Install git on your system

Create a repository on your system

    mkdir repos
    cd repos
    git clone https://github.com/Ashlee1994/rome1.1.2.git


To build
    Linux
        Set up the compiler etc. One of
            source /opt/intel/composerxe/bin/compilervars.csh intel64
            source /opt/intel.2016/compilers_and_libraries/linux/bin/compilervars.csh intel64

        Change to the directory
            cd rome1.1.2

        Make the build output directories
        mkdir bin 
        
        To build MAP:    
            One of
                make -kj4 DEBUG="-debug all" rome_map2d 
                make -kj4 rome_map2d
                make -kj4 rome_map3d
                make -kj4 TBB="-ltbbmalloc_proxy" rome_map2d

                # Set LD_PRELOAD to load the release version of the proxy library
                LD_PRELOAD=libtbbmalloc_proxy.so.2 
                # Link with the release version of the proxy library
                g++ foo.o bar.o -ltbbmalloc_proxy -o a.out

        To build GTM:
                make -kj4 rome_sml

        To build both GTM and MAP:
                make


To run
    The command line should be something based on this pattern
        -i INPUTFILE -o OUTPUTFILE -k NUMBER OF CLASSES -iter -pixel TBD -pool TBD
    or on this pattern
        -unittest NAME
			-unittest MLOptimizer_Kernel_correctness
            -unittest MLOptimizer_Kernel_performance
            NAME such as shiftImageInFourierTransformUnitTestCorrectness

	There are test data and scripts in the testdata_2d and testdata_3d subdirectories

    Linux
        command line which takes 30 secs .. 1 min to run...
            bin/rome_map2d -i testdata_2d/data8_160/data8_160  -o NULL -k 20 -pixel 4. -iter 10 -pool  30 > testdata_2d/data8_160/emit_test_output_stab.txt
        
        running map 3d...
            cd testdata_3d/pdh,testdata_3d/TMV,...
            sh relion_3d.sh // run for relion refine
            sh rome_3d.sh // run for rome ml3d
            result file will be output at refine folder
            use diff to compare the output *.star file
            or _debug.txt to verify each step result.

	Checkpoint restart
		-i ../../testdata_2d/data8_160/data8_160 -o ../../testdata_2d/data8_160/data8_160_output -k 20 -pixel 4. -iter 1 -pool 30 
		-i ../../testdata_2d/data8_160/data8_160_output_iter001 -o NULL -continue 1              -k 20 -pixel 4. -iter 2 -pool 30 
		[Currently seems to crash because of -ve indefinites, not yet debugged]

	Test output (use when src\map2d_optimizer_base.h is selecting emit_test_output)
		-i ../../testdata_2d/data8_160/data8_160 -o NULL -k 20 -pixel 4. -iter 3 -pool 30 

    Guidance support for making tests more deterministic
		Create the guide
			-i ../../testdata_2d/data8_160/data8_160 -o ../../testdata_2d/data8_160/guidance/data8_160_output -k 20 -pixel 4. -iter 5 -pool 30 
		Use the guide
			-i ../../testdata_2d/data8_160/data8_160 -o NULL -k 20 -pixel 4. -iter 5 -pool 30 -testguidance ../../testdata_2d/data8_160/guidance/data8_160_output

	Tandem execution (use when src\map2d_optimizer_base.h is selecting both the new and the original versions)
		-i ../../testdata_2d/data8_160/data8_160 -o NULL -k 20 -pixel 4. -iter 3 -pool 30 

To debug on Linux
    gdb bin/rome_map2d 
    run -i testdata_2d/data8_160/data8_160  -o NULL -k 20 -pixel 4. -iter 10 -pool  30 > testdata_2d/data8_160/emit_test_output_stab.txt

To collect Amplifier data
    Linux
        source /opt/intel.2016/vtune_amplifier_xe/amplxe-vars.csh
        amplxe-gui &
        
            new project
            
            Analysis Target
                application:    /home/nsl/brbrett/project/DanaFaber/repos/ROME2D/bin/rome_map2d
                App params:     -i testdata_2d/data8_160/data8_160  -o NULL -k 20 -pixel 4. -iter 10 -pool  30
                Working dir:    /home/nsl/brbrett/project/DanaFaber/repos/ROME1.1
            
            Analysis Type
                Basic Hotspots
            
            Start
                Output goes to the terminal window
                Takes about 30 seconds
                The only change in the amplixe-gui is the elapsed time ticking
            
        rm -rf r000hs1 ; amplxe-cl -collect hotspots -r r000hs1 bin/rome_map2d -i testdata_2d/data8_160/data8_160  -o NULL -k 20 -pixel 4. -iter 10 -pool  30 > testdata_2d/data8_160/emit_test_output_stab.txt     
                
        amplxe-gui r000hs1/*.amp* &

To collect FTrace data
    Linux
        rm -rf r000hs1 ; amplxe-cl -collect hotspots -r r000hs1 bin/rome_map2d -i testdata_2d/data8_160/data8_160 -o NULL -k 20 -pixel 4. -iter 10 -pool 30 -checker_ftrace testdata_2d/data8_160/ftrace.txt > testdata_2d/data8_160/emit_test_output_stab.txt
        amplxe-gui r000hs1/*.amp* &
        
Testing source changes
    1)map2d_original and map2d_new
    map2d_optimizer_base.h has the following line
        static const bool emit_test_output_possible = true;
    and some simple functions
    which causes it to output data that lets the comparison of these to be useful
        testdata_2d/data8_160/emit_test_output.txt 
        testdata_2d/data8_160/emit_test_output_stab.txt
    2)use -datastream_out and -datastream_in
    map2d_old and map3d_old both base on RELION1.4,set data_stream_out_fn variable in RELION ml_optimiser.h,build and run with '--j 1',that will write 
    datastream file to disk,then for map2d(3d) ,build with NO-openmp and set '-pool 1 -datastream_in relion_datastream_name' ,run and the datastream 
    system will compare the result with the input datastream file.this means the RELION with '--j 1' and NO-openmp map2d(3d) with '-pool 1' will produce 
    totaly same result.
    3)compare the result star file or testguidence file
    example:go to testdata_3d/1xck
    run relion_3d.sh and rome_3d.sh,then compare_3d.sh 10,it will compare the 10th star file

Commiting changes locally
    git status
    git add FILES
    git commit -m "COMMENT"


Push to Bitbucket
    git push origin master

    
Pull the latest changes
    git pull --all