SDP Toolkit Installation Error in SeaDAS 8.2.0 Build from source code

[reema_mathew]

------------------------------------------------------------------------------
Toolkit Installation starting at Wednesday 08 February 2023 09:31:50 AM IST

Note: If your system is CentOS linux, you may need -fPIC compilation flag.
If that is the case you better quit here (using Ctrl-c) and re-start
installation with additional arguments -cc_flags "-fPIC" and/or
-cpp_flags "-fPIC" and -fc_flags "-fPIC" if you have not done so.
You may type bin/INSTALL -h to see notes on how to add additional
compilation flags
The default Toolkit LINUX installation for this machine is 64 bit. Other
available Toolkit LINUX installation mode is 32 bit Mode




Installing in (64 bit) mode...


./makefile.cpp
...file modified
include/makefile.cpp
...file modified
include/CUC/makefile.cpp
...file modified
include/DCW/makefile.cpp
...file modified
include/FF/makefile.cpp
...file modified
include/FW/makefile.cpp
...file modified
src/makefile.cpp
...file modified
src/AA/makefile.cpp
...file modified
src/AA/DCW/makefile.cpp
...file modified
src/AA/VPF/makefile.cpp
...file modified
src/AA/freeform/makefile.cpp
...file modified
src/AA/generic/makefile.cpp
...file modified
src/CBP/makefile.cpp
...file modified
src/CSC/makefile.cpp
...file modified
src/CUC/makefile.cpp
...file modified
src/CUC/ODL/makefile.cpp
...file modified
src/CUC/UDUNITS/makefile.cpp
...file modified
src/EPH/makefile.cpp
...file modified
src/EPH/orbsim/makefile.cpp
...file modified
src/EPH/gbadsim/makefile.cpp
...file modified
src/GCT/makefile.cpp
...file modified
src/GCT/freeware/makefile.cpp
...file modified
src/IO/makefile.cpp
...file modified
src/IO/GEN/makefile.cpp
...file modified
src/IO/L0/makefile.cpp
...file modified
src/IO/L0/L0sim/makefile.cpp
...file modified
src/MEM/makefile.cpp
...file modified
src/MET/makefile.cpp
...file modified
src/MET/support/makefile.cpp
...file modified
src/MET/tools/makefile.cpp
...file modified
src/PC/makefile.cpp
...file modified
src/SMF/makefile.cpp
...file modified
src/TD/makefile.cpp
...file modified
src/DEM/makefile.cpp
...file modified
src/TSF/makefile.cpp
...file modified
src/XML/makefile.cpp
...file modified
src/XML/xml/Makefile.cpp
...file modified
src/XML/xsl/Makefile.cpp
...file modified
message/makefile.cpp
...file modified

Setting ZLIB home directory to: /home/reema/Desktop/ocssw_src/opt

Setting JPEG home directory to: /home/reema/Desktop/ocssw_src/opt

Setting SZIP home directory to: /home/reema/Desktop/ocssw_src/opt

Running the SZIP (with encoding) Installation Script ...
Setting LD_LIBRARY_PATH to /home/reema/Desktop/ocssw_src/opt/lib

Setting HDF home directory to: /home/reema/Desktop/ocssw_src/opt


***** Copying JPEG, ZLIB and SZIP header and library *********

********** files to relevant directories in HDF. **********


Setting HDF5 home directory to: /home/reema/Desktop/ocssw_src/opt
Adding /home/reema/Desktop/ocssw_src/opt/lib to LD_LIBRARY_PATH

Setting HDFEOS home directory to: /home/reema/Desktop/ocssw_src/opt/EOS

Setting HDFEOS5 home directory to: /home/reema/Desktop/ocssw_src/opt/EOS

Running the Toolkit Installation Script ...



Running the Toolkit Installation Script without AA Tool.
bin/INSTALL: 3237: /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/INSTALL-Toolkit: not found
bin/INSTALL: 3239: cannot create /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/linux64/pgs-env.csh: Directory nonexistent



INSTALL: Error: The Toolkit Installation Script failed or had errors.
SDP Toolkit installation cancelled
Unknown error encountered installing sdptk
-----------------------------------------------------------------------------------

I'm not able to debug this error. Is there any solution or workaround for this problem?

[reema_mathew]

Additional details:

OS: Ubuntu 22.04
gcc/g++/gfortran: 11.3.0
cmake: 3.22.1

[gfireman]

Did you perhaps run this twice, in parallel windows or processes? Our installation script will unpack source code directories from the tar file, run the installation, then delete source directories - unless it's run in debug mode, triggered by

Code: Select all

export OCSSW_DEBUG=1

What happens when you try to build the SDP Toolkit by itself?

Code: Select all

cd $LIB3_DIR/src/sdptk
./BuildIt.py 2>&1|tee build.log

[reema_mathew]

I didn't run this parallely. When error comes, I've run it again in the same window.
It was not run in debug mode. I used 'export OCSSW_DEBUG=0'.

When trying to build the toolkit by itself, this is what comes:

patching file bin/INSTALL
patching file bin/INSTALL-Toolkit
patching file include/libxml/Makefile
patching file include/libxml/xmlversion.h
patching file include/PGS_SMF.f
patching file include/PGS_SMF.h
patching file src/EPH/orbsim/makefile
patching file src/XML/xml/Makefile
patching file src/EPH/PGS_EPH_EphemAttit.c
patching file src/EPH/PGS_EPH_EphAtt_unInterpolate.c
patching file src/CUC/UDUNITS/limits.h

Toolkit Installation starting at Wednesday 15 February 2023 09:44:23 AM IST

Note: If your system is CentOS linux, you may need -fPIC compilation flag.
If that is the case you better quit here (using Ctrl-c) and re-start
installation with additional arguments -cc_flags "-fPIC" and/or
-cpp_flags "-fPIC" and -fc_flags "-fPIC" if you have not done so.
You may type bin/INSTALL -h to see notes on how to add additional
compilation flags
The default Toolkit LINUX installation for this machine is 64 bit. Other
available Toolkit LINUX installation mode is 32 bit Mode




Installing in (64 bit) mode...


./makefile.cpp
...file modified
include/makefile.cpp
...file modified
include/CUC/makefile.cpp
...file modified
include/DCW/makefile.cpp
...file modified
include/FF/makefile.cpp
...file modified
include/FW/makefile.cpp
...file modified
src/makefile.cpp
...file modified
src/AA/makefile.cpp
...file modified
src/AA/DCW/makefile.cpp
...file modified
src/AA/VPF/makefile.cpp
...file modified
src/AA/freeform/makefile.cpp
...file modified
src/AA/generic/makefile.cpp
...file modified
src/CBP/makefile.cpp
...file modified
src/CSC/makefile.cpp
...file modified
src/CUC/makefile.cpp
...file modified
src/CUC/ODL/makefile.cpp
...file modified
src/CUC/UDUNITS/makefile.cpp
...file modified
src/EPH/makefile.cpp
...file modified
src/EPH/orbsim/makefile.cpp
...file modified
src/EPH/gbadsim/makefile.cpp
...file modified
src/GCT/makefile.cpp
...file modified
src/GCT/freeware/makefile.cpp
...file modified
src/IO/makefile.cpp
...file modified
src/IO/GEN/makefile.cpp
...file modified
src/IO/L0/makefile.cpp
...file modified
src/IO/L0/L0sim/makefile.cpp
...file modified
src/MEM/makefile.cpp
...file modified
src/MET/makefile.cpp
...file modified
src/MET/support/makefile.cpp
...file modified
src/MET/tools/makefile.cpp
...file modified
src/PC/makefile.cpp
...file modified
src/SMF/makefile.cpp
...file modified
src/TD/makefile.cpp
...file modified
src/DEM/makefile.cpp
...file modified
src/TSF/makefile.cpp
...file modified
src/XML/makefile.cpp
...file modified
src/XML/xml/Makefile.cpp
...file modified
src/XML/xsl/Makefile.cpp
...file modified
message/makefile.cpp
...file modified

Setting ZLIB home directory to: /home/reema/Desktop/ocssw_src/opt

Setting JPEG home directory to: /home/reema/Desktop/ocssw_src/opt

Setting SZIP home directory to: /home/reema/Desktop/ocssw_src/opt

Running the SZIP (with encoding) Installation Script ...
Setting LD_LIBRARY_PATH to /home/reema/Desktop/ocssw_src/opt/lib

Setting HDF home directory to: /home/reema/Desktop/ocssw_src/opt


***** Copying JPEG, ZLIB and SZIP header and library *********

********** files to relevant directories in HDF. **********


Setting HDF5 home directory to: /home/reema/Desktop/ocssw_src/opt
Adding /home/reema/Desktop/ocssw_src/opt/lib to LD_LIBRARY_PATH

Setting HDFEOS home directory to: /home/reema/Desktop/ocssw_src/opt/EOS

Setting HDFEOS5 home directory to: /home/reema/Desktop/ocssw_src/opt/EOS

Running the Toolkit Installation Script ...



Running the Toolkit Installation Script without AA Tool.
bin/INSTALL: 3237: /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/INSTALL-Toolkit: not found
bin/INSTALL: 3239: cannot create /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/linux64/pgs-env.csh: Directory nonexistent



INSTALL: Error: The Toolkit Installation Script failed or had errors.
SDP Toolkit installation cancelled
Extracting SDPTK5.2.20v1.01.tar.Z
bin/INSTALL -notext -batch -fc_path /usr/bin/gfortran -cc_path /usr/bin/gcc -hdfhome /home/reema/Desktop/ocssw_src/opt -hdfeos_home /home/reema/Desktop/ocssw_src/opt/EOS -hdf5home /home/reema/Desktop/ocssw_src/opt -hdfeos5_home /home/reema/Desktop/ocssw_src/opt/EOS -zlibhome /home/reema/Desktop/ocssw_src/opt -jpeghome /home/reema/Desktop/ocssw_src/opt -sziphome /home/reema/Desktop/ocssw_src/opt
Traceback (most recent call last):
File "/home/reema/Desktop/ocssw_src/opt/src/sdptk/./BuildIt.py", line 91, in <module>
sys.exit(install(master))
File "/home/reema/Desktop/ocssw_src/opt/src/sdptk/./BuildIt.py", line 53, in install
subprocess.check_call(cmd)
File "/home/reema/anaconda3/lib/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['bin/INSTALL', '-notext', '-batch', '-fc_path', '/usr/bin/gfortran', '-cc_path', '/usr/bin/gcc', '-hdfhome', '/home/reema/Desktop/ocssw_src/opt', '-hdfeos_home', '/home/reema/Desktop/ocssw_src/opt/EOS', '-hdf5home', '/home/reema/Desktop/ocssw_src/opt', '-hdfeos5_home', '/home/reema/Desktop/ocssw_src/opt/EOS', '-zlibhome', '/home/reema/Desktop/ocssw_src/opt', '-jpeghome', '/home/reema/Desktop/ocssw_src/opt', '-sziphome', '/home/reema/Desktop/ocssw_src/opt']' returned non-zero exit status 1.

[gfireman]

This is very puzzling. I wonder what is deleting your directories.

Please do the following:

Code: Select all

cd /home/reema/Desktop/ocssw_src/opt/src/sdptk/
pwd -P
/bin/rm -rf TOOLKIT
install_ocssw --status
tar xf SDPTK5.2.20v1.01.tar.Z
ls -l /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/INSTALL-Toolkit
ls -l /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/linux64/pgs-env.csh

[gfireman]

One of the install scripts relies on csh - do you have that shell installed?
Please:

Code: Select all

echo $SHELL
ls -l $(which sh) $(which csh)

[reema_mathew]

The command 'ls -l /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/INSTALL-Toolkit' gives the following output:-
-rwxr-xr-x 1 reema reema 177704 Dec 12 2013 /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/INSTALL-Toolkit

The command 'ls -l /home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/linux64/pgs-env.csh' gives the following output:-
ls: cannot access '/home/reema/Desktop/ocssw_src/opt/src/sdptk/TOOLKIT/bin/linux64/pgs-env.csh': No such file or directory

The command 'echo $SHELL 'gives:-
/bin/bash

The command 'ls -l $(which sh) $(which csh)' gives:-
lrwxrwxrwx 1 root root 4 Sep 14 17:58 /usr/bin/sh -> dash

[OB.DAAC - SeanBailey]

Well, that's likely the problem. The installer scripts that comes with the SDTPK package were written for the CSH shell (thus it is listed as a requirement for building OCSSW - see https://seadas.gsfc.nasa.gov/build_ocssw/). Without it, your system will not be able to build the toolkit. Try installing csh and give the sdptk install another whirl.

Sean

[reema_mathew]

Yes. Installing csh solves the SDPTK toolkit Installation error. Thank you.

Now that everything is built successfully, I created the 'build' directory, ran 'cmake' and then while trying to build the OCSSW binaries using the command 'make -j 20' I'm getting the follwing error:

[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/spload.c.o
collect2: error: ld returned 1 exit status
make[2]: *** [oel_util/libgenutils/CMakeFiles/genutils.dir/build.make:657: oel_util/libgenutils/libgenutils.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:1510: oel_util/libgenutils/CMakeFiles/genutils.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/state_plane.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/sterfor.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/sterinv.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/tm.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/vandgfor.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/untfz.c.o
[ 25%] Linking C executable geogen_modis
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/wivfor.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/vandginv.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/wivinv.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/wviifor.c.o
[ 25%] Building C object oel_hdf4/liboli/CMakeFiles/oli.dir/wviiinv.c.o
[ 25%] Linking C executable l1agen_modis
[ 25%] Built target geogen_modis
[ 25%] Built target l1agen_modis
[ 25%] Linking C shared library liboli.so
[ 25%] Built target oli
[ 25%] Linking CXX shared library libcgal_interp.so
[ 25%] Built target cgal_interp
make: *** [Makefile:146: all] Error 2


I don't understand what's going wrong here.