NCGRP/MplusMPI
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To compile: use "make" Usage: m+ varfile datfile [-m mincoresize maxcoresize samplingfreq reps outputfile] [-r] [-k kernelfile] [-a idealcorefile] where, varfile = path to MSTRAT .var file datfile = path to MSTRAT .dat file Options: -m mincoresize maxcoresize samplingfreq reps outputfile = compute the optimal accessions for a given core size using the M+ search algorithm. Arguments are as follows: mincoresize maxcoresize = integers specifying minimum and maximum core size. Usually mincoresize = 2, maxcoresize = total number of accessions samplingfreq = e.g. integer value 5 will cause coresize=2 then coresize=7, then 12, and so on, to be sampled. reps = number of replicate core sets to calculate for a particular core size outputfile = path to output -r use rarefaction to correct for differences in sample size of accessions, applies to M+ algorithm only. -k kernelfile = use an MSTRAT .ker file to specify mandatory members of the core. The number of mandatory accessions must therefore be less than or equal to mincoresize. Option only applies to -m, and cannot be used with -a. -a idealcorefile = compute the minimum set of accessions necessary to retain all variation, i.e. the "ideal" or "best" core, using the A* search algorithm, write output to idealcorefile. Notes: Missing data must be coded as 9999. Option -m uses MPI and -a uses OpenMP. For best performance, avoid combining -m and -a in a single command. Always specify 2 or more processors when invoking -m. Specify 1 processor when using -a. To validate input files, omit all options. Examples (mpirun): mpirun -np 2 ./m+ ./beet.var ./beet.dat -m 3 28 2 3 ./beetout.txt mpirun -np 2 ./m+ ./beet.var ./beet.dat -m 3 28 2 3 ./beetoutk.txt -k beet.ker mpirun -np 1 ./m+ ./beet.var ./beet.dat -a beetideal.txt mpirun -np 16 ./m+ ./orientalis.var ./orientalisIND.dat -m 2 50 1 1 orINDout.txt mpirun -np 1 ./m+ ./orientalis.var ./orientalisIND.dat -a orINDidealout.txt mpirun -np 20 ./m+ ./WheatSNP.var ./WheatSNP.dat -m 20 21 1 20 ./WheatSNPout.txt mpirun -np 10 ./m+ ./At.var ./At.dat -m 2 10 1 1 ./Atout.txt mpirun -np 10 ./m+ ./At.var ./At.dat -m 2 10 1 1 ./Atoutr.txt -r
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MPI implementation of M+ program
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