isce 2.2 on OSX High Sierra

Added by Francisco Delgado over 2 years ago

Dear Isce team

I've been trying to install ISCE 2.2 on a High Sierra Mac with no success, so I wonder if there are specific issues related to this Mac distribution? In short I'm using anaconda3 to install goal and the required libraries, but scons can't find the libraries even though they exist and are correctly installed with conda.

Francisco


Replies (31)

RE: isce 2.2 on OSX High Sierra - Added by Francisco Delgado about 2 years ago

Hi Eric, yes, that's why I said it's pretty stupid, but it works until I properly reinstall the software.
Francisco

RE: isce 2.2 on OSX High Sierra - Added by Francisco Delgado about 2 years ago

Dear ISCE developers,

After removing and reinstalling all the libraries with macports and properly checking that they are correctly installed, I still get the same error as before compiling the software on a Mac with High Sierra

scons: Reading SConscript files ...
Building with scons from python2
Checking for C header file Python.h... (cached) no
Checking for C++ header file Python.h... no
Could not find: Python.h header for python3 header
Error: Install python3-dev or add path to Python.h to CPPPATH
Checking for C header file fftw3.h... no
Checking for C++ header file fftw3.h... yes
Checking for C header file hdf5.h... yes
Checking for C header file X11/Xlib.h... yes
Checking for C header file Xm/Xm.h... yes
Checking for C header file omp.h... yes
Checking for C library hdf5... (cached) no
Could not find: hdf5 lib for libhdf5
Error: Install hdf5 or libhdf5-dev
Checking for C library fftw3f... (cached) no
Could not find: fftw3f lib for libfftw3f
Error: Install fftw3 or libfftw3-dev
Checking for C library Xm... no
Could not find: Xm lib for libXm
Error: Install Xm or libXm-dev
Checking for C library Xt... no
Could not find: Xt lib for libXt
Error: Install Xt or libXt-dev
Checking for F include fftw3 ... yes
GDAL version: 2.3.2

Checking for C++ header file gdal_priv.h... yes
Checking for C library gdal... no
Could not find: libgdal for gdal
Install gdal or include path to libs to LIBPATH
Not all components of ISCE will be installed and can result in errors.

I checked and the files do exist. Why does the software complain if the files actually exist and are properly installed with macports?? I really don't know how to solve this issue so any help is greatly appreciated.

Francisco

RE: isce 2.2 on OSX High Sierra - Added by Jose Uribe about 2 years ago

Hi Francisco,

see the file config.log for more information. This file contains all scons tests when it's trying to detect the required software. Sometimes, even when the file/library exists, it is not detected because it can't compile. Scons not only check for the file, it also tests the compilation with that file.

Regards,
José

RE: isce 2.2 on OSX High Sierra - Added by Francisco Delgado about 2 years ago

Thanks Jose, I also checked that. However, when I manually created the conftest_XY files and then compiled them I got no errors to the same commands that scons complained. For example, ISCE outputs the following

Checking for C++ header file Python.h... no

which I then checked in the config.log file

scons: Configure: Checking for C++ header file Python.h... 
scons: Configure: ".sconf_temp/conftest_1.cpp" is up to date.
scons: Configure: The original builder output was: |.sconf_temp/conftest_1.cpp <- | | | |#include "Python.h" | | | | |
/opt/local/bin/g++ -o .sconf_temp/conftest_1.o -c -O2 -Wall -fPIC -m64 -DNEEDS_F77_TRANSLATION -DF77EXTERNS_LOWERCASE_TRAILINGBAR -I/opt/local/Library/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/opt/local/include -Ibuild/isce/components/iscesys/ImageApi/include -Ibuild/isce/components/iscesys/ImageApi/DataCaster/include -Ibuild/isce/components/isceobj/LineAccessor/include -Ibuild/isce/components/iscesys/StdOE/include -Ibuild/isce/components/isceobj/Util/include - Ibuild/isce/components/isceobj/Util/Library/include .sconf_temp/conftest_1.cpp
g++: error: .sconf_temp/conftest_1.cpp: No such file or directory
g++: fatal error: no input files
compilation terminated.
scons: Configure: no

but if I manually create sconf_temp/conftest_1.cpp and compile it with the above command I get no error at all!

On the other hand, if the file exists and Scons refuses them it might be an issue like that of Eric Fielding who had to add the flag to the openmpi lib for his hdf5. However, the only flags I have added are the +gcc7 to compile fftw-3, hdf5 and that's it

This is even more puzzling, any clue of what's going on here?

Thanks a lot

RE: isce 2.2 on OSX High Sierra - Added by Jose Uribe about 2 years ago

Francisco,

I think it is related with scons temporal database. Try to remove, or even better rename, the following file:

mv .sconsign.dblite .sconsign.dblite_bak

And test again. Scons should recreate the file.

José.

RE: isce 2.2 on OSX High Sierra - Added by Francisco Delgado about 2 years ago

Hi Jose, that's the problem! Thanks a lot! I removed the file and it worked!! That's the reason also why after so many failed installation it would accumulate more and more errors even though the paths were properly set with respect to other failed installations but with less errors.

Francisco

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