On Mon, Jan 09, 2006 at 08:02:35AM -0600, Peng Gu wrote: > Here is where I need your help: > 1) When I was trying to build the flash_benchmark_io code, the > compiler complained that hdf5.h file is missing. I want to know for > sure if this file is necessary for building the code. > # gmake -f Makefile.linux flash_benchmark_io > mpicc -c -I /usr/include/ -DTFLOPS -DN_DIM=3 h5_file_interface.c > h5_file_interface.c:6:18: hdf5.h: No such file or directory
Building flash-io requires a bit of work. it's unlikley to work out of the box. You'll have to modify an existing makefile, but before you do that you need to make sure you've got a properly working software stack (described more below). > Can anybody explained to me what is the relationship between HDF and PVFS. > Are they working on different levels or what? HDF5 and PVFS2 are really quite different things. PVFS2 is a file system, and HDF5 is a library providing several useful abstractions for scientific computing. HDF5 makes MPI-IO calls. those MPI-IO calls (at least in ROMIO) are the ones that talk to PVFS2. The things you need to do are - set up PVFS2 - build, say, MPICH2 with PVFS2 support - build HDF5 with support for parallel IO (the HDF5 documentation has the details) - build FLASH-IO against your HDF5 library (modify Makefile.chiba so that everything points to the correct location) > 2) I can not run mpi_tile_io correctly, the input and output are like: > # mpirun -np 100 mpi-tile-io --nr_tiles_x 25 --nr_tiles_y 4 > --sz_tile_x 100 --sz_tile_y 100 --sz_element 32 --filename > /mnt/pvfs2/foo > problem with execution of mpi-tile-io on cse-wang-server.unl.edu: > [Errno 2] No such file or directory > problem with execution of mpi-tile-io on cse-wang05b.unl.edu: > [Errno 2] No such file or directory > problem with execution of mpi-tile-io on cse-wang-server.unl.edu: > [Errno 2] No such file or directory looks like there's not a common file system between cse-wang-server.unl.edu and cse-wang05b.unl.edu ? Or maybe pvfs2 isn't mounted on those machines? > 3) I could not build the DB for mpiBLAST, here is my input and output > messages: I've never used mpiblast, so i'm not sure what to tell you here ==rob -- Rob Latham Mathematics and Computer Science Division A215 0178 EA2D B059 8CDF Argonne National Labs, IL USA B29D F333 664A 4280 315B _______________________________________________ PVFS2-users mailing list [email protected] http://www.beowulf-underground.org/mailman/listinfo/pvfs2-users
