Re: [FLASH-USERS] HDF5 and problem with myrinet connections

This error indicates that you are not linking correctly to the MPI
library. Please verify that you have MPI with MPIIO support that works on
myrinet, and that it is linked in your makefile.

On Mon, 1 Dec 2003 edpope@soton.ac.uk wrote:

>
> Hi all,
>
> I am attempting to use Flash with the latest version of HDF5(1.6.1) which seems
> to work fine with the normal connections on the computer cluster i am using.
> However, when i alter the makefile so that Flash can run using the fast myrinet
> connection I get the following error message:
>
> In function `H5FD_mpio_open':
> > H5FDmpio.o(.text+0x263c): undefined reference to `MPI_File_open'
> > H5FDmpio.o(.text+0x2913): undefined reference to `MPI_File_get_size'
> > H5FDmpio.o(.text+0x2b32): undefined reference to `MPI_File_set_size'
> > H5FDmpio.o(.text+0x2e04): undefined reference to `MPI_File_close'
> > /scratch1/edpope/hdf5/new5-1.6.1-linux-pgipp/lib/libhdf5.a(H5FDmpio.o): In
> > function `H5FD_mpio_close':
> > H5FDmpio.o(.text+0x2f23): undefined reference to `MPI_File_close'
> > /scratch1/edpope/hdf5/new5-1.6.1-linux-pgipp/lib/libhdf5.a(H5FDmpio.o): In
> > function `H5FD_mpio_read':
> > H5FDmpio.o(.text+0x3acb): undefined reference to `MPI_File_set_view'
> > H5FDmpio.o(.text+0x3be6): undefined reference to `MPI_File_read_at'
> > H5FDmpio.o(.text+0x3d00): undefined reference to `MPI_File_read_at_all'
> > H5FDmpio.o(.text+0x3eb0): undefined reference to `MPI_File_set_view'
> > /scratch1/edpope/hdf5/new5-1.6.1-linux-pgipp/lib/libhdf5.a(H5FDmpio.o): In
> > function `H5FD_mpio_write':
> > H5FDmpio.o(.text+0x45c1): undefined reference to `MPI_File_set_view'
> > H5FDmpio.o(.text+0x48bb): undefined reference to `MPI_File_write_at'
> > H5FDmpio.o(.text+0x49d5): undefined reference to `MPI_File_write_at_all'
> > H5FDmpio.o(.text+0x4b88): undefined reference to `MPI_File_set_view'
> > /scratch1/edpope/hdf5/new5-1.6.1-linux-pgipp/lib/libhdf5.a(H5FDmpio.o): In
> > function `H5FD_mpio_flush':
> > H5FDmpio.o(.text+0x4f91): undefined reference to `MPI_File_set_size'
> > H5FDmpio.o(.text+0x518d): undefined reference to `MPI_File_sync'
> > gmake[1]: *** [flash2] Error 2
> > gmake[1]: Leaving directory
> `/import/blue03/scratch1/edpope/FLASH2.3/object'
> > gmake: *** [default] Error 2
>
> I noticed that Flash has only been tested with HDF5-1.4 or so. Has anyone else
> has encountered such problems or, indeed, over come them?
>
> Thanks,
>
> Ed
>
> Edward Pope
> Postgraduate student
> Astronomy Group
> School of Physics and Astronomy
> University of Southampton,
> UK
> SO17 1BJ
>
> email:edpope@soton.ac.uk
> phone: 02380 592087
>

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