[Dock-fans] Compiling dock to run parallel multicore on Mac OS X

Julio Dominguez acheron24 at hotmail.com
Tue Jan 21 17:54:33 PST 2014

HI y'all

I am kinda busy so forgive the quick and dirty answer.
To get mpi working on a mac you need to modify/create a makefile with the correct data. The way I went about it was to take a look at the gnu.parallel makefile and use it as a base for a new one. I called this one intel.mkl.parallel since I use the intel C and fortran compilers.My intel.mkl.parallel looks like this:
CC=          iccCXX=         /sw/bin/mpicxxCFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK -DMPICH_SKIP_MPICXX -I$(MPICH_HOME)/include -O2FC=          ifortFFLAGS=      -O2LIBS=        -L$(MKL_HOME)/lib/em64t -lvml -lmkl_lapack -lmkl -lguide -lpthreadLIBS=        $(MKL)LINK_WITHOUT_FORTRAN_MAIN= -nofor_mainLOAD=        /sw/bin/mpicxxDOCK_SUFFIX= .mpi
AR=          ar rvLEX=         flexOCFLAGS=     -O3 -ipo -D_ANSI_SOURCERANLIB=      ranlib
I left all the comments out for clarity. Notice that I indicated the specific location of my mpicxx as well as some intel libraries. For GNU in mac, you will have to compile mpirun and identify its location for dock. In my hands, this method has worked for Dock 6.5 and 6.6
Best regards
Date: Tue, 21 Jan 2014 13:05:58 -0800
From: dkhsu at ucdavis.edu
To: dock-fans at docking.org
Subject: [Dock-fans] Compiling dock to run parallel multicore on Mac OS X


    Hi All


      Would anyone have a link/brief instructions to make this happen on
      a Mac (e.g. Lion OS)? The serial installation works and generates
      OK output on the 'check' process; parallel installation runs with
      warnings that look no different from serial, but the 'test'
      terminates at 'parallel dock6 test mpi' with the following:




      cd mpi && make test 

      cd ../grid_generation && make test

      # Construct box to enclose spheres

      ../../../bin/showbox < box.in > /dev/null

      ../dockdif box.pdb.save box.pdb

      diffing box.pdb.save with box.pdb



      # Compute scoring grids

      ../../../bin/grid -i grid.in -o grid.out

      ../dockdif grid.out.save grid.out

      diffing grid.out.save with grid.out

      possible FAILURE:  check grid.out.dif



      Processing parallel dock6 test mpi

      /bin/mpirun -np 2 ../../../bin/dock6.mpi -i mpi.dockin -o

      make[3]: /bin/mpirun: No such file or directory

      make[3]: *** [mpi.dockmpiout] Error 1

      make[2]: *** [test] Error 2

      make[1]: *** [parallel] Error 2

      make: *** [timed_test] Error 2



      The location of 'mpirun' above is incorrect, but I cant find where
      hand editing can
      be done in the mpi 'Makefile' and associated '.h' files. Other


    Thanks much for any help!



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