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Installation guide

How to install RSMAS InSAR code.

  • Set the required environment variables ($RSMASINSAR_HOME, $JOBSCHEDULER, $QUEUENAME, $SCRATCHDIR) in your .bashrc and .bash_profile. There are several other customizable environment variables. The defaults are given here. 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 directtory.

git clone https://github.com/geodesymiami/accounts.git ~/accounts ;
  • Go to the area where you want to install the code:
cd ~/test/test1
  • Install the code using the commands below (you need a reasonable recent git version (the default on pegasus is too old, get a local version, or use an old rsmas_insar version).
bash
[ -f ~/local_git/miniconda3/bin/git ] && alias git=~/local_git/miniconda3/bin/git	

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/geodesymiami/geodmod.git sources/geodmod;
git clone https://github.com/bakerunavco/SSARA.git 3rdparty/SSARA
git clone https://github.com/yunjunz/pyaps3.git 3rdparty/PyAPS/pyaps3
git clone https://github.com/geodesymiami/MimtPy.git sources/MimtPy ;
git clone https://github.com/TACC/launcher.git 3rdparty/launcher ;

git clone https://github.com/isce-framework/isce2.git 3rdparty/isce2
mkdir -p sources/isceStack
cp -r 3rdparty/isce2/contrib/stack/topsStack sources/isceStack
cp -r 3rdparty/isce2/contrib/stack/stripmapStack sources/isceStack
rm -rf 3rdparty/isce2
########  Done with critical code.  ########

# Install tippecanoe for insarmaps (need gcc 4.9.1 or younger):
module load gcc/4.9.4
git clone https://github.com/mapbox/tippecanoe.git 3rdparty/tippecanoe
make -C 3rdparty/tippecanoe install PREFIX=3rdparty/tippecanoe
  • Install your python environment:
cd setup
#cd ../3rdparty; ln -s /nethome/famelung/MINICONDA3_GOOD miniconda3; cd ..; 
#../3rdparty/miniconda3/bin/conda env create -f ../docs/conda_env.yml; #works but creates minsar environment, not base
rm -r ../3rdparty/miniconda3
miniconda_version=Miniconda3-4.5.12-MacOSX-x86_64.sh
miniconda_version=Miniconda3-4.5.12-Linux-x86_64.sh
miniconda_version=Miniconda3-4.6.14-MacOSX-x86_64.sh
miniconda_version=Miniconda3-4.6.14-Linux-x86_64.sh
wget http://repo.continuum.io/miniconda/$miniconda_version --no-check-certificate #; if ($? != 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 isce2 -c conda-forge --yes

../3rdparty/miniconda3/bin/conda install --yes --file ../sources/MintPy/docs/conda.txt
../3rdparty/miniconda3/bin/conda install --yes --file ../docs/conda.txt
../3rdparty/miniconda3/bin/pip install --upgrade pip
../3rdparty/miniconda3/bin/pip install opencv-python
../3rdparty/miniconda3/bin/pip install geocoder
#../3rdparty/miniconda3/bin/pip install git+https://github.com/matplotlib/basemap.git#egg=mpl_toolkits #needed for ARIA products
../3rdparty/miniconda3/bin/conda install basemap python=3.7 --yes
../3rdparty/miniconda3/bin/pip install git+https://github.com/tylere/pykml.git
  • Source the environment and create aux directories. Install credential files for data download:
source ~/accounts/platforms_defaults.bash;
source environment.bash;
mkdir -p $SENTINEL_ORBITS $SENTINEL_AUX $OPERATIONS/LOGS;
$RSMASINSAR_HOME/setup/install_credential_files.csh;

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/ .

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