[Smeagol-discuss] Fw: Re: fw:parallel compilation problem
ambavale sagar
sagarambavale at yahoo.co.in
Mon Jan 19 17:56:28 GMT 2009
Hi Ivan and all,
I told in my previous mail that transport calculation of example is running well with 4 nodes. But when i tried with more nodes (8 nodes) it gives segmentation fault at random places. I changed my arch.make file as suggested i.e put mpif90 and removed "/" (mpif90 is in path). Few more things are changed as I searched in siesta forum though problem persists. Please have a look at my arch.make file given below and suggest if any changes should be made..
Thanks a lot.
my new arch.make file is :
..SUFFIXES:
..SUFFIXES: .f .F .o .a .f90 .F90
SIESTA_ARCH=intel10
SOURCE_DIR=/home/phy/para-smgl/smeagol.1.0b/
EXEC = smglpara
FPP=
FPP_OUTPUT=
#FC=/opt/MPI/lam-7.1.4/lam/bin/mpif90
FC=mpif90
FC_ASIS=$(FC)
RANLIB=ranlib
SYS=nag
SP_KIND=4
DP_KIND=8
KINDS=$(SP_KIND)
$(DP_KIND)
#FFLAGS=-g
#FFLAGS= -O2 -mtune=pentium4 -zero
FFLAGS= -O1
FPPFLAGS= -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT -DGRID_DP
LDFLAGS= -Vaxlib
TRANSPORTFLAGS= -O1
ARFLAGS_EXTRA=
FCFLAGS_fixed_f=
FCFLAGS_free_f90=
FPPFLAGS_fixed_F=
FPPFLAGS_free_F90=
COMP_LIBS=linalg.a
#COMP_LIBS=dc_lapack.a liblapack.a libblas.a
NETCDF_LIBS=-lnetcdf
NETCDF_INTERFACE=libnetcdf_f90.a
DEFS_CDF=-DCDF
#LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)
#SIESTA needs an F90 interface to MPI
#This will give you SIESTA's own implementation
#If your compiler vendor offers an alternative, you may change
#to it here.
MPI_INTERFACE=libmpi_f90.a
MPI_INCLUDE=/opt/MPI/lam-7.1.4/lam/include/
#MPI_LIBS= -L/opt/MPI/lam-7.1.4/lam/lib -llamf77mpi -lmpi -llam -lnsl
DEFS_MPI=-DMPI
DEFS= $(DEFS_CDF)
$(DEFS_MPI)
GUIDE=/opt/intel/mkl/10.0.1.014/lib/em64t/libguide.a
#BLAS_LIBS=libblas.a
#LAPACK_LIBS=dc_lapack.a liblapack.a
#BLACS_LIBS=/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_blacs_ilp64.a
#SCALAPACK_LIBS=/opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_scalapack_ilp64.a
#this also gives segmentation fault)
#SCALAPACK_LIBS= /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_scalapack.a
#BLACS_LIBS= /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
#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
#LIBS_PATH=-L/opt/intel/mkl/10.0.1.014/lib/em64t
#LIBS= $(LIBS_PATH) $(NETCDF_LIBS) $(SCALAPACK_LIBS) $(BLACS_LIBS) $(GUIDE) $(BLACS) $(BLAS) \
# $(LAPACK)
$(OTHER_LIBS) /home/phy/siesta-2.0.1-para/Src/MPI/Interfaces.o -lpthread -lguide
#LIBS= $(LIBS_PATH) $(NETCDF_LIBS) $(SCALAPACK_LIBS) $(BLACS_LIBS) $(GUIDE) $(LAPACK) $(BLAS) \
# $(OTHER_LIBS) -lpthread -lguide
#sagar
MKLPATH=/opt/intel/cmkl/10.0.1.014/lib/em64t
LIBS=-L$(MKLPATH) -lmkl_scalapack_lp64 -lmkl_blacs_lp64 -lmkl_intel_lp64 -Wl,--start-group -lmkl_sequential -lmkl_core -Wl,--end-group -lpthread
#Dependency rules are created by autoconf according to whether
#discrete preprocessing is necessary or not.
..F.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<
..F90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
..f.o:
$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<
..f90.o:
$(FC) -c $(FFLAGS) $(INCFLAGS)
$(FCFLAGS_free_f90) $<
--- On Sun, 18/1/09, 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
Cc: "smeagol-post" <smeagol-discuss at lists.tchpc.tcd.ie>
Date: Sunday, 18 January, 2009, 11:12 PM
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
> >
>
>
> >
> >
>
------------------------------------------------------------------------
> > 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
> =================================================
>
>
>
>
>
> ------------------------------------------------------------------------
> Add more friends to your messenger and enjoy! Invite them now.
>
<http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/>
--
=================================================
Ivan Rungger,
School of Physics and CRANN,
Trinity College Dublin,
Dublin 2,
IRELAND
Phone: +353-1-8968454
Email: runggeri at tcd.ie
=================================================
Add more friends to your messenger and enjoy! Invite them now.
Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://lists.tchpc.tcd.ie/pipermail/smeagol-discuss/attachments/20090119/f3c66d80/attachment-0001.html
More information about the Smeagol-discuss
mailing list