VLOCAL1: 99.0% of the norm of Vloc inside 34.126 Ry > VLOCAL1: 99.9% of the norm of Vloc inside 77.774 Ry > atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.37759 > atom: Maximum radius for r*vlocal+2*Zval: 1.18566 > GHOST: No ghost state for L = 0 > GHOST: No ghost state for L = 1 > GHOST: No ghost state for L = 2 > GHOST: No ghost state for L = 3 > > KBgen: Kleinman-Bylander projectors: > l= 0 rc= 1.294105 el= -1.742414 Ekb= 9.135903 kbcos= > 0.326910 > l= 1 rc= 1.294105 el= -0.676589 Ekb= -8.124878 kbcos= > -0.395047 > l= 2 rc= 1.448233 el= 0.002386 Ekb= -2.039267 kbcos= > -0.003484 > l= 3 rc= 1.561052 el= 0.003508 Ekb= -0.799141 kbcos= > -0.000344 > > KBgen: Total number of Kleinman-Bylander projectors: 16 > atom: > ------------------------------------------------------------------------- > > atom: SANKEY-TYPE ORBITALS: > atom: Selected multiple-zeta basis: split > > SPLIT: Orbitals with angular momentum L= 0 > > SPLIT: Basis orbitals for state 2s > > SPLIT: PAO cut-off radius determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 3.305093 > energy = -1.723766 > kinetic = 1.614911 > potential(screened) = -3.338677 > potential(ionic) = -11.304675 > > izeta = 2 > rmatch = 2.510382 > splitnorm = 0.150000 > energy = -1.471299 > kinetic = 2.446434 > potential(screened) = -3.917732 > potential(ionic) = -12.476133 > > SPLIT: Orbitals with angular momentum L= 1 > > SPLIT: Basis orbitals for state 2p > > SPLIT: PAO cut-off radius determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 3.937239 > energy = -0.658841 > kinetic = 5.005986 > potential(screened) = -5.664827 > potential(ionic) = -13.452360 > > izeta = 2 > rmatch = 2.541963 > splitnorm = 0.150000 > energy = -0.367441 > kinetic = 7.530509 > potential(screened) = -7.897949 > potential(ionic) = -16.611953 > > POLgen: Perturbative polarization orbital with L= 2 > > POLgen: Polarization orbital for state 2p > > izeta = 1 > rc = 3.937239 > energy = 2.398520 > kinetic = 4.716729 > potential(screened) = -2.318209 > potential(ionic) = -8.603170 > atom: Total number of Sankey-type orbitals: 13 > > atm_pop: Valence configuration (for local Pseudopot. screening): > 2s( 2.00) > 2p( 4.00) > Vna: chval, zval: 6.00000 6.00000 > > Vna: Cut-off radius for the neutral-atom potential: 3.937239 > > atom: > _________________________________________________________________________ > > <basis_specs> > =============================================================================== > H Z= 1 Mass= 1.0100 Charge= 0.17977 > +309 > Lmxo=0 Lmxkb= 2 BasisType=split Semic=F > L=0 Nsemic=0 Cnfigmx=1 > n=1 nzeta=2 polorb=1 > splnorm: 0.15000 > vcte: 0.0000 > rinn: 0.0000 > rcs: 0.0000 0.0000 > lambdas: 1.0000 1.0000 > ------------------------------------------------------------------------------- > L=0 Nkbl=1 erefs: 0.17977+309 > L=1 Nkbl=1 erefs: 0.17977+309 > L=2 Nkbl=1 erefs: 0.17977+309 > =============================================================================== > </basis_specs> > > atom: Called for H (Z = 1) > > read_vps: Pseudopotential generation method: > read_vps: ATM3 Troullier-Martins > Total valence charge: 1.00000 > > xc_check: Exchange-correlation functional: > xc_check: Ceperley-Alder > V l=0 = -2*Zval/r beyond r= 1.2343 > V l=1 = -2*Zval/r beyond r= 1.2189 > V l=2 = -2*Zval/r beyond r= 1.2189 > All V_l potentials equal beyond r= 1.2343 > This should be close to max(r_c) in ps generation > All pots = -2*Zval/r beyond r= 1.2343 > > VLOCAL1: 99.0% of the norm of Vloc inside 28.493 Ry > VLOCAL1: 99.9% of the norm of Vloc inside 64.935 Ry > atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 1.45251 > atom: Maximum radius for r*vlocal+2*Zval: 1.21892 > GHOST: No ghost state for L = 0 > GHOST: No ghost state for L = 1 > GHOST: No ghost state for L = 2 > > KBgen: Kleinman-Bylander projectors: > l= 0 rc= 1.364359 el= -0.467325 Ekb= -2.005361 kbcos= > -0.336422 > l= 1 rc= 1.434438 el= 0.001430 Ekb= -0.501708 kbcos= > -0.021697 > l= 2 rc= 1.470814 el= 0.002365 Ekb= -0.190555 kbcos= > -0.002281 > > KBgen: Total number of Kleinman-Bylander projectors: 9 > atom: > ------------------------------------------------------------------------- > > atom: SANKEY-TYPE ORBITALS: > atom: Selected multiple-zeta basis: split > > SPLIT: Orbitals with angular momentum L= 0 > > SPLIT: Basis orbitals for state 1s > > SPLIT: PAO cut-off radius determined from an > SPLIT: energy shift= 0.020000 Ry > > izeta = 1 > lambda = 1.000000 > rc = 4.828263 > energy = -0.449375 > kinetic = 0.929372 > potential(screened) = -1.378747 > potential(ionic) = -1.915047 > > izeta = 2 > rmatch = 3.854947 > splitnorm = 0.150000 > energy = -0.336153 > kinetic = 1.505294 > potential(screened) = -1.841447 > potential(ionic) = -2.413582 > > POLgen: Perturbative polarization orbital with L= 1 > > POLgen: Polarization orbital for state 1s > > izeta = 1 > rc = 4.828263 > energy = 0.706972 > kinetic = 1.396397 > potential(screened) = -0.689424 > potential(ionic) = -1.169792 > atom: Total number of Sankey-type orbitals: 5 > > atm_pop: Valence configuration (for local Pseudopot. screening): > 1s( 1.00) > Vna: chval, zval: 1.00000 1.00000 > > Vna: Cut-off radius for the neutral-atom potential: 4.828263 > > atom: > _________________________________________________________________________ > > prinput: Basis input > ---------------------------------------------------------- > > PAO.BasisType split > > %block ChemicalSpeciesLabel > 1 8 O # Species index, atomic number, > species label > 2 1 H # Species index, atomic number, > species label > %endblock ChemicalSpeciesLabel > > %block PAO.Basis # Define Basis set > O 2 # Species label, number of > l-shells > n=2 0 2 # n, l, Nzeta > 3.305 2.510 > 1.000 1.000 > n=2 1 2 P 1 # n, l, Nzeta, Polarization, > NzetaPol > 3.937 2.542 > 1.000 1.000 > H 1 # Species label, number of > l-shells > n=1 0 2 P 1 # n, l, Nzeta, Polarization, > NzetaPol > 4.828 3.855 > 1.000 1.000 > %endblock PAO.Basis > > prinput: > ---------------------------------------------------------------------- > > coor: Atomic-coordinates input format = Cartesian coordinates > coor: (in Angstroms) > > siesta: Atomic coordinates (Bohr) and species > siesta: 0.00000 0.00000 0.00000 1 1 > siesta: 1.43052 1.10738 0.00000 2 2 > siesta: -1.43052 1.10738 0.00000 2 3 > > siesta: Automatic unit cell vectors (Ang): > siesta: 7.286412 0.000000 0.000000 > siesta: 0.000000 5.746952 0.000000 > siesta: 0.000000 0.000000 5.621012 > > siesta: System type = molecule > > initatomlists: Number of atoms, orbitals, and projectors: 3 23 > 34 > > siesta: ******************** Simulation parameters > **************************** > siesta: > siesta: The following are some of the parameters of the simulation. > siesta: A complete list of the parameters used, including default > values, > siesta: can be found in file out.fdf > siesta: > redata: Non-Collinear-spin run = F > redata: SpinPolarized (Up/Down) run = F > redata: Number of spin components = 1 > redata: Long output = F > redata: Number of Atomic Species = 2 > redata: Charge density info will appear in .RHO file > redata: Write Mulliken Pop. = NO > redata: Mesh Cutoff = 100.0000 Ry > redata: Net charge of the system = 0.0000 |e| > redata: Max. number of SCF Iter = 50 > redata: Mixing is linear > redata: Mix DM in first SCF step ? = F > redata: Write Pulay info on disk? = F > redata: Discard 1st Pulay DM after kick = F > redata: New DM Mixing Weight = 0.2500 > redata: New DM Occupancy tolerance = 0.000000000001 > redata: No kicks to SCF > redata: DM Mixing Weight for Kicks = 0.5000 > redata: DM Tolerance for SCF = 0.000100 > redata: Require Energy convergence for SCF = F > redata: DM Energy tolerance for SCF = 0.000100 eV > redata: Require Harris convergence for SCF = F > redata: DM Harris energy tolerance for SCF = 0.000100 eV > redata: Using Saved Data (generic) = F > redata: Use continuation files for DM = F > redata: Neglect nonoverlap interactions = F > redata: Method of Calculation = Diagonalization > redata: Divide and Conquer = T > redata: Electronic Temperature = 0.0019 Ry > redata: Fix the spin of the system = F > redata: Dynamics option = Verlet MD run > redata: Initial MD time step = 1 > redata: Final MD time step = 1 > redata: Length of MD time step = 1.0000 fs > redata: Initial Temperature of MD run = 0.0000 K > redata: Perform a MD quench = F > redata: > *********************************************************************** > Total number of electrons: 8.000000 > Total ionic charge: 8.000000 > Kpoints in: 1 . Kpoints trimmed: 1 > > siesta: k-grid: Number of k-points = 1 > siesta: k-grid: Cutoff (effective) = 2.811 Ang > siesta: k-grid: Supercell and displacements > siesta: k-grid: 1 0 0 0.000 > siesta: k-grid: 0 1 0 0.000 > siesta: k-grid: 0 0 1 0.000 > > * Maximum dynamic memory allocated = 2 MB > > siesta: ============================== > Begin MD step = 1 > ============================== > > outcell: Unit cell vectors (Ang): > 7.286412 0.000000 0.000000 > 0.000000 5.746952 0.000000 > 0.000000 0.000000 5.621012 > > outcell: Cell vector modules (Ang) : 7.286412 5.746952 > 5.621012 > outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 > 90.0000 > outcell: Cell volume (Ang**3) : 235.3780 > New_DM. Step: 1 > Initializing Density Matrix... > > InitMesh: MESH = 48 x 36 x 36 = 62208 > InitMesh: Mesh cutoff (required, used) = 100.000 108.450 Ry > > * Maximum dynamic memory allocated = 5 MB > > stepf: Fermi-Dirac step function > > siesta: Program's energy decomposition (eV): > siesta: Ebs = -124.137313 > siesta: Eions = 815.854478 > siesta: Ena = 175.154321 > siesta: Ekin = 341.667405 > siesta: Enl = -52.736757 > siesta: DEna = -0.000002 > siesta: DUscf = 0.000000 > siesta: DUext = 0.000000 > siesta: Exc = -109.897180 > siesta: eta*DQ = 0.000000 > siesta: Emadel = 0.000000 > siesta: Emeta = 0.000000 > siesta: Emolmec = 0.000000 > siesta: Ekinion = 0.000000 > siesta: Eharris = -466.544769 > siesta: Etot = -461.666691 > siesta: FreeEng = -461.666691 > > siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) > siesta: 1 -466.5448 -461.6667 -461.6667 1.4337 -4.4227 > timer: Routine,Calls,Time,% = IterSCF 1 1.366 63.42 > elaps: Routine,Calls,Wall,% = IterSCF 1 1.367 62.59 > siesta: 2 -467.2759 -465.0105 -465.0105 0.2142 0.2483 > siesta: 3 -465.9404 -465.3142 -465.3142 0.0606 -1.4657 > siesta: 4 -465.8369 -465.4507 -465.4507 0.0240 -1.9332 > siesta: 5 -465.8277 -465.5455 -465.5455 0.0123 -2.0651 > siesta: 6 -465.8268 -465.6159 -465.6159 0.0073 -2.1009 > siesta: 7 -465.8266 -465.6686 -465.6686 0.0049 -2.1094 > siesta: 8 -465.8266 -465.7081 -465.7081 0.0034 -2.1104 > siesta: 9 -465.8266 -465.7377 -465.7377 0.0024 -2.1098 > siesta: 10 -465.8266 -465.7599 -465.7599 0.0017 -2.1090 > siesta: 11 -465.8266 -465.7766 -465.7766 0.0013 -2.1083 > siesta: 12 -465.8266 -465.7891 -465.7891 0.0009 -2.1079 > siesta: 13 -465.8266 -465.7985 -465.7985 0.0007 -2.1076 > siesta: 14 -465.8266 -465.8055 -465.8055 0.0005 -2.1074 > siesta: 15 -465.8266 -465.8108 -465.8108 0.0004 -2.1073 > siesta: 16 -465.8266 -465.8147 -465.8147 0.0003 -2.1072 > siesta: 17 -465.8266 -465.8177 -465.8177 0.0002 -2.1071 > siesta: 18 -465.8266 -465.8199 -465.8199 0.0002 -2.1071 > siesta: 19 -465.8266 -465.8216 -465.8216 0.0001 -2.1070 > siesta: 20 -465.8266 -465.8228 -465.8228 0.0001 -2.1070 > > siesta: E_KS(eV) = -465.8238 > > siesta: E_KS - E_eggbox = -465.8238 > > siesta: Atomic forces (eV/Ang): > ---------------------------------------- > Tot 0.000002 -0.055942 0.000000 > ---------------------------------------- > Max 0.760263 > Res 0.448208 sqrt( Sum f_i^2 / 3N ) > ---------------------------------------- > Max 0.760263 constrained > > Stress-tensor-Voigt (kbar): -7.22 -3.17 -1.00 > 0.00 0.00 0.00 > (Free)E + p*V (eV/cell) -465.2660 > Target enthalpy (eV/cell) -465.8238 > > siesta: Stress tensor (static) (eV/Ang**3): > -0.004508 0.000000 0.000000 > 0.000000 -0.001978 0.000000 > 0.000000 0.000000 -0.000623 > > siesta: Pressure (static): 3.79671742 kBar > > siesta: Stress tensor (total) (eV/Ang**3): > -0.004508 0.000000 0.000000 > 0.000000 -0.001978 0.000000 > 0.000000 0.000000 -0.000623 > > siesta: Pressure (total): 3.79671742 kBar > > siesta: Temp_ion = 0.000 K > > * Maximum dynamic memory allocated = 5 MB > > siesta: Program's energy decomposition (eV): > siesta: Ebs = -104.303586 > siesta: Eions = 815.854478 > siesta: Ena = 175.154321 > siesta: Ekin = 353.764171 > siesta: Enl = -63.087297 > siesta: DEna = -3.350829 > siesta: DUscf = 0.755638 > siesta: DUext = 0.000000 > siesta: Exc = -113.205320 > siesta: eta*DQ = 0.000000 > siesta: Emadel = 0.000000 > siesta: Emeta = 0.000000 > siesta: Emolmec = 0.000000 > siesta: Ekinion = 0.000000 > siesta: Eharris = -465.826592 > siesta: Etot = -465.823794 > siesta: FreeEng = -465.823794 > > siesta: Final energy (eV): > siesta: Band Struct. = -104.303586 > siesta: Kinetic = 353.764171 > siesta: Hartree = 385.167523 > siesta: Ext. field = 0.000000 > siesta: Exch.-corr. = -113.205320 > siesta: Ion-electron = -1080.072468 > siesta: Ion-ion = -11.477701 > siesta: Ekinion = 0.000000 > siesta: Total = -465.823794 > > siesta: Atomic forces (eV/Ang): > siesta: 1 0.000002 -0.760263 0.000000 > siesta: 2 0.700707 0.352161 0.000000 > siesta: 3 -0.700707 0.352160 0.000000 > siesta: ---------------------------------------- > siesta: Tot 0.000002 -0.055942 0.000000 > > siesta: Stress tensor (static) (eV/Ang**3): > siesta: -0.004508 0.000000 0.000000 > siesta: 0.000000 -0.001978 0.000000 > siesta: 0.000000 0.000000 -0.000623 > > siesta: Cell volume = 235.378012 Ang**3 > > siesta: Pressure (static): > siesta: Solid Molecule Units > siesta: 0.00002581 0.00000274 Ry/Bohr**3 > siesta: 0.00236970 0.00025189 eV/Ang**3 > siesta: 3.79671742 0.40357634 kBar > (Free)E+ p_basis*V_orbitals = -465.238627 > (Free)Eharris+ p_basis*V_orbitals = -465.242381 > > siesta: Electric dipole (a.u.) = 0.000000 0.557772 0.000000 > siesta: Electric dipole (Debye) = 0.000000 1.417716 0.000000 > > * Maximum dynamic memory allocated : Node 0 = 5 MB > > * Maximum memory occured during poison > > timer: CPU execution times: > timer: Routine Calls Time/call Tot.time % > timer: siesta 1 3.613 3.613 100.00 > timer: Setup 1 0.340 0.340 9.41 > timer: bands 1 0.000 0.000 0.00 > timer: writewave 1 0.000 0.000 0.00 > timer: KSV_init 1 0.001 0.001 0.03 > timer: IterMD 1 3.267 3.267 90.40 > timer: hsparse 1 0.001 0.001 0.03 > timer: overlap 1 0.445 0.445 12.31 > timer: IterSCF 20 0.131 2.629 72.74 > timer: kinefsm 2 0.165 0.331 9.16 > timer: nlefsm 2 0.452 0.904 25.01 > timer: DHSCF 21 0.074 1.550 42.89 > timer: DHSCF1 1 0.016 0.016 0.44 > timer: DHSCF2 1 0.068 0.068 1.88 > timer: REORD 170 0.000 0.074 2.05 > timer: POISON 22 0.011 0.239 6.61 > timer: DHSCF3 21 0.064 1.347 37.27 > timer: rhoofd 21 0.021 0.432 11.95 > timer: cellXC 21 0.015 0.314 8.69 > timer: vmat 21 0.011 0.224 6.20 > timer: MolMec 2 0.000 0.000 0.00 > timer: diagon 20 0.001 0.010 0.28 > timer: r-eigvec 20 0.001 0.010 0.28 > timer: r-buildHS 20 0.000 0.001 0.03 > timer: rdiag 20 0.000 0.009 0.25 > timer: rdiag1 20 0.000 0.000 0.00 > timer: rdiag2 20 0.000 0.000 0.00 > timer: rdiag3 20 0.000 0.007 0.19 > timer: rdiag4 20 0.000 0.000 0.00 > timer: r-buildD 20 0.000 0.000 0.00 > timer: DHSCF4 1 0.115 0.115 3.18 > timer: dfscf 1 0.102 0.102 2.82 > timer: overfsm 1 0.001 0.001 0.03 > timer: optical 1 0.000 0.000 0.00 > > > elaps: ELAPSED times: > elaps: Routine Calls Time/call Tot.time % > elaps: siesta 1 3.968 3.968 100.00 > elaps: Setup 1 0.368 0.368 9.27 > elaps: bands 1 0.001 0.001 0.03 > elaps: writewave 1 0.000 0.000 0.00 > elaps: KSV_init 1 0.000 0.000 0.00 > elaps: IterMD 1 3.591 3.591 90.50 > elaps: hsparse 1 0.000 0.000 0.00 > elaps: overlap 1 0.446 0.446 11.24 > elaps: IterSCF 20 0.147 2.945 74.22 > elaps: kinefsm 2 0.167 0.333 8.39 > elaps: nlefsm 2 0.452 0.903 22.76 > elaps: DHSCF 21 0.074 1.550 39.06 > elaps: DHSCF1 1 0.015 0.015 0.38 > elaps: DHSCF2 1 0.068 0.068 1.71 > elaps: REORD 170 0.000 0.066 1.66 > elaps: POISON 22 0.011 0.239 6.02 > elaps: DHSCF3 21 0.064 1.345 33.90 > elaps: rhoofd 21 0.021 0.431 10.86 > elaps: cellXC 21 0.015 0.315 7.94 > elaps: vmat 21 0.011 0.224 5.65 > elaps: MolMec 2 0.000 0.000 0.00 > elaps: diagon 20 0.001 0.013 0.33 > elaps: r-eigvec 20 0.001 0.012 0.30 > elaps: r-buildHS 20 0.000 0.001 0.03 > elaps: rdiag 20 0.001 0.011 0.28 > elaps: rdiag1 20 0.000 0.001 0.03 > elaps: rdiag2 20 0.000 0.001 0.03 > elaps: rdiag3 20 0.000 0.009 0.23 > elaps: rdiag4 20 0.000 0.000 0.00 > elaps: r-buildD 20 0.000 0.000 0.00 > elaps: DHSCF4 1 0.115 0.115 2.90 > elaps: dfscf 1 0.102 0.102 2.57 > elaps: overfsm 1 0.000 0.000 0.00 > elaps: optical 1 0.000 0.000 0.00 > > >> End of run: 18-JAN-2014 12:26:19 > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 6 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =================================================================================== > YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6) > This typically refers to a problem with your application. > Please see the FAQ page for debugging suggestions > > > > On Fri, Jan 17, 2014 at 5:36 PM, Nick Papior Andersen > <[email protected]> wrote: > What? > > That was not what I told you. :) > > > Try: > LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) > $(BLAS_LIBS) $(NETCDF_LIBS) > -L/home/sprakash/mpich2-install/lib > > > Please, it's not plz... :) > > > / Nick > > > 2014/1/17 Swati Khatta <[email protected]> > I add MPI_LIBS= -L/home/sprakash/mpich2-install/lib > > in LIBS line. > > I do many changes in my arch.make file but get the > same error > > /usr/bin/ld: cannot find -lmpichf90 > collect2: ld returned 1 exit status > make: *** [siesta] Error 1 > > plz help me out > > > > On Fri, Jan 17, 2014 at 3:18 PM, Nick Papior Andersen > <[email protected]> wrote: > Add -L/home/sprakash/mpich2-install/lib > > to your LIBS line. > I would suggest you read about how linking > programs work. Consider reading this: > > http://www3.ntu.edu.sg/home/ehchua/programming/cpp/gcc_make.html > Even though it describes C-code linking it is > basically the same for fortran (consider *.h > files as *.mod files). > > > / Nick > > > 2014/1/17 Swati Khatta > <[email protected]> > thanks for your help I make that line > a coment line but now I get error > > /usr/bin/ld: cannot find -lmpichf90 > collect2: ld returned 1 exit status > make: *** [siesta] Error 1 > > > > > On Fri, Jan 17, 2014 at 12:56 PM, Nick > Papior Andersen <[email protected]> > wrote: > A couple of things... > > 1) Didn't you just acknowledge > that you completed the 2.0.2 > scalapack installation > successfully? In that case I > would recommend you to use > that library. (However, there > can be other reasons you wish > to use the "old" library, in > that case disregard this > point). Remember if you use > 2.0.2 to remove the BLACS_LIBS > line, it is not necessary. > 2) The COMP_LIBS is only > required if you lack the > LAPACK/BLAS libraries, which > you don't. So you should > simply out-comment that line > and try to recompile. > 3) NetLIB lapack has been > updated to 3.5.0, it does not > affect any calculations in > regards of siesta, the > bugfixes are to my knowledge > in other routines. > > > Kind regards Nick > > > > > 2014/1/17 Swati Khatta > <[email protected]> > Dear siesta users > > > I am trying to install > siesta in parallel but > after editing my > arch.make file as > given below when I try > to make it it will > shown me the error > Compilation > architecture to be > used: > > x86_64-unknown-linux-gnu--unknown > If this is not what > you want, create the > right > arch.make file using > the models in Src/Sys > > Hit ^C to abort... > > ==> Incorporating > information about > present compilation > (compiler and flags) > make[1]: Entering > directory > > `/home/sprakash/siesta-3.1/Obj' > > /home/sprakash/mpich2-install/bin/mpif90 -c -g -O2 `FoX/FoX-config > --fcflags` -DFC_HAVE_FLUSH -DFC_HAVE_ABORT compinfo.F90 > make[1]: Leaving > directory > > `/home/sprakash/siesta-3.1/Obj' > #@rm -f compinfo.F90 > > make: *** No rule to > make target > `Libs/lapack.f', > needed by > `liblapack.a'. Stop. > > > ############################################################################ > > # arch .make file > .SUFFIXES: > .SUFFIXES: .f .F .o .a .f90 > .F90 > > > SIESTA_ARCH=x86_64-unknown-linux-gnu--unknown > > FPP= > FPP_OUTPUT= > > FC=/home/sprakash/mpich2-install/bin/mpif90 > RANLIB=ranlib > > SYS=nag > > SP_KIND=4 > DP_KIND=8 > KINDS=$(SP_KIND) > $(DP_KIND) > > FFLAGS=-g -O2 > FPPFLAGS= > -DFC_HAVE_FLUSH > -DFC_HAVE_ABORT > LDFLAGS= > ARFLAGS_EXTRA= > > FCFLAGS_fixed_f= > FCFLAGS_free_f90= > FPPFLAGS_fixed_F= > FPPFLAGS_free_F90= > > > BLAS_LIBS=/home/sprakash/libraries/BLAS/blas_LINUX.a > > LAPACK_LIBS=/home/sprakash/libraries/lapack-3.4.2/liblapack.a > > BLACS_LIBS=/home/sprakash/libraries/BLACS/LIB/blacsF77init_MPI-LINUX-0.a \ > > /home/sprakash/libraries/BLACS/LIB/blacsCinit_MPI-LINUX-0.a \ > > /home/sprakash/libraries/BLACS/LIB/blacs_MPI-LINUX-0.a > > SCALAPACK_LIBS=/home/sprakash/libraries/scalapack-1.8.0/libscalapack.a > > COMP_LIBS= blapack.a > libblas.a dc_lapack.a > > NETCDF_LIBS= > NETCDF_INTERFACE= > > LIBS=$(SCALAPACK_LIBS) > $(BLACS_LIBS) > $(LAPACK_LIBS) > $(BLAS_LIBS) > $(NETCDF_LIBS) > #SIESTA needs an F90 > interface to MPI > #This will give you > SIESTA's own > implementation > #If your compiler > vendor offers an > alternative, you may > change > #to it here. > MPI_INTERFACE=libmpi_f90.a > > MPI_INCLUDE=./home/sprakash/mpich2-install/include > > MPI_LIBS=/home/sprakash/mpich2-install/lib > > #Dependency rules are > created by autoconf > according to whether > #discrete > preprocessing is > necessary or not. > .F.o: > $(FC) -c > $(FFLAGS) $(INCFLAGS) > $(FPPFLAGS) > $(FPPFLAGS_fixed_F) > $< > .F90.o: > $(FC) -c > $(FFLAGS) $(INCFLAGS) > $(FPPFLAGS) > $(FPPFLAGS_free_F90) > $< > .f.o: > $(FC) -c > $(FFLAGS) $(INCFLAGS) > $(FCFLAGS_fixed_f) $< > .f90.o: > $(FC) -c > $(FFLAGS) $(INCFLAGS) > $(FCFLAGS_free_f90) > $< > > > > > > > > > -- > Kind regards Nick > > > > > > > -- > Kind regards Nick > > > > > > > -- > Kind regards Nick > > > > >
