Re: [FLASH-USERS] version of flash 2.3 compatible with mpich-1.2.5.2 ??

Is it only MPI_Wtime that you are having trouble with in linking now, or
other mpi functions as well ?

You also mentioned using debugger in your earlier mail, you can use a
debugger only when you have the executable built.

Also try to do a build with IO/null and see if you have better luck.

On Thu, 12 Aug 2004, Victor Shum wrote:

>
>
> Hi Anshu,
>
> I always try to cleanly redo the compilation and the
> linking by rm -f *.o inside the flash2.3/object dir.
>
>
> My includes in my mpif90 compilation goes like this:
>
> mpif90 -c -r8 -i4 -f90=ifc -quiet
> -I/usr/local/mpich-1.2.5/ch_p4/include-I/usr/src/hdf5-1.4.3/src/include
> -DN_DIM=2 -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1
>
>
> so I'd think that BOTH the hdf5 headers and the mpich
> headers should be there already!
>
> Mind boggling.
>
> -Vic
>
> --- Anshu Dubey <dubey@tagore.uchicago.edu> wrote:
>
> >
> > Victor,
> >
> > If you are using mpif90 for compilation and linking,
> > you shouldn't need to
> > link the mpich library explicitly. Did you also
> > verify that your hdf5 was
> > compiled using the right versions of compilers and
> > mpi includes ?
> >
> > On Thu, 12 Aug 2004, Victor Shum wrote:
> >
> > > Hi Tomak and flash users,
> > >
> > > I removed the -fast, -ipo, -ipo_obj and the no
> > action
> > > performed warning disappeared!
> > > Thanks a lot!
> > >
> > > However, on the link side I still have problems
> > after
> > > doing clean reinstall of mpich and hdf5.
> > >
> > > I did notice that I need the syntax:
> > > LIB_HDF5 = -L/usr/src/hdf5-1.4.3/src/.libs -lhdf5
> > >
> > > for mpif90 to link the hdf5 library without the
> > > undefined reference hdf5 variable errors but if I
> > try
> > > to mimic that and use :
> > > LIB_HDF5 = -L/usr/local/mpich-1.2.5/lib -lmpich
> > > it didn't work!
> > > What is the syntax to -lmpich (I just guessed this
> > one
> > > as -lhdf5 is to the libhdf5.a, I have in the mpich
> > dir
> > >
> > > the library libmpich.a) .
> > >
> > > I still have those mpi_wtime undefined errors.
> > >
> > > Any help on this is most welcome!
> > >
> > > Much Appreciated!
> > >
> > > Bst,
> > > Vic
> > > --- Tomasz Plewa <tomek@flash.uchicago.edu> wrote:
> > >
> > > > Victor -
> > > >
> > > > I think it might be a good idea to cleanly
> > install
> > > > intel compiler,
> > > > recompile mpich, make sure the output from
> > > >
> > > > mpif90 -show
> > > >
> > > > points to the right place, that your
> > /etc/ld.so.conf
> > > > points to
> > > > where you installed your libraries (if you use
> > > > shared libraries),
> > > > eventually set up and compile the code.
> > > >
> > > > Did you install mpich in
> > > >
> > > > /usr/src/mpich-1.2.5.2/include
> > > >
> > > > this is rather unusual place reserved for
> > > > distribution sources rather
> > > > than compiled tools. Try
> > > >
> > > > ./configure
> > --prefix=/usr/local/mpich-1.2.5.2-ifc80
> > > >
> > > > Make sure you defined environemnt prior to
> > > > installation as follows:
> > > >
> > > > setenv FC ifort
> > > > setenv F77 ifort
> > > > setenv F90 ifort
> > > > setenv F9X ifort
> > > > setenv CC icc
> > > > setenv CXX icc
> > > >
> > > > and you may need
> > > >
> > > > setenv RSHCOMMAND ssh
> > > >
> > > > depending whether rsh or ssh is available on
> > your
> > > > system.
> > > >
> > > > You may have followed all those steps already,
> > but I
> > > > am finding
> > > > your diagnostic information a little difficult
> > to
> > > > decipher.
> > > >
> > > > Also, can you lower optimization options and at
> > > > least temporarily
> > > > eliminate -fast -ipo -ipo_obj.
> > > >
> > > > Best -
> > > >
> > > > Tomek
> > > > --
> > > > On Thu, Aug 12, 2004 at 04:57:09PM -0700, Victor
> > > > Shum wrote:
> > > > >
> > > > > Hi,
> > > > >
> > > > > I checked the include library for
> > > > > mpich-1.2.5.2/include
> > > > > and I can see the definitions of MPI_WTIME
> > etc.
> > > > there
> > > > >
> > > > > In my compile script I used:
> > > > > mpif90 -c -fast -ipo -ipo_obj -r8 -i4 -I
> > > > > /usr/src/mpich-1.2.5.2/include -DN_DIM=2
> > > > > -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1
> > xx.f90
> > > > >
> > > > > so the mpif.h should have been incorporated
> > right?
> > > > >
> > > > >
> > > > > Also I still get the no action performed
> > warning
> > > > for a
> > > > > lot of files, maybe that is related? :
> > > > >
> > > > > mpif90 -c -fast -ipo -ipo_obj -r8 -i4 -I
> > > > > /usr/src/mpich-1.2.5.2/include -DN_DIM=2
> > > > > -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1
> > > > > get_argument.F90
> > > > > ifort: Command line warning: no action
> > performed
> > > > for
> > > > > specified file(s)
> > > > > mpif90 -c -fast -ipo -ipo_obj -r8 -i4 -I
> > > > > /usr/src/mpich-1.2.5.2/include -DN_DIM=2
> > > > > -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1
> > > > > current_date_time.F90
> > > > > ifort: Command line warning: no action
> > performed
> > > > for
> > > > > specified file(s)
> > > > > mpif90 -c -fast -ipo -ipo_obj -r8 -i4 -I
> > > > > /usr/src/mpich-1.2.5.2/include -DN_DIM=2
> > > > > -DMAXBLOCKS=1000 -DNXB=8 -DNYB=8 -DNZB=1
> > > > get_opt.F90
> > > > >
> > > > >
> > > > > --- Tomasz Plewa <tomek@flash.uchicago.edu>
> > wrote:
> > > > >
> > > > > > Victor -
> > > > > >
> > > > > > It is likely that you are linking against
> > wrong
> > > > > > library (static
> > > > > > vs. shared, for example).
> > > > > >
> > > > > > Tomek
> > > > > > --
> > > > > > On Thu, Aug 12, 2004 at 04:07:14PM -0700,
> > Victor
> > > > > > Shum wrote:
> > > > > > >
> > > > > > >
> > > > > > > Thanks for the info.
> > > > > > >
> > > > > > > I did that and still it was the same.
> > > > > > >
> > > > > > > When linking, the make did :
> > > > > > > mpif90 -o flash2 Cosmology.o
> > > > > > CosmologicalFunctions.o
> > > > > > > ..
> > > > > > > flashModules.o -L
> > > > /usr/src/hdf5-1.4.3/src/.libs
> > > > > > > -lhdf5
> > > > > > >
> > > > > > > However, after linking I got many
> > undefined
> > > > > > reference
> > > > > > > :
> > > > > > >
> > > > > > > amr_morton.o(.text+0x3356): undefined
> > > > reference to
> > > > > > > `mpi_irecv_'
> > > > > > > amr_morton.o(.text+0x33ae): undefined
> > > > reference to
> > > > > > > `mpi_ssend_'
> > > > > > > amr_morton.o(.text+0x33fb): undefined
> > > > reference to
> > > > > > > `mpi_waitall_'
> > > > > > > amr_morton.o(.text+0x34c3): undefined
> >
> === message truncated ===
>

-- 
Anshu Dubey
Astronomy & Astrophysics
University of Chicago
5640 S. Ellis Ave.  Chicago IL 60637
Tel : (773) 834 2999
Fax : (773) 834 3230