16-Oct-2006
heimbach@mit.edu, cnh@mit.edu

Brief instructions for building and running

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Exp. 1: For advect diffuse test (injects dye every timestep at one point and advects with a fixed flow field)
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 cd build
 rm -fr *
 ../../../tools/genmake2 -mods  ../code
 make depend
 make 
 ln -s ../input/* .
 ln -s ../input_fields/* .
 ./mitgcmuv >& output

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Exp. 2a: Adjoint of advect-diffuse: 
-------  --->>> 1 tile per cube face (32x32), single-processor <<<---

 cd build_ad/
 rm -fr *
 \cp -f ../code_ad/topol_32x32/* .
 ../../../tools/genmake2 -mods ../code_ad
### ../../../../MITgcm/tools/genmake2 -rootdir ../../../../MITgcm -mods ../code_ad
 make depend
 make adtaf
 make adall

 ln -s ../input_ad/* .
 ln -s ../input_fields/* .
 ./mitgcmuv_ad >! output_adm.txt &


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Exp. 2b: Adjoint of advect-diffuse: 
-------  --->>> 4 tiles per cube face (16x16), single-processor <<<---

 cd build_ad/
 rm -fr *
 \cp -f ../code_ad/topol_16x16/* .
 ../../../tools/genmake2 -mods ../code_ad
### ../../../../MITgcm/tools/genmake2 -rootdir ../../../../MITgcm -mods ../code_ad
 make depend
 make adtaf
 make adall

 ln -s ../input_ad/* .
 ln -s ../input/*.bin .
 ln -s ../input/*.mitgrid .
 ./mitgcmuv_ad >! output_adm.txt &

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Exp. 2c: Adjoint of advect-diffuse: 
-------  --->>> 4 tiles per cube face (16x16), 4-processor MPI <<<---

 cd build_ad/
 rm -fr *
 \cp -f ../code_ad/topol_16x16/* .
 \cp -f SIZE.h_mpi SIZE.h
 ../../../tools/genmake2 -mpi -mods ../code_ad
### ../../../../MITgcm/tools/genmake2 -rootdir ../../../../MITgcm -mpi -mods ../code_ad
 make depend
 make adtaf
 make adall

 ln -s ../input_ad/* .
 ln -s ../input/*.bin .
 ln -s ../input/*.mitgrid .
 mpirun -np 4 ./mitgcmuv_ad

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Exp. 4: Adjoint of full code:
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 cd build_ad_full/
 rm -fr *
 ../../../tools/genmake2 -mods ../code_ad_full
 make depend
 make adtaf
 make adall

 ln -s ../input_ad_full/* .
 ./mitgcmuv_ad >! output_adm.txt &

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Exp. 5: TLM of full code:
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 cd build_ad_full/
 rm -fr *
 ../../../tools/genmake2 -mods ../code_ad_full
 make depend
 make ftltaf
 make ftlall

 ln -s ../input_ad_full/* .
 ./mitgcmuv_ftl >! output_tlm.txt &