Dear All Thanks for your help. How to solve the following WARNING Siesta Version: siesta-3.0-rc2 Architecture : x86_64-unknown-linux-gnu--unknown Compiler flags: mpif90 -g -O3 PARALLEL version
* Running on 4 nodes in parallel >> Start of run: 2-MAR-2011 10:58:02 *********************** * WELCOME TO SIESTA * *********************** reinit: Reading from standard input ************************** Dump of input data file **************************** # $Id: Fe.fdf,v 1.1 1999/04/20 12:52:43 emilio Exp $ # ----------------------------------------------------------------------------- # FDF for bcc iron # # GGA, Ferromagnetic. # Scalar-relativistic pseudopotential with non-linear partial-core correction # # E. Artacho, April 1999 # ----------------------------------------------------------------------------- SystemName bcc Fe ferro GGA # Descriptive name of the system SystemLabel Fe # Short name for naming files # Output options WriteCoorStep WriteMullikenPop 1 WriteXML F # Species and atoms NumberOfSpecies 1 NumberOfAtoms 1 %block ChemicalSpeciesLabel 1 26 Fe %endblock ChemicalSpeciesLabel # Basis PAO.EnergyShift 50 meV PAO.BasisSize DZP %block PAO.Basis Fe 2 0 2 P 6. 0. 2 2 0. 0. %endblock PAO.Basis LatticeConstant 2.87 Ang %block LatticeVectors 0.50000 0.500000 0.500000 0.50000 -0.500000 0.500000 0.50000 0.500000 -0.500000 %endblock LatticeVectors KgridCutoff 15. Ang %block BandLines 1 0.00000 0.000000 0.000000 \Gamma 40 2.00000 0.000000 0.000000 H 28 1.00000 1.000000 0.000000 N 28 0.00000 0.000000 0.000000 \Gamma 34 1.00000 1.000000 1.000000 P %endblock BandLines xc.functional GGA # Exchange-correlation functional xc.authors PBE # Exchange-correlation version SpinPolarized true # Logical parameters are: yes or no MeshCutoff 150. Ry # Mesh cutoff. real space mesh # SCF options MaxSCFIterations 40 # Maximum number of SCF iter DM.MixingWeight 0.1 # New DM amount for next SCF cycle DM.Tolerance 1.d-3 # Tolerance in maximum difference # between input and output DM DM.UseSaveDM true # to use continuation files DM.NumberPulay 3 SolutionMethod diagon # OrderN or Diagon ElectronicTemperature 25 meV # Temp. for Fermi smearing # MD options MD.TypeOfRun cg # Type of dynamics: MD.NumCGsteps 0 # Number of CG steps for # coordinate optimization MD.MaxCGDispl 0.1 Ang # Maximum atomic displacement # in one CG step (Bohr) MD.MaxForceTol 0.04 eV/Ang # Tolerance in the maximum # atomic force (Ry/Bohr) # Atomic coordinates AtomicCoordinatesFormat Fractional %block AtomicCoordinatesAndAtomicSpecies 0.000000000000 0.000000000000 0.000000000000 1 %endblock AtomicCoordinatesAndAtomicSpecies ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: bcc Fe ferro GGA reinit: ----------------------------------------------------------------------- reinit: System Label: Fe reinit: ----------------------------------------------------------------------- initatom: Reading input for the pseudopotentials and atomic orbitals ---------- Species number: 1 Label: Fe Atomic number: 26 Ground state valence configuration: 4s02 3d06 Reading pseudopotential information in formatted form from Fe.psf Pseudopotential generated from a relativistic atomic calculation There are spin-orbit pseudopotentials available Spin-orbit interaction is not included in this calculation Valence configuration for pseudopotential generation: 4s( 2.00) rc: 2.00 4p( 0.00) rc: 2.00 3d( 6.00) rc: 2.00 4f( 0.00) rc: 2.00 For Fe, 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. Warning: Empty PAO shell. l = 1 Will have a KB projector anyway... <basis_specs> =============================================================================== Fe Z= 26 Mass= 55.850 Charge= 0.17977+309 Lmxo=2 Lmxkb=3 BasisType=split Semic=F L=0 Nsemic=0 Cnfigmx=4 n=1 nzeta=2 polorb=1 splnorm: 0.15000 vcte: 0.0000 rinn: 0.0000 rcs: 6.0000 0.0000 lambdas: 1.0000 1.0000 L=1 Nsemic=0 Cnfigmx=4 L=2 Nsemic=0 Cnfigmx=3 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=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 Fe (Z = 26) read_vps: Pseudopotential generation method: read_vps: ATM3 Troullier-Martins Total valence charge: 8.00000 read_vps: Pseudopotential includes a core correction: read_vps: Pseudo-core for xc-correction xc_check: Exchange-correlation functional: xc_check: GGA Perdew, Burke & Ernzerhof 1996 V l=0 = -2*Zval/r beyond r= 2.7645 V l=1 = -2*Zval/r beyond r= 2.7645 V l=2 = -2*Zval/r beyond r= 2.7645 V l=3 = -2*Zval/r beyond r= 2.7645 All V_l potentials equal beyond r= 1.9726 This should be close to max(r_c) in ps generation All pots = -2*Zval/r beyond r= 2.7645 Using large-core scheme for Vlocal atom: Estimated core radius 2.76453 atom: Maximum radius for 4*pi*r*r*local-pseudopot. charge 3.05528 atom: Maximum radius for r*vlocal+2*Zval: 2.79930 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= 2.047986 el= -0.388305 Ekb= 4.259322 kbcos= 0.262992 l= 1 rc= 2.047986 el= -0.097543 Ekb= 2.850785 kbcos= 0.194191 l= 2 rc= 2.022544 el= -0.553241 Ekb=-12.567334 kbcos= -0.683368 l= 3 rc= 2.047986 el= 0.003178 Ekb= -1.649997 kbcos= -0.006611 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 4s izeta = 1 lambda = 1.000000 rc = 6.000769 energy = -0.359899 kinetic = 0.368794 potential(screened) = -0.728693 potential(ionic) = -6.200046 WARNING: Minimum split_norm parameter: 0.52689. Will not be able to generate orbital with split_norm = 0.15000 See manual for new split options ERROR STOP from Node: 0 --- On Tue, 3/1/11, Marcos Veríssimo Alves <[email protected]> wrote: From: Marcos Veríssimo Alves <[email protected]> Subject: Re: [SIESTA-L] Parallel_version To: [email protected] Date: Tuesday, March 1, 2011, 3:50 PM Michael, I'm pretty sure this issue has already been discussed before on the list, but here goes the short version of the story. Siesta needs infiniband or myrinet (in general, a low latency internode connection) to work properly in parallel, otherwise you should try to run it in parallel only on one node with many cores, using mpi. If you have to use many nodes, Gigabit interconnection won't do the job. Even in the case of mpi on only one node with many cores, if your system is too small, parallelism will not work efficiently. No modifications in the fdf file are needed to run siesta in parallel, except for the Parallel Over Orbitals, and Parallel Over K modes. Check the manual and the list archives for that. Marcos On Tue, Mar 1, 2011 at 6:32 PM, Michael Shin <[email protected]> wrote: Hello out Huan, It works and I successfully compiled parallel SIESTA. However, When I run the example of Fe, I found the computational time increases with increasing the number of nodes. For example with 1 node it takes about 3 mints, and with 2 nodes it takes about 4 mints. But with 4 nodes, it took about 30 mints. See the attached arch,make file, and two output files. Do I have to make any special changes in FDF file when I want to run parallel calculations. Any help from any one is welcome. --- On Sat, 2/26/11, Huan Tran <[email protected]> wrote: From: Huan Tran <[email protected]> Subject: Re: [SIESTA-L] Parallel_version To: [email protected] Date: Saturday, February 26, 2011, 11:10 AM For those who need to install parallel siesta, here is something I found on the web. For me, it works. Installation of SIESTA-3.0-b(parallel version): 1. Installation of MPICH2: a) to get mpich2 http://www-unix.mcs.anl.gov/mpi/mpich/ b) installation instruction: http://hydra.nac.uci.edu/~sev/docs/mpich2-readme.txt $ tar xfz mpich2.tar.gz $ cd mpich2-1.0.1 $ ./configure # default installation directory (/urs/local/bin/) $ make $ make install ( need to be a root) $ which mpd # (print /usr/local/bin ) $ which mpiexec #(print /usr/local/bin/) $ which mpirun #(print /usr/local/bin/) $ cd #(go to home directory) $ vi .mpd.conf #(type secretword = what ever you want and save) $ chmod 600 .mpd.conf $ mpd $ $ mpdtrace (print the localhost name) $ mpdallexit $ vi hostfile (type localhost X no, X = no of core of that machine ) 2. BLAS installation: to get BLAS http://www.netlib.org/blas/blas.tgz for installation http://wiki.ifca.es/e-ciencia/index.php/BLAS or $ tar -zxvf blas.tgz $ cd BLAS $ vi make.inc (need to edit ---see below) $ make edit FORTRAN = /usr/local/bin/mpif90 LOADER = /usr/lcoal/bin/mpif90 $ make clean (for cleaning) 3. lapack installation: to get http://www.netlib.org/blas/lapack.tgz for installation go to http://wiki.ifca.es/e-ciencia/index.php/LAPACK or $ tar -zxvf lapack.tgz $ cd lapack-3.2/ $ cp make.inc.example make.inc $ vi make.inc (need to edit ...see below) $ make all edit FORTRAN = /usr/local/bin/mpif90 LOADER = /usr/local/bin/mpif90 TIMER = EXT_ETIME BLASLIB = /home/../../BLAS/blas$(PLAT).a (give the full path) for cleaning $ rm *.a #(make clean is not going to work) 4. BLACS installation: to get http://www.netlib.org/blacs/mpiblacs.tgz http://www.netlib.org/blacs/mpiblacs-patch03.tgz for installation http://wiki.ifca.es/e-ciencia/index.php/BLACS or $ tar -zxvf mpiblacs.tgz $ tar -zxvf mpiblacs-patch03.tgz $ cd BLACS/ $ cp BMAKES/Bmake.MPI-LINUX ./Bmake.inc $ vi Bmake.inci (need to edit .....see below) $ make mpi edit BTOPdir = $(HOME)/Software/BLACS # directory we're compiling BLACS at MPIdir = /usr/local/ # Open MPI directory MPILIBdir = MPIINCdir = /usr/local/include/ MPILIB = /usr/local/lib/libmpich.a SYSINC = INTFACE = -DAdd_ TRANSCOMM = -DUseMpich F77 = /usr/local/bin/mpif90 # MPI wrapper for Fortran compiler CC = /usr/local/bin/mpicc # MPI wrapper for C compiler CCFLAGS = -O3 for cleaning $ find ./* -name '*.o' | xargs rm 5. Scalapack installation: to get http://www.netlib.org/scalapack/scalapack.tgz for installation http://wiki.ifca.es/e-ciencia/index.php/ScaLAPACK or $ tar -zxvf TARs/scalapack.tgz $ cd scalapack-1.8.0/ $ cp SLmake.inc.example SLmake.inc $ vi SLmake.inc (need to edit ...see below) $ make for cleaning $ make clean $ rm libscalapack.a edit home = $(HOME)/Software/scalapack-1.8.0 BLACSdir = $(HOME)/Software/BLACS/LIB SMPLIB = /usr/local/bin/libmpich.a BLACSFINIT = $(BLACSdir)/blacsF77init_MPI-$(PLAT)-$(BLACSDBGLVL).a BLACSCINIT = $(BLACSdir)/blacsCinit_MPI-$(PLAT)-$(BLACSDBGLVL).a BLACSLIB = $(BLACSdir)/blacs_MPI-$(PLAT)-$(BLACSDBGLVL).a F77 = /usr/local/bin/mpif90 CC = /usr/local/bin/mpicc F77FLAGS = -O2 $(NOOPT) CCFLAGS = CDEFS = -DAdd_ -DNO_IEEE $(USEMPI) BLASLIB = $(HOME)/Software/BLAS/blas_LINUX.a LAPACKLIB = $(HOME)/Software/lapack-3.2/lapack_LINUX.a 6. Siesta installation: go to http://wiki.ifca.es/e-ciencia/index.php/SIESTA#Serial_version 1. $ tar -zxvf siesta-3.0-b.tgz 2. $ cd siesta-3.0-b/Obj/ 3. $ sh ../Src/obj_setup.sh 4. $ ../Src/configure 5. $ vi arch.make (need to edit this file .... see the web page...as it depends on where did you install the other libraries.... ... ) 6. $ make ( this is for siesta, for transiesta see below ) 7 $ make clean (to clean the *.o file and recompile again to compile transiesta type make transiesta instead of make) edit FC= /usr/local/bin/mpif9 FFLAGS=-g -O2 FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT BLAS_LIBS=$(HOME)/../BLAS/blas_LINUX.a LAPACK_LIBS=$(HOME)/../lapack-3.2/lapack_LINUX.a BLACS_LIBS=$(HOME)/../BLACS/LIB/blacsF77init_MPI-LINUX-0.a \ $(HOME)/../BLACS/LIB/blacs_MPI-LINUX-0.a \ $(HOME)/../BLACS/LIB/blacsCinit_MPI-LINUX-0.a SCALAPACK_LIBS=$(HOME)/../scalapack-1.8.0/libscalapack.a COMP_LIBS=dc_lapack.a MPI_INTERFACE=libmpi_f90.a MPI_INCLUDE=. 7. To run siesta from any directory $ cd yourdirectory $ ln -s ../path to siesta/Obj/siesta . ( to link the siesta ) $ mpdboot -n 1 -f hostfile $ mpiexec -n <np> ./siesta < xyz.fdf | tee xyz.out & **** make sure to kill the mpd after every run **** $ mpdallexit On Sat, Feb 26, 2011 at 9:47 AM, Michael Shin <[email protected]> wrote: Dear All Can any one guide me and send me some related steps for installation of parallel version of SIESTA-3.0-rc2. I will be grateful if some has successfully installed the parallel version of SIESTA-3.0-rc2 and can send me arch.make file. Also tell me the FORTRAN compiler name which can support parallel version of SIESTA-3.0-rc2 Regrads
