[Smeagol-discuss] compiling siesta in parallel

Mon Mar 10 04:10:02 GMT 2008

>
>
>> hi, 
>
>
> in continuation to my last email i made some progress....
>
>>
>> i have  been able to compile and run this version of siesta on two 
>> machines.
>> 1. one with itanium cpu and RHEL3 using ifort9
>> 2. the other a xeon cpu with RHEL4 and ifort10
>>
>> however on the parallel compilation....i have compiled on the #2 
>> machine.
>> but the job does not run......
>> i am enclosing the out which sahopws the error.....
>> i am also enclosing the arch.make file. please suggest something....
>>
>> s.auluck
>>
>>
>>> make[1]: Leaving directory 
>>> `/home/slakxncf/update35/siesta/siesta-2.0.2-rc-9/Src'
>>> #@rm -f compinfo.F90
>>>  
>>> mpif90    -o siesta \
>>>         automatic_cell.o arw.o  atomlwf.o bands.o bessph.o cgwf.o 
>>> chkdim.o chkgmx.o chempot.o coceri.o constr.o coxmol.o cross.o 
>>> denmat.o denmatlomem.o detover.o dfscf.o dhscf.o diagon.o digcel.o 
>>> fft3d.o diagg.o diagk.o diagkp.o diag2g.o diag2k.o diagpol.o 
>>> diagsprl.o dipole.o dismin.o dnaefs.o dot.o efield.o egandd.o 
>>> ener3.o ener3lomem.o extrapol.o extrapolon.o fixed.o fsiesta.o 
>>> gradient.o gradientlomem.o grdsam.o hsparse.o idiag.o  initatom.o 
>>> initdm.o inver.o iodm.o iohs.o iolwf.o iozm.o ipack.o iopipes.o 
>>> kgrid.o kgridinit.o kinefsm.o ksv.o ksvinit.o kpoint_grid.o 
>>> find_kgrid.o linpack.o madelung.o matel.o meshmatrix.o memory.o 
>>> meshsubs.o m_check_supercell.o mulliken.o minvec.o naefs.o neighb.o 
>>> ordern.o outcell.o outcoor.o paste.o pdos.o pdosg.o pdosk.o pdoskp.o 
>>> phirphi.o pixmol.o plcharge.o propor.o pulayx.o ranger.o ran3.o 
>>> reclat.o redcel.o reinit.o reord.o rhoofd.o rhoofdsp.o rhooda.o 
>>> savepsi.o shaper.o timer.o vmb.o vmat.o vmatsp.o volcel.o xc.o 
>>> xijorb.o cellxc.o cdiag.o rdiag.o cgvc.o cgvc_zmatrix.o iocg.o 
>>> ioeig.o iofa.o iokp.o iomd.o repol.o typecell.o ofc.o poison.o 
>>> readsp.o radfft.o siesta.o io.o spin_init.o coor.o atm_transfer.o 
>>> broadcast_basis.o eggbox.o dsyevds.o zheevds.o optical.o 
>>> phirphi_opt.o reoptical.o transition_rate.o initparallel.o 
>>> show_distribution.o setspatial.o setatomnodes.o uncell.o cart2frac.o 
>>> obc.o precision.o sys.o m_cell.o recipes.o files.o spatial.o 
>>> parallel.o parallelsubs.o  parsing.o chemical.o xcmod.o atom.o 
>>> atmparams.o m_mpi_utils.o m_fdf_global.o m_history.o m_iorho.o 
>>> atmfuncs.o listsc.o memoryinfo.o m_memory.o numbvect.o sorting.o 
>>> atomlist.o atm_types.o old_atmfuncs.o radial.o m_smearing.o alloc.o 
>>> phonon.o spher_harm.o periodic_table.o version.o timestamp.o 
>>> basis_types.o xml.o pseudopotential.o basis_specs.o basis_io.o 
>>> onmod.o densematrix.o writewave.o on_subs.o fermid.o m_broyddj.o 
>>> electrostatic.o mneighb.o globalise.o siesta_cmlsubs.o siesta_cml.o 
>>> units.o zmatrix.o m_broyden_mixing.o forhar.o m_walltime.o 
>>> m_wallclock.o m_iostruct.o nlefsm.o overfsm.o conjgr.o conjgr_old.o 
>>> redata.o m_broyddj_nocomm.o broyden_optim.o ioxv.o dynamics.o 
>>> md_out.o nag.o pxf.o libfdf.a libwxml.a libxmlparser.a libmpi_f90.a\
>>>                  -L/opt/intel/cmkl/10.0.011/lib/em64t 
>>> -lmkl_scalapack_ilp64 -lmkl_scalapack -lmkl_blacs_intelmpi20_ilp64 
>>> -lmkl_lapack -lmkl_em64t -lguide -lpthread -lrt -lsvml -lmkl_core
>>> [slakxncf at master Src]$ ls -l siesta
>>> -rwxrwxr-x  1 slakxncf slakxncf 14643324 Mar  9 14:16 siesta
>>> [slakxncf at master Src]$ cd ../Examples/SiH/
>>> [slakxncf at master SiH]$ mpdtrace
>>> master
>>> [slakxncf at master SiH]$ mpirun -n 2 ../../Src/siesta < sih.fdf
>>> [cli_0]: aborting job:
>>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x5b, rank=0x11ca864) failed
>>> MPI_Comm_rank(65).: Invalid communicator
>>> [cli_1]: aborting job:
>>> Fatal error in MPI_Comm_rank: Invalid communicator, error stack:
>>> MPI_Comm_rank(107): MPI_Comm_rank(comm=0x5b, rank=0x11ca864) failed
>>> MPI_Comm_rank(65).: Invalid communicator
>>> rank 0 in job 7  master.iitk.com_48605   caused collective abort of 
>>> all ranks
>>>   exit status of rank 0: return code 1
>>> [slakxncf at master SiH]$
>>
>>
>
> -- 
> **************************************************************************** 
>
> Prof. Sushil Auluck            Phone: +91-512-6798177(Home)        
> Department of Physics                     
> +91-512-6797306/7092(Work)       
> Indian Institute of Technology      Mobile: +91-9358470794  Kanpur 
> 208016 (UP)                   e-mail: sauluck at iitk.ac.in     
> India                           e-mail: sauluck at gmail.com         
> http://www.iitk.ac.in/phy/People/phy_facvis.html
> http://www.iitk.ac.in/phy/New01/profile_SA.html
> **************************************************************************** 
>
>
>------------------------------------------------------------------------
>
>SIESTA_ARCH=intel9-cmkl8-mpi
>#
># arch.make created by Lucas Fernandez Seivane, quevedin at gmail.com
># You may need to change the name of the compiler, location of libraries...
># Modified by Alberto Garcia to suit cryst at the UPV.
>#
># Note: The -mp1 option is necessary to recover IEEE floating point precision,
>#       but it sometimes leads to bad code. Use -mp instead.
>#       In this released .make file, we not use the highest optimization.
>#
>LANG=
>#FC=mpiifort
>FC=mpif90   
>FC_ASIS=$(FC)
>#
>FFLAGS=-O1 
>FFLAGS_DEBUG= -g -O0
>RANLIB=echo 
>#MPI_INCLUDE=/opt/intel/mpi/2.0/include
>MPI_INCLUDE=/opt/mpich-1.2.6/include   
>MPI_INTERFACE=libmpi_f90.a
>DEFS_MPI=-DMPI
>#
>#LIBS=-L/opt/intel/cmkl/8.0/lib/32  -lmkl_scalapacktesting_intel80  \
>#      -lmkl_scalapack -lmkl_blacs_intelmpi20  \
>#      -lmkl_lapack -lmkl_ia32 -lguide -lpthread -lrt -lsvml
>LIBS=-L/opt/intel/cmkl/10.0.011/lib/em64t -lmkl_scalapack_ilp64  \
>      -lmkl_scalapack -lmkl_blacs_intelmpi20_ilp64  \
>      -lmkl_lapack -lmkl_em64t -lguide -lpthread -lrt -lsvml -lmkl_core
>SYS=nag
>DEFS= $(DEFS_MPI) $(DEFS_CDF)
>#
>.F.o:
>	$(FC) -c $(FFLAGS) $(INCFLAGS)  $(DEFS) $<
>.f.o:
>	$(FC) -c $(FFLAGS) $(INCFLAGS)   $<
>.F90.o:
>	$(FC) -c $(FFLAGS) $(INCFLAGS)  $(DEFS) $<
>.f90.o:
>	$(FC) -c $(FFLAGS) $(INCFLAGS)   $<
>#
>  
>

-- 
****************************************************************************
Prof. Sushil Auluck			Phone: +91-512-6798177(Home)        
Department of Physics	       	  	+91-512-6797306/7092(Work)    	
Indian Institute of Technology  	Mobile: +91-9358470794  
Kanpur 208016 (UP)          		 e-mail: sauluck at iitk.ac.in     
India			      		 e-mail: sauluck at gmail.com         
http://www.iitk.ac.in/phy/People/phy_facvis.html
http://www.iitk.ac.in/phy/New01/profile_SA.html
****************************************************************************

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