fastDNAml on Solaris 10 x86 with mpi

I have been using this app called fastDNAml, written by Gary J. Olsen, a very useful bio-app that finds out the maximum likelyhood phylogenetic trees from nucleotide sequences. I am interested in the parallel version of the same app, developed by the Indiana University. You can download the same here.
To make it work on Solaris 10 x86 mpi 1.2 . The only tweaks to be done are.
  1. un-tar  the  source package.
  2. Switch to the source directory.
  3. You would want to make changes to Makefile.LINUX.
  4. Open the Makefile.LINUX , and change
    1. gcc path.
    2. set the MPI_ROOT appropriately.
    3. make the MPICC variable point to the $MPI_ROOT/bin/mpicc
  5. Build the project using this command #make -f Makefile.LINUX mpi .
  6. Create a file called machines that looks like this. I have done so cause I need to run four process of fastDNAmlp mpi_foreman, mpi_worker, mpi_fastDNAml, mpi_fastDNAml_mon.
  7. For the mpirun to pick this up we need to use a tool to change the file and assign each of these nodes a process to run on.
    • run this command 'fastDNAml_1.2.2p/testdata/mkp4pg  fastDNAml_1.2.2p/src/machines 1  mpi_dnaml_mon  ~/dev/fastDNAml_1.2.2p/src' > myProc.pg
    • this command generates a proc group file that looks like this.
    • the arguments it takes are
      • the machines file we generated.
      • the number of processor in each node.
      • the first process to be run.
      • the absolute path of the place where all the executables.
  8. Use this command to run the app, I use a test case already bundled with fastDNAml.
    • mpirun -v -p4pg  fastDNAml_1.2.2p/myProc.pg fastDNAml_1.2.2p/src/mpi_dnaml_mon -d4 -nmpi56 -s  fastDNAml_1.2.2p/testdata/test56.phy
    • It should take about 12 minutes to complete this on an Ultra 20 with 1 GB of RAM.
The folks at Indiana have written a nice help file that covers all options, please refer to this fastDNAml_1.2.2p/docs/fastDNAml_1.2.2.txt . I have uploaded it here for your benefit.

Myself and Prem Kumar L (my colleague and friend), have compiled these steps together.




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