[Smeagol-discuss] fw:parallel compilation problem
Ivan Rungger
runggeri at tcd.ie
Sun Jan 18 17:42:56 GMT 2009
Hello Sagar,
>I tried leads calculation with 1 processor and then
> transport calculation with 4 processors. It ran smoothly.
This sounds good. The problem with compiling siesta is probably that you
specify FC with slashes ("/") in it, which will not work with the
Makefile as it is. Try to change FC=/opt/MPI/lam-7.1.4/lam/bin/mpif90
with FC=mpif90 (and make sure that the directory
/opt/MPI/lam-7.1.4/lam/bin/ is the first in your PATH environment
variable), that should work.
Regarding the problem of siesta2.0 running a set of serial jobs instead
of one parallel, I don't know what can be the origin.
Anyway the good thing is that smeagol runs in parallel.
Cheers,
Ivan
ambavale sagar wrote:
> Dear Ivan,
> I tried leads calculation with 1 processor and then transport
> calculation with 4 processors. It ran smoothly.
> Then as per your advice i tried to compile siesta 1.3f1p (without
> smeagol patch) with same arch.make file, but it couldn't be compiled.
> In the very beginning it gave the error like:
>
> ==> Incorporating information about present compilation (compiler and
> flags)
> sed: -e expression #1, char 11: unknown option to`s'
> make: *** [version] error 1
>
> Then I tried compilation of siesta2.0 which compiled without error but
> for what ever number of nodes i give in run command , it runs
> serially. It neither gives the error message nor stops. With some
> minutely changed arch.make file it runs same process on all nodes and
> writes same output 4 times (for 4 nodes).
>
> Please help me about this. I am completely clueless..
>
> Regards
> Sagar
>
>
>
> --- On *Thu, 15/1/09, Ivan Rungger /<runggeri at tcd.ie>/* wrote:
>
> From: Ivan Rungger <runggeri at tcd.ie>
> Subject: Re: [Smeagol-discuss] fw:parallel compilation problem
> To: sagarambavale at yahoo.co.in, "smeagol-post"
> <smeagol-discuss at lists.tchpc.tcd.ie>
> Date: Thursday, 15 January, 2009, 4:42 PM
>
> 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
> >
> >
> >
> >
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> > Smeagol-discuss at lists.tchpc.tcd.ie
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>
>
> --
>
> =================================================
> Ivan Rungger,
>
> School of Physics and CRANN,
> Trinity College Dublin,
> Dublin 2, IRELAND
> Phone: +353-1-8968454
> Email: runggeri at tcd.ie
> =================================================
>
>
>
>
>
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--
=================================================
Ivan Rungger,
School of Physics and CRANN,
Trinity College Dublin,
Dublin 2, IRELAND
Phone: +353-1-8968454
Email: runggeri at tcd.ie
=================================================
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