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error when installing galtoolslib

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subho

Post subject: Re: error when installing galtoolslib

Posted: Tue Apr 23, 2019 7:31 pm

Joined: Mon Mar 31, 2014 9:14 pm
Posts: 12

Good job with the Healpix libraries

.

For psht, please use the libsharp path as mentioned here: For Healpix version 3.10 and above, spherical harmonics library (psht) is replaced by the libsharp (https://healpix.sourceforge.io/doc/html/install.htm).

Some related issues that I want to touch upon for future bug cleaning.

1. As you can see that the compiler cannot recognize where pointing.h is. 'pointing.h' is necessary because this header file contains a class that defines a point in an unit sphere. This file should be
located (if properly installed) inside the include directory in your generic_gcc folder within Healpix.

But your path for include directory for Healpix is wrong. Very primitive mistake. You can do a 'grep' search to deal with finding files or strings inside file.

2. Path where Healpix is installed: You can give path till generic_gcc folder.

3. Also another suggestion: Probably in an ideal case you will always separate your GALPROP and its dependencies from the ubuntu (or whatever linux distribution you are using) /usr folder.
So maybe just like any other dependencies (CCfits, cfitsio etc..) you can install gsl within GALPROP folder and give path to that installation.

Happy Debugging !!

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Yan-Ping

Post subject: Re: error when installing galtoolslib

Posted: Thu May 09, 2019 12:21 am

Joined: Mon Jun 04, 2018 12:44 am
Posts: 6

Thank you very much !
With your help, I made a big step forward.
now the healpix part in CMakeCache.txt is

Code:

//Path to a file.
HEALPix_INCLUDE_DIR:PATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include

//Location where Healpix is installed
HEALPix_PREFIX:PATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc

//Path to a library.
HEALPix_c_utils:FILEPATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libc_utils.a

//Path to a library.
HEALPix_cxxsupport:FILEPATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libcxxsupport.a

//Path to a library.
HEALPix_fftpack:FILEPATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libfftpack.a

//Path to a library.
HEALPix_healpix_cxx:FILEPATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libhealpix_cxx.a

//Path to a library.
HEALPix_psht:FILEPATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libsharp.a

//Path to a library.
HEALPix_sharp:FILEPATH=/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libsharp.a

is it right for the dir of HEALPix_sharp?

then i run
cmake ../ -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CC_COMPILER=gcc
the output is

Quote:

-- Looking for C++ include alm_healpix_tools.h
-- Looking for C++ include alm_healpix_tools.h - found
-- Looking for C++ include lsconstants.h
-- Looking for C++ include lsconstants.h - found
-- Looking for C++ include alm_powspec_tools.h
-- Looking for C++ include alm_powspec_tools.h - found
-- Looking for C++ include alloc_utils.h
-- Looking for C++ include alloc_utils.h - found
-- Performing Test HEALPIX_STD_COMPLEX
-- Performing Test HEALPIX_STD_COMPLEX - Success
-- Found HEALPix: /home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libhealpix_cxx.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libsharp.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libc_utils.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libfftpack.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libcxxsupport.a
-- Found WCS: /usr/local/lib/libwcs.so
-- Using GSL from /usr/local
-- Found Xerces-C: /usr/local/lib/libxerces-c.so
-- : /usr/local/include
-- Version: 3.2.1
-- CMAKE_BUILD_TYPE not set, defaulting to RelWithDebInfo.
Set in cache or on command line to override.
-- The configure script will now override the cached CMAKE_CXX_FLAGS_RELWITHDEBINFO variable to a hand crafted value for most compilers.
CMAKE_CXX_FLAGS can be used to add compiler flags. To manually define the build flags a CMAKE_BUILD_TYPE other than RelWithDebInfo (the default) and Release should be used.
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP Fortran flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp
-- Using CXX flags -std=c++11 -fopenmp -g -pipe -O3 -Wall for compiler /usr/bin/g++
-- Using Fortran flags -fopenmp -g -pipe -O3 -Wall for compiler /usr/bin/gfortran
-- Detecting Fortran/C Interface
-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
-- Verifying Fortran/CXX Compiler Compatibility
-- Verifying Fortran/CXX Compiler Compatibility - Success
compile_result='TRUE'
run_result='0'
compile_output='Change Dir: /home/congyanping/Software/galtoolslib/galtoolslib/build/CMakeFiles/CMakeTmp

Run Build Command:"/usr/bin/make" "cmTC_099ef/fast"
/usr/bin/make -f CMakeFiles/cmTC_099ef.dir/build.make CMakeFiles/cmTC_099ef.dir/build
make[1]:into dir“/home/congyanping/Software/galtoolslib/galtoolslib/build/CMakeFiles/CMakeTmp”
Building CXX object CMakeFiles/cmTC_099ef.dir/regex.cxx.o
/usr/bin/g++ -std=c++11 -fopenmp -O3 -DNDEBUG -fPIE -o CMakeFiles/cmTC_099ef.dir/regex.cxx.o -c /home/congyanping/Software/galtoolslib/galtoolslib/build/CMakeFiles/CMakeTmp/regex.cxx
Linking CXX executable cmTC_099ef
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_099ef.dir/link.txt --verbose=1
/usr/bin/g++ -std=c++11 -fopenmp -O3 -DNDEBUG -rdynamic CMakeFiles/cmTC_099ef.dir/regex.cxx.o -o cmTC_099ef
make[1]: leave dir“/home/congyanping/Software/galtoolslib/galtoolslib/build/CMakeFiles/CMakeTmp”
'
run_output=''
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:

CMAKE_CC_COMPILER

-- Build files have been written to: /home/congyanping/Software/galtoolslib/galtoolslib/build

then make step
the output is

Quote:

[ 1%] Building CXX object utils/CMakeFiles/utils.dir/ErrorLogger.cc.o
[ 3%] Building CXX object utils/CMakeFiles/utils.dir/Timer.cc.o
[ 5%] Building CXX object utils/CMakeFiles/utils.dir/Parameters.cc.o
[ 6%] Building CXX object utils/CMakeFiles/utils.dir/StatusIndicator.cc.o
[ 8%] Building CXX object utils/CMakeFiles/utils.dir/Interpolation.cc.o
[ 10%] Building CXX object utils/CMakeFiles/utils.dir/ReaderErrorReporter.cc.o
[ 11%] Building CXX object utils/CMakeFiles/utils.dir/Reader.cc.o
[ 13%] Building CXX object utils/CMakeFiles/utils.dir/Variables.cc.o
[ 15%] Building CXX object utils/CMakeFiles/utils.dir/md5.cc.o
[ 16%] Building CXX object utils/CMakeFiles/utils.dir/Malloc.cc.o
[ 18%] Linking CXX static library libutils.a
[ 18%] Built target utils
Scanning dependencies of target galstruct
[ 20%] Building CXX object galstruct/CMakeFiles/galstruct.dir/radialprofiles.cpp.o
[ 22%] Building CXX object galstruct/CMakeFiles/galstruct.dir/spiralarms.cpp.o
[ 23%] Building CXX object galstruct/CMakeFiles/galstruct.dir/planeprofiles.cpp.o
[ 25%] Building CXX object galstruct/CMakeFiles/galstruct.dir/cylindricalprofiles.cpp.o
[ 27%] Linking CXX static library libgalstruct.a
[ 27%] Built target galstruct
Scanning dependencies of target skymap
[ 28%] Building CXX object libskymap/CMakeFiles/skymap.dir/Coordinate.cc.o
[ 30%] Building CXX object libskymap/CMakeFiles/skymap.dir/HealpixBaseExtended.cc.o
In file included from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/HealpixBaseExtended.h:10:0,
from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/HealpixBaseExtended.cc:1:
/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include/healpix_base.h:56:14: warning: inline function ‘I T_Healpix_Base<I>::ring_above(double) const [with I = int]’ used but never defined
inline I ring_above (double z) const;
^~~~~~~~~~
[ 32%] Building CXX object libskymap/CMakeFiles/skymap.dir/Region.cc.o
[ 33%] Building CXX object libskymap/CMakeFiles/skymap.dir/SkySelection.cc.o
[ 35%] Building CXX object libskymap/CMakeFiles/skymap.dir/Skymap.cc.o
[ 37%] Building CXX object libskymap/CMakeFiles/skymap.dir/BaseSky.cc.o
In file included from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.cc:1:0:
/home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.h: In member function ‘std::unique_ptr<SM::BaseSky<T> > SM::BaseSky<T>::CoordinateConversion(SM::CoordSys) const’:
/home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.h:677:47: error: no matching function for call to ‘rangeset<int>::toVector()’
for ( int np : newPixels.toVector() )
^
In file included from /home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include/healpix_base.h:39:0,
from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/HealpixBaseExtended.h:10,
from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.h:4,
from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.cc:1:
/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include/rangeset.h:187:10: note: candidate: void rangeset<T>::toVector(std::vector<T>&) const [with T = int]
void toVector (std::vector<T> &res) const
^~~~~~~~
/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include/rangeset.h:187:10: note: candidate expects 1 argument, 0 provided
In file included from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.cc:1:0:
/home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.h: In member function ‘void SM::BaseSky<T>::Interpolate(SM::BaseSky<T>&, bool) const’:
/home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.h:764:45: error: no matching function for call to ‘rangeset<int>::toVector()’
for ( auto np : newPixels.toVector() )
^
In file included from /home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include/healpix_base.h:39:0,
from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/HealpixBaseExtended.h:10,
from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.h:4,
from /home/congyanping/Software/galtoolslib/galtoolslib/libskymap/BaseSky.cc:1:
/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include/rangeset.h:187:10: note: candidate: void rangeset<T>::toVector(std::vector<T>&) const [with T = int]
void toVector (std::vector<T> &res) const
^~~~~~~~
/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/include/rangeset.h:187:10: note: candidate expects 1 argument, 0 provided
libskymap/CMakeFiles/skymap.dir/build.make:182: recipe for target 'libskymap/CMakeFiles/skymap.dir/BaseSky.cc.o' failed
make[2]: *** [libskymap/CMakeFiles/skymap.dir/BaseSky.cc.o] Error 1
CMakeFiles/Makefile2:195: recipe for target 'libskymap/CMakeFiles/skymap.dir/all' failed
make[1]: *** [libskymap/CMakeFiles/skymap.dir/all] Error 2
Makefile:162: recipe for target 'all' failed
make: *** [all] Error 2

I can't figure it out :cry:

, any idea?

Top

subho

Post subject: Re: error when installing galtoolslib

Posted: Wed May 22, 2019 6:21 pm

Joined: Mon Mar 31, 2014 9:14 pm
Posts: 12

Then I run

Code:

cmake ../ -DCMAKE_CXX_COMPILER=g++ -DCMAKE_CC_COMPILER=gcc

This is not the correct way to write the makefile. You need to mention the galtoolslib directory.
As mentioned in the readme file you can follow the steps
1. Extract galtoolslib tar file.
2. Create a build and binary directory for galtoolslib.
3. Inside the build directory

Code:

cmake -DCMAKE_INSTALL_PREFIX=/home/congyangping/.../binary/galtoolslib <space> /home/congyangping/.../galtoolslib-1.0.855-Source

4. make
5. make install
Did you follow these steps ? The binary directory creation isn't a mandatory option but I do it to separate the binary files from the build files. You can find these inside the readme files in galtoolslib extracted folder.

libsharp is okay.

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Yan-Ping

Post subject: Re: error when installing galtoolslib

Posted: Wed May 22, 2019 11:34 pm

Joined: Mon Jun 04, 2018 12:44 am
Posts: 6

yes, i followed your steps doing that:

Quote:

congyanping@congyanping-OptiPlex-7040:~/Software/galtoolslib/galtoolslib/build$ cmake -DCMAKE_INSTALL_PREFIX=/home/congyanping/Software/galtoolslib/galtoolslib/binary/galtoolslib /home/congyanping/Software/galtoolslib/galtoolslib

my directory of galtoolslib is ~/Software/galtoolslib/galtoolslib

Code:

-- Looking for C++ include alm_healpix_tools.h
-- Looking for C++ include alm_healpix_tools.h - found
-- Looking for C++ include lsconstants.h
-- Looking for C++ include lsconstants.h - found
-- Looking for C++ include alm_powspec_tools.h
-- Looking for C++ include alm_powspec_tools.h - found
-- Looking for C++ include alloc_utils.h
-- Looking for C++ include alloc_utils.h - found
-- Performing Test HEALPIX_STD_COMPLEX
-- Performing Test HEALPIX_STD_COMPLEX - Success
-- Found HEALPix: /home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libhealpix_cxx.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libsharp.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libc_utils.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libfftpack.a;/home/congyanping/Software/healpix/Healpix_311/src/cxx/generic_gcc/lib/libcxxsupport.a  
-- Found WCS: /usr/local/lib/libwcs.so  
-- Using GSL from /usr/local
-- Found Xerces-C: /usr/local/lib/libxerces-c.so
--               : /usr/local/include
--        Version: 3.2.1
-- CMAKE_BUILD_TYPE not set, defaulting to RelWithDebInfo.
 Set in cache or on command line to override.
-- The configure script will now override the cached CMAKE_CXX_FLAGS_RELWITHDEBINFO variable to a hand crafted value for most compilers.
CMAKE_CXX_FLAGS can be used to add compiler flags.  To manually define the build flags a CMAKE_BUILD_TYPE other than RelWithDebInfo (the default) and Release should be used.
-- Try OpenMP C flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP CXX flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Try OpenMP Fortran flag = [-fopenmp]
-- Performing Test OpenMP_FLAG_DETECTED
-- Performing Test OpenMP_FLAG_DETECTED - Success
-- Found OpenMP: -fopenmp  
-- Using CXX flags  -std=c++11 -fopenmp -g -pipe -O3 -Wall for compiler /usr/bin/g++
-- Using Fortran flags  -fopenmp -g -pipe -O3 -Wall for compiler /usr/bin/gfortran
-- Detecting Fortran/C Interface
-- Detecting Fortran/C Interface - Found GLOBAL and MODULE mangling
-- Verifying Fortran/CXX Compiler Compatibility
-- Verifying Fortran/CXX Compiler Compatibility - Success
compile_result='TRUE'
run_result='0'
compile_output='Change Dir: /home/congyanping/Software/galtoolslib/galtoolslib/build/CMakeFiles/CMakeTmp

then i run make && make install, i got the result of :

Quote:

the error information have not been eliminated. :roll:

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subho

Post subject: Re: error when installing galtoolslib

Posted: Tue May 28, 2019 1:29 am

Joined: Mon Mar 31, 2014 9:14 pm
Posts: 12

Please check your C/C++ version because they need to be higher than 4.9.
If that is not the problem then you need to activate C++11 standard inside CMake. Set this manually inside the config file.
Hopefully it works !
Also you can take a look at the Appendix of the paper by Troy Porter for a better installation guide

https://iopscience.iop.org/article/10.3847/1538-4357/aa844d/meta

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pratham

Post subject: Re: error when installing galtoolslib

Posted: Sun Jul 16, 2023 1:41 pm

Joined: Tue Mar 17, 2020 4:39 am
Posts: 1

facing the same issue, any luck here?
https://vidmate.click https://myfiosgateway.win/

_________________
https://vidmateapp.win https://momix.uno

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