Installation

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 ~/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
if [ "$(uname)" == "Linux" ]; then
   module purge
   export PATH=/bin
fi
git clone https://github.com/geodesymiami/rsmas_insar.git ;
cd rsmas_insar

git clone https://github.com/insarlab/MintPy.git tools/MintPy ;
git clone https://github.com/isce-framework/isce2.git tools/isce2
git clone https://github.com/insarlab/MiaplPy.git tools/MiaplPy 
git clone https://github.com/geodesymiami/geodmod.git tools/geodmod ;
git clone https://github.com/geodesymiami/insarmaps_scripts.git tools/insarmaps_scripts ;
git clone https://github.com/geodesymiami/SSARA.git tools/SSARA ;
git clone https://github.com/geodesymiami/MimtPy.git tools/MimtPy ;
git clone https://github.com/TACC/launcher.git tools/launcher ;
########  Done with critical code.  ########

############################################
### Install your python environment: #######
cd setup
rm -rf ../tools/miniconda3
miniconda_version=Miniconda3-latest-Linux-x86_64.sh
if [ "$(uname)" == "Darwin" ]; then miniconda_version=Miniconda3-latest-MacOSX-arm64.sh ; fi
wget http://repo.continuum.io/miniconda/$miniconda_version --no-check-certificate -O $miniconda_version #; if ($? != 0) exit; 
chmod 755 $miniconda_version
bash ./$miniconda_version -b -p ../tools/miniconda3
../tools/miniconda3/bin/conda install -n base conda-libmamba-solver --yes
../tools/miniconda3/bin/conda config --set solver libmamba
../tools/miniconda3/bin/conda config --add channels conda-forge
../tools/miniconda3/bin/conda install --yes --file ../tools/MintPy/requirements.txt
sed -i.bak "s|isce2|#isce2|g" ../tools/MiaplPy/docs/requirements.txt
../tools/miniconda3/bin/conda install --yes --file ../tools/MiaplPy/docs/requirements.txt

../tools/miniconda3/bin/conda install isce2 -c conda-forge --yes 
../tools/miniconda3/bin/conda install --yes --file ../minsar/requirements.txt
../tools/miniconda3/bin/conda install --yes --file ../tools/insarmaps_scripts/requirements.txt
../tools/miniconda3/bin/conda install --yes --file ../tools/MimtPy/mimtpy/docs/requirements.txt 
# faster:  ../tools/miniconda3/bin/conda install --yes --file  ../tools/MintPy/requirements.txt  isce2 -c conda-forge (but needs the memory of a node)
############################################
### Compile MiaplPy and install SNAPHU #####
export MIAPLPY_HOME="${PWD%/*}/tools/MiaplPy"
cd $MIAPLPY_HOME/miaplpy/lib;
 ../../../../tools/miniconda3/bin/python  setup.py

cd $MIAPLPY_HOME;
wget --no-check-certificate  https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/snaphu-v2.0.4.tar.gz
tar -xvf snaphu-v2.0.4.tar.gz
mv snaphu-v2.0.4 snaphu;
rm snaphu-v2.0.4.tar.gz;
sed -i.bak 's/\/usr\/local/$(MIAPLPY_HOME)\/snaphu/g' snaphu/src/Makefile
cd snaphu/src; make

############################################
cd ../../../../setup/
### Adding not-commited MintPy fixes
cp -p ../minsar/additions/mintpy/save_hdfeos5.py ../tools/MintPy/src/mintpy/
cp -p ../minsar/additions/mintpy/cli/save_hdfeos5.py ../tools/MintPy/src/mintpy/cli/

### Adding ISCE fixes and copying checked-out ISCE version (the latest) into miniconda directory ###
cp -p ../minsar/additions/isce/logging.conf ../tools/miniconda3/lib/python3.?/site-packages/isce/defaults/logging/logging.conf
cp -p ../minsar/additions/isce2/topsStack/FilterAndCoherence.py ../tools/isce2/contrib/stack/topsStack
cp -p ../minsar/additions/isce2/stripmapStack/prepRawCSK.py ../tools/isce2/contrib/stack/stripmapStack
cp -p ../minsar/additions/isce2/stripmapStack/unpackFrame_TSX.py ../tools/isce2/contrib/stack/stripmapStack
cp -p ../minsar/additions/isce2/DemStitcher.py ../tools/isce2/contrib/demUtils/demstitcher
#cp -p ../minsar/additions/isce2/topo.py ../tools/isce2/contrib/stack/stripmapStack                           #(uses method isce instead of gdal)
cp -p ../minsar/additions/isce2/VRTManager.py ../tools/isce2/contrib/stack/topsStack                          # 1/23 np.int issue
cp -p ../minsar/additions/isce2/TOPSSwathSLCProduct.py ../tools/isce2/components/isceobj/Sensor/TOPS          # 1/23 np.int issue
cp -p ../minsar/additions/isce2/Sentinel1.py  ../tools/isce2/components/isceobj/Sensor/TOPS                   # 2/23 np.int issue
cp -p ../minsar/additions/isce2/stripmapStack/cropFrame.py ../tools/isce2/contrib/stack/stripmapStack         # 1/23 np.int issue

### Copying ISCE fixes into miniconda directory ###
cp -r ../tools/isce2/contrib/stack/* ../tools/miniconda3/share/isce2
cp -r ../tools/isce2/components/isceobj/Sensor/TOPS ../tools/miniconda3/share/isce2 
cp ../tools/isce2/components/isceobj/Sensor/TOPS/TOPSSwathSLCProduct.py ../tools/miniconda3/lib/python3.?/site-packages/isce/components/isceobj/Sensor/TOPS
cp ../minsar/additions/isce2/Sentinel1.py  ../tools/miniconda3/lib/python3.?/site-packages/isce/components/isceobj/Sensor/TOPS/    # 4/23 np.int issue, not clear why need to copy
cp ../tools/isce2/contrib/demUtils/demstitcher/DemStitcher.py  ../tools/miniconda3/lib/python3.?/site-packages/isce/components/contrib/demUtils 

############################################
### Source the environment and create aux directories. Install credential files for data download: ###
./install_credential_files.bash;

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

############################################
### create your `miniconda3.tar` and `minsar.tar`  (removing `pkgs` saves space, could cause problems with environments) (needed for `install_code_to_tmp.bash) ###
tar cf ../minsar.tar ../tools/launcher ../minsar ../setup ../tools/MintPy/src ../tools/MimtPy/mimtpy ../tools/MiaplPy/miaplpy ../tools/MiaplPy/snaphu/bin ../tools/insarmaps_scripts ../tools/isce2/contrib/stack
rm -rf ../tools/miniconda3/pkgs
tar cf ../tools/miniconda3.tar -C ../tools/ miniconda3 
echo "Installation DONE"

#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/tools/miniconda3.tarand$WORKDIR/S1orbits.tarif 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.

Installation guide#

#Orbits and aux files#

#Keep copys in the case your $SCRATCHDIR gets purged#

Next steps and possible problems#

*. Set-up in Miami#

#Keep copys in the case your `$SCRATCHDIR` gets purged#

*. Set-up in Miami #