AMSTer Installation Errors:

I did the installation of AMSTre distribution with the provided bash file. However, I am still facing state variables path missing in bashrc (although these paths are present in bashrc file). Similarly for 3rf party software and Specific system-based functions, I am getting directory missing warning.

Testing components for AMSTer Software

1) STATE VARIABLES in bashrc or bash_profile

--> PATHGNU: passed Value : export PATHGNU=/usr/bin export PATHGNU=$/usr/bin/gnuplot export PATHGNU=/usr/bin export PATHGNU=$/usr/bin/gnuplot PATHGNU not /usr/bin as expected for Linux. Please check --> PATHFIJI: passed Value : export PATHFIJI=$/home/contec/Softwares/Fiji.app/ export PATHFIJI=$/home/contec/Softwares/Fiji.app/ --> PATHCONV: missing --> PATHTOCPXFIDDLE: passed Value : export PATHTOCPXFIDDLE=$/home/contec/Softwares/EXEC/ export PATHTOCPXFIDDLE=$/home/contec/Softwares/EXEC/ --> PATH_1650: missing --> PATH_3600: missing --> PATH_3601: missing --> PATH_3602: missing --> PATH_DataSAR: missing --> PATH_SCRIPTS: missing --> S1_ORBITS_DIR: passed Value : export S1_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/S1_ORB export S1_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/S1_ORB --> ENVISAT_PRECISES_ORBITS_DIR: passed Value : export ENVISAT_PRECISES_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/ENV_ORB export ENVISAT_PRECISES_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/ENV_ORB --> EARTH_GRAVITATIONAL_MODELS_DIR: passed Value : export EARTH_GRAVITATIONAL_MODELS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/EGM export EARTH_GRAVITATIONAL_MODELS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/EGM --> EXTERNAL_DEMS_DIR: passed Value : export EXTERNAL_DEMS_DIR=${PATH_DataSAR}/DEMS export EXTERNAL_DEMS_DIR=${PATH_DataSAR}/DEMS EXTERNAL_DEMS_DIR is not mandatrory and actually not used with AMSTer Toolbox

2) AMSTer Software main components

Directories in $PATH in bashrc: dirname: missing operand Try 'dirname --help' for more information. ./Check_Installation.sh: line 459: $/usr/bin/gnuplot/grep: No such file or directory --> AMSTerEngine in $PATH: failed
dirname: missing operand Try 'dirname --help' for more information. ./Check_Installation.sh: line 469: $/usr/bin/gnuplot/grep: No such file or directory --> AMSTer Software SCRIPTS in $PATH: failed
./Check_Installation.sh: line 568: $/usr/bin/gnuplot/grep: No such file or directory --> /SAR/EXEC in $PATH: failed

Executables and versions: --> AMSTerEngine failed: missing at least initInSAR --> AMSTerEngine MSBAStools failed: missing at least getLineThroughStack dirname: missing operand Try 'dirname --help' for more information. --> AMSTer Software SCRIPTS failed: missing at least FUNCTIONS_FOR_MT.sh is in:

3) Third party software

--> parallel: passed Version GNU parallel 20161222 (in: /usr/bin) --> gmt: passed Version 6.0.0 (in: /usr/bin) --> gnuplot: passed Version gnuplot 5.4 patchlevel 1 (in: /usr/local/bin) Gnu version not in $PATHGNU? Please check! --> bc : passed Version bc 1.07.1 (in: /usr/bin) --> convert: passed Version Version: ImageMagick 6.9.10-23 Q16 x86_64 20190101 https://imagemagick.org (in: /usr/bin) --> gdalinfo: passed Version GDAL 3.6.2, released 2023/01/02 (in: /home/contec/Softwares/anaconda3/bin) ./Check_Installation.sh: line 226: $/usr/bin/gnuplot/grep: No such file or directory --> snaphu: passed Version (in: /usr/local/bin/snaphu) ./Check_Installation.sh: line 231: $/usr/bin/gnuplot/grep: No such file or directory --> cpxfiddle: passed Version (in: /home/contec/SAR/EXEC/cpxfiddle) --> wget: passed Version GNU Wget 1.20.3 built on linux-gnu. (in: /home/contec/Softwares/anaconda3/bin) --> curl: passed Version curl 8.5.0 (x86_64-conda-linux-gnu) libcurl/8.5.0 OpenSSL/3.1.5 zlib/1.2.13 libssh2/1.10.0 nghttp2/1.57.0 (in: /home/contec/Softwares/anaconda3/bin)

gsed    has more than one GNU version ? - pelase check: 
/bin/gsed
/usr/bin/gsed
 sed has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory sed: passed Version sed (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory sed: passed Version sed (in: /usr/bin). same as GNU version

gawk    has more than one GNU version ? - pelase check: 
/bin/gawk
/usr/bin/gawk
 awk has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory awk: passed Version awk (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory awk: passed Version awk (in: /usr/bin). same as GNU version

ggrep   has more than one GNU version ? - pelase check: 
/bin/ggrep
/usr/bin/ggrep
 grep has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory grep: passed Version grep (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory grep: passed Version grep (in: /usr/bin). same as GNU version

gseq    has more than one GNU version ? - pelase check: 
/bin/gseq
/usr/bin/gseq
 seq has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory seq: passed Version seq (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory seq: passed Version seq (in: /usr/bin). same as GNU version

gfind   has more than one GNU version ? - pelase check: 
/bin/gfind
/usr/bin/gfind
 find has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory find: passed Version find (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory find: passed Version find (in: /usr/bin). same as GNU version

gstat   has more than one GNU version ? - pelase check: 
/bin/gstat
/usr/bin/gstat
 stat has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory stat: passed Version stat (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory stat: passed Version stat (in: /usr/bin). same as GNU version

gdate   has more than one GNU version ? - pelase check: 
/bin/gdate
/usr/bin/gdate
 date has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory date: passed Version date (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory date: passed Version date (in: /usr/bin). same as GNU version

guniq   has more than one GNU version ? - pelase check: 
/bin/guniq
/usr/bin/guniq
 uniq has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory uniq: passed Version uniq (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory uniq: passed Version uniq (in: /usr/bin). same as GNU version

greadlink   has more than one GNU version ? - pelase check: 
/bin/greadlink
/usr/bin/greadlink
 readlink has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory readlink: passed Version readlink (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory readlink: passed Version readlink (in: /usr/bin). same as GNU version

gxargs  has more than one GNU version ? - pelase check: 
/bin/gxargs
/usr/bin/gxargs
 xargs has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory xargs: passed Version xargs (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory xargs: passed Version xargs (in: /usr/bin). same as GNU version

gdu has more than one GNU version ? - pelase check: 
/bin/gdu
/usr/bin/gdu
 du has more than one version:

./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory du: passed Version du (in: /bin). same as GNU version ./Check_Installation.sh: line 164: $/usr/bin/gnuplot/gsed: No such file or directory ./Check_Installation.sh: line 165: $/usr/bin/gnuplot/gsed: No such file or directory du: passed Version du (in: /usr/bin). same as GNU version

--> python: passed Need V3 for AMSTer. Python 3.11.6 found in /opt/local/bin Warning: a python exist in a default directory that is not the expected /opt/local/bin, i.e.:
/bin/python /home/contec/Softwares/anaconda3/bin/python /usr/bin/python --> python3: passed Python 3.11.6 required for AMSTer found in /opt/local/bin Warning: a python3 exist in a default directory that is not the expected /opt/local/bin, i.e.:
/bin/python3 /home/contec/Softwares/anaconda3/bin/python3 /usr/bin/python3

--> Check modules for /opt/local/bin/python
numpy: passed Version 1.26.4 scipy: passed Version 1.11.4 matplotlib: passed Version 3.8.0 utm: passed Version nr is missing though
osgeo: passed Version 3.6.2 (gdal) pip: passed Version 24.2 networkx: passed Version 3.1 PyQt6: missing Traceback (most recent call last): File "", line 1, in ImportError: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.35' not found (required by /home/contec/Softwares/anaconda3/lib/python3.11/site-packages/PyQt6/QtGui.abi3.so) opencv: missing

4) Specific system-based functions

Testing libraries for MSBAS, AMSTerEngine etc... ./Check_Installation.sh: line 373: $/usr/bin/gnuplot/grep: No such file or directory --> clang: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libfftw3-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libfftw3-long3: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libfftw3-single3: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libgeotiff-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libtiff-dev: failed
./Check_Installation.sh: line 373: $/usr/bin/gnuplot/grep: No such file or directory --> libxml2: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libxml2-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> liblapack-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libomp-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libopenblas-dev: failed
./Check_Installation.sh: line 373: $/usr/bin/gnuplot/grep: No such file or directory --> mpich: failed
./Check_Installation.sh: line 799: $/usr/bin/gnuplot/grep: No such file or directory ./Check_Installation.sh: line 799: $/usr/bin/gnuplot/gawk: No such file or directory --> ImageMagick : passed Version ./Check_Installation.sh: line 373: $/usr/bin/gnuplot/grep: No such file or directory --> gdal: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libgdal-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libhdf5-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libnetcdf-dev: failed
./Check_Installation.sh: line 356: $/usr/bin/gnuplot/grep: No such file or directory --> libgsl-dev: failed
./Check_Installation.sh: line 373: $/usr/bin/gnuplot/grep: No such file or directory --> gfortran: failed
./Check_Installation.sh: line 818: $/usr/bin/gnuplot/grep: No such file or directory ./Check_Installation.sh: line 818: $/usr/bin/gnuplot/gawk: No such file or directory --> g++: passed Version

Testing specific Linux features: --> x-terminal-emulator: passed Version (in: /usr/bin/x-terminal-emulator) --> espeak: passed Version (in: /usr/bin/espeak) --> OPENBLAS_NUM_THREADS=: passed Value : export OPENBLAS_NUM_THREADS=1 export OPENBLAS_NUM_THREADS=1

5) Testing access to mandatory disk/directories:

--> /SAR_AUX_FILES: unreachable ! --> /SAR_AUX_FILES/DEM: unreachable ! --> /SAR_AUX_FILES/ORBITS: unreachable ! --> /SAR_AUX_FILES/ORBITS/ENV_ORB: unreachable ! --> /SAR_AUX_FILES/ORBITS/ENV_ORB/vor_gdr_d: unreachable ! --> /SAR_AUX_FILES/ORBITS/ERS: unreachable ! --> /SAR_AUX_FILES/ORBITS/S1_ORB: unreachable ! --> /SAR_AUX_FILES/ORBITS/S1_ORB/AUX_POEORB: unreachable ! --> /SAR_AUX_FILES/ORBITS/S1_ORB/AUX_RESORB: unreachable ! --> /SAR_AUX_FILES/Param_files: unreachable ! --> /SAR_AUX_FILES/EGM/EGM96: unreachable !

6) Testing some configs in mandatory files (Linux only):

ImageMagick config file contains read & write rights for PS: OK ImageMagick config file contains read & write rights for EPS: OK ImageMagick config file contains height value up to 32KP: OK ImageMagick config file contains width value up to 32KP: OK ImageMagick config file contains disk value up to 8GiB: OK

7) Testing usefull stuffs though not mandatory:

--> Gitkraken: passed Version 10.1.1 --> GIMP: passed Version GNU Image Manipulation Program version 2.10.38 --> JAVA: passed Version java.version = 11.0.24 --> ImageJ-Fiji : failed, though it is not mnadatory --> ImageJ-Fiji: failed
--> QGIS: passed Version QGIS 3.10.4-A Coruña 'A Coruña' (exported) QGIS : You may want to install the following plugins (to do from within QGIS):

point sampling tool
PointConnetor
Profile tool
Qdraw
QuickMapServices
RasterDataPlotting (may require to install python first)
Serval
Temporal/Spectal Profile Tool
Value Tool

// As final notes: if you intend to run cron jobs, // 1) ensure that the following lines are commented in your .bashrc (if any) !! :

If not running interactively, don't do anything
```
            case hB in
                *i*) ;;
                *) return;;
            esac
```
// 2) ensure that the following state variable are exported at the beginning or the crontab !! : export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/cuda/bin export LD_LIBRARY_PATH=:/usr/local/cuda/lib64 export LD_INCLUDE_PATH=:/usr/local/cuda/include export LD_LIBRARY_PATH=:/usr/local/cuda/extras/CUPTI/lib64 export PATH="/home/contec/Softwares/anaconda3/bin:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/stripmapStack:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/topsStack:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/stripmapStack:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/topsStack:$PATH" export PATH="/home/contec/Softwares/StaMPS/StaMPS_CONFIG.bash:$PATH" export PATH="home/contec/Softwares/TRAIN/APS_CONFIG.sh:$PATH" export GMTSAR=/home/contec/Softwares/GMTSAR export PATH=$GMTSAR/bin:"$PATH" export isbas=/home/contec/Softwares/isbas/ export PATH=isbas:"$PATH" export PATHGNU=/usr/bin export JAVA_HOME=$/usr/lib/jvm/java-11-openjdk-amd64 export PATHFIJI=$/home/contec/Softwares/Fiji.app/ export PATHTOCPXFIDDLE=$/home/contec/Softwares/EXEC/ export PATHGNU=$/usr/bin/gnuplot export OPENBLAS_NUM_THREADS=1 export PATH_HOMEDATA=/media/hdd3/AMSTer/PATH_HOMEDATA export PATH_SynoData=/media/hdd3/AMSTer/PATH_SynoData export PATH_3610=/media/hdd3/AMSTer/PATH_1650 export PATH_3610=/media/hdd3/AMSTer/PATH_3600 export PATH_3610=/media/hdd3/AMSTer/PATH_3601 export PATH_3610=/media/hdd3/AMSTer/PATH_3602 export PATH_1660=/media/hdd3/AMSTer/PATH_1660 export PATH_3610=/media/hdd3/AMSTer/PATH_DataSAR export PATH_3610=/media/hdd3/AMSTer/PATH_SCRIPTS export EXTERNAL_DEMS_DIR=${PATH_DataSAR}/DEMS export EARTH_GRAVITATIONAL_MODELS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/EGM export ENVISAT_PRECISES_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/ENV_ORB export S1_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/S1_ORB export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/usr/local/cuda/bin export LD_LIBRARY_PATH=:/usr/local/cuda/lib64 export LD_INCLUDE_PATH=:/usr/local/cuda/include export LD_LIBRARY_PATH=:/usr/local/cuda/extras/CUPTI/lib64 export PATH="/home/contec/Softwares/anaconda3/bin:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/stripmapStack:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/topsStack:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/stripmapStack:$PATH" export PATH="/home/contec/Softwares/ISCE/isce2/contrib/stack/topsStack:$PATH" export PATH="/home/contec/Softwares/StaMPS/StaMPS_CONFIG.bash:$PATH" export PATH="home/contec/Softwares/TRAIN/APS_CONFIG.sh:$PATH" export GMTSAR=/home/contec/Softwares/GMTSAR export PATH=$GMTSAR/bin:"$PATH" export isbas=/home/contec/Softwares/isbas/ export PATH=isbas:"$PATH" export PATHGNU=/usr/bin export JAVA_HOME=$/usr/lib/jvm/java-11-openjdk-amd64 export PATHFIJI=$/home/contec/Softwares/Fiji.app/ export PATHTOCPXFIDDLE=$/home/contec/Softwares/EXEC/ export PATHGNU=$/usr/bin/gnuplot export OPENBLAS_NUM_THREADS=1 export PATH_HOMEDATA=/media/hdd3/AMSTer/PATH_HOMEDATA export PATH_SynoData=/media/hdd3/AMSTer/PATH_SynoData export PATH_3610=/media/hdd3/AMSTer/PATH_1650 export PATH_3610=/media/hdd3/AMSTer/PATH_3600 export PATH_3610=/media/hdd3/AMSTer/PATH_3601 export PATH_3610=/media/hdd3/AMSTer/PATH_3602 export PATH_1660=/media/hdd3/AMSTer/PATH_1660 export PATH_3610=/media/hdd3/AMSTer/PATH_DataSAR export PATH_3610=/media/hdd3/AMSTer/PATH_SCRIPTS export EXTERNAL_DEMS_DIR=${PATH_DataSAR}/DEMS export EARTH_GRAVITATIONAL_MODELS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/EGM export ENVISAT_PRECISES_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/ENV_ORB export S1_ORBITS_DIR=${PATH_DataSAR}/SAR_AUX_FILES/ORBITS/S1_ORB

8) Check the .netrc file for accessing S1 orbits

You already have a .netrc file in your home directroy
And it seems to have a line with login and password to dataspace.copernicus.eu Nevertheless it the download of S1 orbits fails, double check your .netrc file contains a line as follow: machine identity.dataspace.copernicus.eu login password

AMSTerUsers / AMSTer_Distribution