[Smeagol-discuss] fw:parallel compilation problem

[Ivan Rungger]

Hello Sagar,

   the leads calculation in smeagol can only be done on 1 processor. Try
running the leads calculation with 1 processor, and then the smeagol
transport calculation in the /examples/gamma directory with more processors.

However from your output is seems that the code is crashing rather at
the beginning of the calculation, in which case it would be a siesta
problem. Try to compile the bare siesta code (without the smeagol
patch), and see if that runs for the siesta examples.

Cheers,

 Ivan

ambavale sagar wrote:
> Hi,
> I tried many ways. But can not make it run in parallel. Can you please
> look at the problem and my arch.make file.. I am sorry to post the
> same mail again.
>
> Sagar
>
> --- On *Wed, 7/1/09, ambavale sagar /<sagarambavale at yahoo.co.in>/* wrote:
>
>     From: ambavale sagar <sagarambavale at yahoo.co.in>
>     Subject: parallel compilation problem
>     To: "smeagol-post" <smeagol-discuss at lists.tchpc.tcd.ie>
>     Date: Wednesday, 7 January, 2009, 11:37 AM
>
>     Dear All and Alex,
>
>     I compiled parallel smeagol on Xeon dual processor quad core
>     workstation with lam-mpi and intel-mkl. the program compiled
>     without giving any error message. Now when I tried to run the
>     /examples/gamma/leads/Au.fdf on 2 or 4 nodes using command mpirun
>     -np 4 ~/para-smgl/smeagol.1.0b/Src/smglpara <Au.fdf>Au.out
>
>     it gives me the "forrtl: severe (174): SIGSEGV, segmentation fault
>     occurred" error and stops at particular point :
>
>
>     SIESTA 1.3.7  -- [1.3f1 release] (04 Feb 2004)
>     Architecture  : intel-parallel-sagar
>     Compiler flags: 
>     PARALLEL version
>     NetCDF-capable
>
>     * Running on    4 nodes in parallel
>     >> Start of run:   7-JAN-2009  10:44:33
>
>
>     .....
>
>     ......
>
>     siesta: overlap: 12.1666 5.4652 2
>     siesta: overlap: rmaxh veclen direction
>     siesta: overlap: 12.1666 7.7290 3
>
>     superc: Internal auxiliary supercell: 5 x 5 x 3 = 75
>     superc: Number of atoms, orbitals, and projectors: 150 150 600
>      
>     * Maximum dynamic memory allocated = 2 MB
>
>     siesta: ===============================
>       Begin MD step = 1
>       ===============================
>
>     superc: Internal auxiliary supercell: 5 x 5 x 3 = 75
>     superc: Number of atoms, orbitals, and projectors: 150 150 600
>
>     **********************
>
>     But when i use single node in a command i.e. 
>
>     mpirun -np 1 ~/para-smgl/smeagol.1.0b/Src/smglpara <Au.fdf>Au.out
>
>     it runs successfully and ends normally. 
>
>     Where might be a mistake in compilation?
>
>     Below is my arch.make file:
>
>     ****************
>
>     SIESTA_ARCH=intel-parallel-sagar
>     #
>     FC=/opt/MPI/lam-7.1.4/lam/bin/mpif90
>     FC_ASIS=$(FC)
>
>     #FFLAGS=  -O2
>     FFLAGS= -w -xP -O3 -mp1
>     LDFLAGS= -Vaxlib
>     COMP_LIBS=
>     TRANSPORTFLAGS= -c -tpp7 -O3
>
>     SOURCE_DIR=/home/phy/para-smgl/smeagol.1.0b/
>     EXEC = smglpara
>
>     NETCDF_LIBS=-lnetcdf
>     NETCDF_INTERFACE=libnetcdf_f90..a
>     DEFS_CDF=-DCDF
>
>     MPI_INTERFACE=libmpi_f90.a
>     MPI_INCLUDE=/opt/MPI/lam-7.1.4/lam/include/
>     DEFS_MPI=-DMPI
>
>     GUIDE=/opt/intel/mkl/10.0.1.014/lib/em64t/libguide.a
>     LAPACK=/opt/intel/mkl/10.0.1..014/lib/em64t/libmkl_lapack.a
>     BLAS=/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_blas95.a
>     #sagar
>     BLACS= /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_blacs_ilp64.a 
>     /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_em64t.a 
>     /opt/intel/mkl/10.0.1.014/lib/em64t/libiomp5.a
>
>     SCALAPACK_LIBS= /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_scalapack.a
>
>     LIBS_PATH=-L/opt/intel/mkl/10.0.1.014/lib/em64t
>
>     LIBS= $(LIBS_PATH) $(NETCDF_LIBS) $(SCALAPACK_LIBS) $(BLACS_LIBS)
>     $(BLAS) $(LAPACK_LIBS) $(BLAS_LIBS)
>     /home/guest/sagar/tran/smeagol.1.0b/Src/MPI/Interfaces.o   
>     $(BLACS) $(OTHER_LIBS) -lpthread
>
>     #
>     RANLIB=echo
>     SYS=bsd
>     DEFS= $(DEFS_CDF) $(DEFS_MPI)
>     #DEFS= $(DEFS_MPI)
>
>     #
>     .F.o:
>         $(FC) -c $(FFLAGS)  $(DEFS) $<
>     .f.o:
>         $(FC) -c $(FFLAGS)   $<
>     .F90.o:
>         $(FC) -c $(FFLAGS)  $(DEFS) $<
>     .f90.o:
>         $(FC) -c $(FFLAGS)   $<
>                    
>     #
>     ***************************************
>
>
>
>     Thanks
>
>     Sagar Ambavale
>
>     Research student..
>
>     The M.S. University of Baroda
>
>     India
>
>
>
>     ------------------------------------------------------------------------
>     Connect with friends all over the world. Get Yahoo! India
>     Messenger.
>     <http://in.rd.yahoo.com/tagline_messenger_1/*http://in.messenger.yahoo.com/?wm=n/>
>
>
> ------------------------------------------------------------------------
> Add more friends to your messenger and enjoy! Invite them now.
> <http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Smeagol-discuss mailing list
> Smeagol-discuss at lists.tchpc.tcd.ie
> http://lists.tchpc.tcd.ie/listinfo/smeagol-discuss


-- 
=================================================
Ivan Rungger,

School of Physics and CRANN,  
Trinity College Dublin,  
Dublin 2,  IRELAND  
Phone: +353-1-8968454  
Email: runggeri at tcd.ie
=================================================