[Smeagol-discuss] fw:parallel compilation problem
ambavale sagar
sagarambavale at yahoo.co.in
Sat Jan 17 05:27:25 GMT 2009
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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=================================================
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School of Physics and CRANN,
Trinity College Dublin,
Dublin 2, IRELAND
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Email: runggeri at tcd.ie
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