I want to test I/O performance on PVFS2, so I what to know what kind of benchmark do shall we typically use?
Currently, I am trying the follows, but none of them are working correctly right now. 1) flash_benchmark_io, 2) mpi_tile_io 3) mpiBLAST If you are familiar with any of them and are readily to offer some help, please read on; otherwise pleasing ignore the following messages to save your precious time. Thanks! Frankly speaking, I am not quite familiar with any of them currently. As far as I know/guess, ( I might be wrong here), flash_benchmark_io is a component of Flash (an adaptive mesh hydrodynamics code for modeling astrophysical thermonuclear flashes) from University of Chicago. This is simply a guess because I currently don't have access to the entire flash software suite. 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 Can anybody explained to me what is the relationship between HDF and PVFS. Are they working on different levels or what? 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 ... ... ... I don't what file is missing and was complained by the program by repeatedly printing out "No Such file or directory". 3) I could not build the DB for mpiBLAST, here is my input and output messages: # mpiformatdb -N 5 -i yeast.aa Reading input file Done, read 46527 lines Reordering 6298 sequence entries Database type unspecified, assuming protein Breaking yeast.aa (2 MB) into 5 fragments Executing: formatdb -i /tmp/reorderAtVnfq -p T -N 5 -n /mnt/pvfs2/mpiblast/yeast.aa -o T [formatdb] FATAL ERROR: /mnt/pvfs2/mpiblast/data/seqcode.valInput tag mismatch on Seq-code-set I have no idea what was been complained and how to resolve it. Thank you in advance for your time and help! Sincerely Peng _______________________________________________ PVFS2-users mailing list [email protected] http://www.beowulf-underground.org/mailman/listinfo/pvfs2-users
