Re: Need help in compiling Gadget

From: Robert Fisher <rfisher_at_flash.uchicago.edu>
Date: Wed, 8 Feb 2006 08:24:05 -0600 (CST)

Hi Shasikant :

  What is certainly true is that your linker is failing to locate the
unresolved symbols. You may wish to confirm that the library was compiled
properly. You may do so using the unix command "nm" on the ".a" library
file, checking whether the unresolved symbols exist in the linked library
or not.

  Also, note that the mp "compilers" are actually scripts which should
automatically link to MPI -- you should not need to link to MPI
explicitly. In some case you may need to provide the relevant paths for
headers and libraries. The standard location for these on IBM machines is

 -I/usr/lpp/ppe.poe/include
 -L/usr/lpp/ppe.poe/lib

Check with your sysadmin if these do not work on your machine.

  Best,

  Bob

On Wed, 8 Feb 2006, Shashikant wrote:

>
> Hi,
> fftw and gsl are ok. I have checked both using "make check".
> I am using fftw-2.1.5 and gsl-1.7. I am using poe instead of mpich.
> The part of Gadget Makefile is as follows-
>
> ifeq ($(SYSTYPE),"Regatta")
> CC = mpcc_r -qipa -q64
> OPTIMIZE = -O5 -qstrict
> GSL_INCL = -I/home/phd/03/astskant/soft_inst/GSL/include
> GSL_LIBS = -L/home/phd/03/astskant/soft_inst/GSL/lib
> FFTW_INCL= -I/home/phd/03/astskant/soft_inst/FFTW/include
> FFTW_LIBS= -L/home/phd/03/astskant/soft_inst/FFTW/lib
> MPICHLIB = -L/usr/bin/poe -lpoe
> #HDF5INCL = -I/afs/rzg/u/vrs/hdf5_psi64/include
> #HDF5LIB = -L/afs/rzg/u/vrs/hdf5_psi64/lib -lhdf5 -lz
> endif
>
> Why it is happening ?
>
> Regards
> Shashikant
>
>
> On Tue, 7 Feb 2006, Yves Revaz wrote:
> > Dear Shashikant,
> > It seems that gsl and fftw libraries are missing or
> > badly installed.
> > I just re-installed Gadget on a new computer yesterday and used the
> > following libraries :
> > fftw-2.1.5.tar.gz
> > and
> > gsl-1.7.tar.gz
> > I installed those libraries with the commands :
> > [for fftw]
> > ./configure --prefix=/home/revaz/local --enable-type-prefix --enable-mpi --enable-float
> > make
> > make install
> >
> > [for gsl]
> > ./configure --prefix=/home/revaz/local
> > make
> > make install
> >
> > and my gadget makefile looks like :
> >
> > ifeq ($(SYSTYPE),"revaz/local")
> > CC = mpicc
> > OPTIMIZE = -O3 -Wall -g
> > GSL_INCL = -I/home/revaz/local/include
> > GSL_LIBS = -L/home/revaz/local/lib
> > FFTW_INCL= -I/home/revaz/local/include
> > FFTW_LIBS= -L/home/revaz/local/lib
> > MPICHLIB = -L/home/revaz/local/mpich-1.2.5/ch_p4/lib -lmpich
> > HDF5INCL =
> > HDF5LIB =
> > endif
> >
> > (of course, you also need mpi to be installed, I use mpich in this example)
> >
> > I never get compilation errors with this configuration.
> > Hope it will help...
> >
> > Cheers.
> >
> > Shashikant wrote:
> >
> > >Hi,
> > > I have just started with Gadget2 on a supercomputer(regatta)at
> > >Indian Institute of Science, Bangalore. I am having some problems in
> > >compiling the code. Can someone help me ?
> > >
> > >I am getting the following error-
> > >
> > >mpcc_r -qipa -q64 main.o run.o predict.o begrun.o endrun.o global.o
> > >timestep.o init.o restart.o io.o accel.o read_ic.o ngb.o system.o
> > >allocate.o density.o gravtree.o hydra.o driftfac.o domain.o allvars.o
> > >potential.o forcetree.o peano.o gravtree_forcetest.o pm_periodic.o
> > >pm_nonperiodic.o longrange.o -g -lmpi
> > >-L/home/phd/03/astskant/soft_inst/GSL/lib -lgsl -lgslcblas -lm
> > >-L/home/phd/03/astskant/soft_inst/FFTW/lib -lsrfftw_mpi -lsfftw_mpi
> > >-lsrfftw -lsfftw -o Gadget2
> > >"system.o" 1586-233 (I) Duplicate definition of symbol
> > >"MPI_F_STATUS_IGNORE" ignored.
> > >"system.o" 1586-233 (I) Duplicate definition of symbol
> > >"MPI_F_STATUSES_IGNORE" ignored.
> > >1586-206 (S) Unresolved reference to symbol "gsl_rng_uniform".
> > >1586-206 (S) Unresolved reference to symbol "gsl_rng_alloc".
> > >1586-206 (S) Unresolved reference to symbol "gsl_rng_ranlxd1".
> > >1586-206 (S) Unresolved reference to symbol "gsl_rng_set".
> > >1586-206 (S) Unresolved reference to symbol
> > >"gsl_integration_workspace_alloc".
> > >1586-206 (S) Unresolved reference to symbol
> > >"gsl_integration_workspace_free".
> > >1586-206 (S) Unresolved reference to symbol "gsl_integration_qag".
> > >1586-206 (S) Unresolved reference to symbol "gsl_rng_state".
> > >1586-206 (S) Unresolved reference to symbol "gsl_rng_size".
> > >1586-206 (S) Unresolved reference to symbol "rfftw3d_mpi_create_plan".
> > >1586-206 (S) Unresolved reference to symbol "rfftwnd_mpi_local_sizes".
> > >1586-206 (S) Unresolved reference to symbol "rfftwnd_mpi".
> > >1586-204 (S) Unresolved references to objects are detected.
> > >1586-341 (U) Code generation was not performed due to previously detected
> > >errors. Object file not created.
> > >make: *** [Gadget2] Error 1
> > >
> > >Thanks in advance
> > >Regards
> > >shashikant
> -----------------------------------------------------------------------------------------
> Shashikant Gupta
> Joint Astrophysics Program
> Dept. of Physics
> Indian Institute of Science
> Bangalore 560012
> Ph : +91 080 2293 3277
> ------------------------------------------------------------------------------------------
>
>
>
>
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Received on 2006-02-08 15:20:12

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