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Installation guide

How to install RSMAS InSAR code.

  • Set $RSMASINSAR_HOME in your .bashrc and .bash_profile. You may want to set your variables in an external file as we do in Miami (see example).

  • Create an ~/accounts directory with your data download credentials (for contents see here). If you have access to the RSMAS accounts repo clone it into your /home or $WORK2 directory

git clone https://github.com/geodesymiami/accounts.git $WORK2/accounts ;
  • Go to the area where you want to install the code:
cd $WORK2/code
  • Install the code using the commands below (you need a reasonable recent git version).
bash
module purge
export PATH=/bin
git clone https://github.com/geodesymiami/rsmas_insar.git ;
cd rsmas_insar

git clone https://github.com/insarlab/MintPy.git sources/MintPy ;
git clone https://github.com/isce-framework/isce2.git sources/isce2
git clone https://github.com/geodesymiami/MiNoPy.git sources/MiNoPy 
git clone https://github.com/geodesymiami/geodmod.git sources/geodmod ;
git clone https://github.com/geodesymiami/insarmaps_scripts.git sources/insarmaps_scripts ;
git clone https://github.com/geodesymiami/SSARA.git 3rdparty/SSARA ;
git clone https://github.com/geodesymiami/MimtPy.git sources/MimtPy ;
git clone https://github.com/TACC/launcher.git 3rdparty/launcher ;

########  Done with critical code.  ########
  • #Install your python environment:
cd setup
rm -rf ../3rdparty/miniconda3
#miniconda_version=Miniconda3-latest-MacOSX-x86_64.sh    # python 3.8  - does not seem to work
miniconda_version=Miniconda3-latest-Linux-x86_64.sh
miniconda_version=Miniconda3-py38_4.9.2-Linux-x86_64.sh
wget http://repo.continuum.io/miniconda/$miniconda_version --no-check-certificate -O $miniconda_version #; if ($? != 0) exit; 
chmod 755 $miniconda_version
mkdir -p ../3rdparty
./$miniconda_version -b -p ../3rdparty/miniconda3
../3rdparty/miniconda3/bin/conda config --add channels conda-forge
../3rdparty/miniconda3/bin/conda install --yes --file ../sources/MintPy/docs/requirements.txt
../3rdparty/miniconda3/bin/pip install git+https://github.com/insarlab/PySolid.git
../3rdparty/miniconda3/bin/conda install --yes --file ../sources/MiNoPy/docs/requirements.txt
../3rdparty/miniconda3/bin/conda install --yes --file ../sources/insarmaps_scripts/docs/requirements.txt


export MINOPY_HOME="${PWD%/*}/sources/MiNoPy"
export PATH="${PWD%/*}/3rdparty/miniconda3/bin:/bin"
bash +x $MINOPY_HOME/docs/install
  • #Adding ISCE fixes and copying latest version into miniconda directory
cp -p ../minsar/additions/isce/logging.conf ../3rdparty/miniconda3/lib/python3.*/site-packages/isce/defaults/logging/logging.conf
cp -p ../minsar/additions/isce2/topsStack/FilterAndCoherence.py ../sources/isce2/contrib/stack/topsStack
cp -p ../minsar/additions/isce2/topsStack/fetchOrbit.py ../sources/isce2/contrib/stack/topsStack
cp -p ../minsar/additions/isce2/stripmapStack/prepRawCSK.py ../sources/isce2/contrib/stack/stripmapStack
cp -p ../minsar/additions/isce2/topo.py ../sources/isce2/contrib/stack/stripmapStack    #(uses method isce instead of gdal)

cp -r ../sources/isce2/contrib/stack/* ../3rdparty/miniconda3/share/isce2 

#cp -p ../minsar/additions/mintpy/plot_smallbaselineApp.sh ../sources/MintPy/mintpy/sh/
#cp -p ../minsar/additions/isce/invertMisreg.py ../sources/isce2/contrib/stack/stripmapStack
#cp -p ../minsar/additions/stackStripMap.py $ISCE_STACK/stripmapStack
#cp -p ../minsar/additions/isce/stackSentinel.py $ISCE_STACK/topsStack
  • #create your miniconda3.tar and minsar.tar (removing pkgs saves space, could cause problems with environments) (needed for `install_code_to_tmp.bash)
rm -rf ../3rdparty/miniconda3/pkgs
tar cf ../3rdparty/miniconda3.tar -C ../3rdparty/ miniconda3 &
tar cf ../minsar.tar ../3rdparty/launcher ../minsar ../setup ../sources/MintPy/mintpy ../sources/MimtPy/mimtpy ../sources/MiNoPy/minopy ../sources/MiNoPy/snaphu/bin ../sources/insarmaps_scripts ../sources/isce2/contrib/stack
  • #Source the environment and create aux directories. Install credential files for data download:
./install_credential_files.csh;

source ~/accounts/platforms_defaults.bash;
export RSMASINSAR_HOME=$(dirname $PWD)
source environment.bash;
mkdir -p $SENTINEL_ORBITS $SENTINEL_AUX $OPERATIONS/LOGS;

#Orbits and aux files

This has created directories for the orbits for Sentinel-1 ($SENTINEL_ORBITS), which The can be downloaded using dloadOrbits.py. The IPF calibration files (SENTINEL_AUX) are downloaded from: https://qc.sentinel1.eo.esa.int/aux_cal/ .

#Keep copys in the case your $SCRATCHDIR gets purged

The $SENTINEL_ORBITS and miniconda3.tar are located on $SCRATCHDIR which gets purged every couple of weeks. minsarApp.bash uses $RSMASINSAR_HOME/3rdparty/miniconda3.tarand $WORKDIR/S1orbits.tar if files have been purged.

Next steps and possible problems

  • To check your installation, run the testdata as explained here. You need to have the testdata in your $TESTDATA_ISCE directory.
ls  $TESTDATA_ISCE
unittestGalapagosSenDT128  unittestKrakatoaSenAT171

ll $TESTDATA_ISCE/unittestGalapagosSenDT128/SLC/
total 17528848
-rw-rw--w-+ 1 famelung insarlab        782 Jan 17 17:10 files.csv
-rw-rw--w-+ 1 famelung insarlab        644 Jan 17 17:13 log
-rw-rw--w-+ 1 famelung insarlab        777 Jan 17 17:10 new_files.csv
-rw-rw-rw-+ 1 famelung insarlab 2382498740 Jan 17 17:08 S1A_IW_SLC__1SSV_20160605T114943_20160605T115018_011575_011AEF_98EA.zip
-rw-rw-rw-+ 1 famelung insarlab 2596328889 Jan 17 17:10 S1A_IW_SLC__1SSV_20160629T114944_20160629T115019_011925_0125EE_41E2.zip
-rw-rw-rw-+ 1 famelung insarlab 2538509057 Jan 17 17:08 S1A_IW_SLC__1SSV_20160711T114945_20160711T115020_012100_012BB7_AD1C.zip
-rw-rw-rw-+ 1 famelung insarlab 2658073568 Jan 17 17:08 S1A_IW_SLC__1SSV_20160723T114945_20160723T115021_012275_01315B_4BF1.zip
-rw-rw-rw-+ 1 famelung insarlab 2619635729 Jan 17 17:09 S1A_IW_SLC__1SSV_20160804T114946_20160804T115022_012450_01372F_C4E2.zip
-rw-rw-rw-+ 1 famelung insarlab 2576452600 Jan 17 17:09 S1A_IW_SLC__1SSV_20160816T114947_20160816T115022_012625_013CEA_AD2C.zip
-rw-rw-rw-+ 1 famelung insarlab 2578011015 Jan 17 17:09 S1A_IW_SLC__1SSV_20160828T114947_20160828T115023_012800_0142DE_D868.zip
drwxrws-w-+ 2 famelung insarlab       4096 Jan 17 16:58 test
//login4/nethome/dwg11/insarlab/TESTDATA_ISCE[59]
  • For possible problems, check here.

*. Set-up in Miami