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Matrix Market is ASCII with variable-length lines, so the byte offset of nonzero k cannot be computed without scanning the file: reading it in parallel is impossible without a redistribution pass. psb_mm2bin converts it once into a row-sorted binary layout, and psb_binmat_mod reads that layout in parallel. Layout, 8-byte native-endian throughout: a header carrying a magic number, the index and real kinds the file was written with, and the dimensions; then row_ptr(nrows+1), col_idx(nnz) and values(nnz). The kinds are recorded so a mismatched reader fails loudly instead of reinterpreting the bytes. Each rank reads the header, then only its own slice of row_ptr, and from that seeks straight to the nonzeros of the rows it owns. Because the block-row partition is implicit in the file order, psb_matdist is not needed at all -- that scatter alone accounted for 28 s of MPI time at 448 ranks. Geo_1438, 1.44M rows, 63.2M nonzeros: Matrix Market read, serial 27.0 s conversion, once 27.9 s binary read at 8 ranks, including assembly and one SpMV 0.98 s Verified: byte-for-byte layout check on a 4x4 symmetric matrix with the lower triangle expanded; A*1 identical at 1, 2, 3 and 4 ranks there, the 3-rank case covering the uneven split; sum(A*1) identical to sixteen digits at 1, 4 and 8 ranks on Geo_1438. Positioned stream reads rather than MPI-IO: the ranks touch disjoint byte ranges, so there is nothing to coordinate. If collective buffering turns out to matter at high rank counts, MPI_File_read_at_all is a change local to psb_binmat_mod.
107 lines
3.5 KiB
Fortran
107 lines
3.5 KiB
Fortran
!
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! Convert a Matrix Market file into a row-sorted binary CSR-like layout that can
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! be read in parallel.
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!
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! Why this exists: Matrix Market is ASCII with variable-length lines, so the byte
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! offset of nonzero k cannot be computed without scanning the file. Reading it in
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! parallel is therefore impossible without a redistribution step. Converting once
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! to a fixed-record binary layout lets every rank seek straight to its own rows,
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! which also removes the need for psb_matdist -- at 448 ranks that scatter cost
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! 28 s of MPI time on its own.
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!
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! Layout, all 8-byte native-endian:
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!
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! header magic, version, ipk_bytes, rpk_bytes, nrows, ncols, nnz, reserved
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! row_ptr nrows+1 entries, 1-based, row i occupies row_ptr(i)..row_ptr(i+1)-1
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! col_idx nnz entries, 1-based global column indices
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! values nnz doubles
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!
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! Native endianness on purpose: this is an intermediate for local runs, and the
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! header records the kinds so a mismatched reader fails loudly instead of
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! producing garbage.
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!
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program psb_mm2bin
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use psb_base_mod
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use psb_util_mod
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implicit none
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integer(psb_lpk_), parameter :: bin_magic = 6510534141251461121_psb_lpk_
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integer(psb_lpk_), parameter :: bin_version = 1_psb_lpk_
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type(psb_ldspmat_type) :: aux
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type(psb_ld_coo_sparse_mat) :: coo
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character(len=1024) :: infile, outfile
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integer(psb_ipk_) :: info, iout
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integer(psb_lpk_) :: nr, nc, nz, k, irow
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integer(psb_lpk_), allocatable :: row_ptr(:)
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real(psb_dpk_) :: t0, t1
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if (command_argument_count() < 2) then
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write(psb_err_unit,*) 'usage: psb_mm2bin <in.mtx> <out.psb>'
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stop 1
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end if
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call get_command_argument(1, infile)
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call get_command_argument(2, outfile)
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call cpu_time(t0)
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call mm_mat_read(aux, info, filename=trim(infile))
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if (info /= psb_success_) then
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write(psb_err_unit,*) 'cannot read ', trim(infile), ' info=', info
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stop 2
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end if
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call cpu_time(t1)
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write(psb_out_unit,'("read : ",f8.2," s")') t1-t0
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nr = aux%get_nrows()
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nc = aux%get_ncols()
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! Move the storage into a COO object and sort it row-major: fix() is what
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! guarantees the entries of a row are contiguous, which is the whole premise
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! of the layout below.
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call cpu_time(t0)
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call aux%mv_to(coo)
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call coo%fix(info)
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if (info /= psb_success_) then
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write(psb_err_unit,*) 'fix failed, info=', info
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stop 3
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end if
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nz = coo%get_nzeros()
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call cpu_time(t1)
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write(psb_out_unit,'("sort : ",f8.2," s")') t1-t0
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write(psb_out_unit,'("rows ",i0," cols ",i0," nonzeros ",i0)') nr, nc, nz
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! row_ptr from the sorted row indices
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allocate(row_ptr(nr+1), stat=info)
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if (info /= 0) stop 4
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row_ptr = 0
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do k = 1, nz
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irow = coo%ia(k)
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row_ptr(irow+1) = row_ptr(irow+1) + 1
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end do
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row_ptr(1) = 1
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do k = 1, nr
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row_ptr(k+1) = row_ptr(k+1) + row_ptr(k)
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end do
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if (row_ptr(nr+1) /= nz+1) then
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write(psb_err_unit,*) 'row_ptr inconsistent: ', row_ptr(nr+1), nz+1
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stop 5
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end if
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call cpu_time(t0)
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iout = 91
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open(unit=iout, file=trim(outfile), access='stream', form='unformatted', &
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& status='replace', action='write', iostat=info)
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if (info /= 0) stop 6
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write(iout) bin_magic, bin_version, &
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& int(storage_size(nz)/8, psb_lpk_), int(storage_size(coo%val(1))/8, psb_lpk_), &
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& nr, nc, nz, 0_psb_lpk_
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write(iout) row_ptr
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write(iout) coo%ja(1:nz)
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write(iout) coo%val(1:nz)
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close(iout)
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call cpu_time(t1)
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write(psb_out_unit,'("write : ",f8.2," s")') t1-t0
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write(psb_out_unit,'("output : ",a)') trim(outfile)
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end program psb_mm2bin
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