Issue installing Repast HPC 4.2.1 on MacOS with M1 - netcdf

When I run the ./install.sh netcdf' I get the following error:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/type_traits:421:
../version:1:1: error: expected external declaration
-n 4.2
^
../version:1:2: error: unknown type name 'n'
-n 4.2
^
../version:1:4: error: expected unqualified-id
-n 4.2
^
In file included from netcdf.cpp:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:37:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:214:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:520:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:22:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/exception:85:
../version:1:1: error: expected external declaration
-n 4.2
^
../version:1:2: error: unknown type name 'n'
-n 4.2
^
../version:1:4: error: expected unqualified-id
-n 4.2
^
In file included from netcdf.cpp:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:37:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:214:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:520:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:23:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/new:95:
../version:1:1: error: expected external declaration
-n 4.2
^
../version:1:2: error: unknown type name 'n'
-n 4.2
^
../version:1:4: error: expected unqualified-id
-n 4.2
^
In file included from netcdf.cpp:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:37:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:214:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:520:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:26:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/utility:214:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__utility/cmp.h:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/limits:121:
../version:1:1: error: expected external declaration
-n 4.2
^
../version:1:2: error: unknown type name 'n'
-n 4.2
^
../version:1:4: error: expected unqualified-id
-n 4.2
^
In file included from netcdf.cpp:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:37:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:214:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:520:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional_base:26:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/utility:228:
../version:1:1: error: expected external declaration
-n 4.2
^
../version:1:2: error: unknown type name 'n'
-n 4.2
^
../version:1:4: error: expected unqualified-id
-n 4.2
^
In file included from netcdf.cpp:13:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/iostream:37:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/ios:214:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__locale:15:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/string:522:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/algorithm:653:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/functional:495:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/bind_front.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/__functional/perfect_forward.h:14:
In file included from /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/tuple:164:
../version:1:1: error: expected external declaration
-n 4.2
^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make[2]: *** [libnetcdf_c___la-netcdf.lo] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
It seems as though the installer is seeing the wrong versions (4.1.1 and 4.2.1) of netcdf, but both versions are in the same directory. I'm following the INSTALL.txt instructions but can't see how to resolve this error.
I was getting errors as I had no Fortran compiler, these have now been solved as I installed the NAG Fortran compiler. However, I don't know whether that could be causing these errors.

Related

fatal error: lipo: can't open input file: wireguard-go-bridge/libwg-go-arm64.a (No such file or directory

I have developed a framework which was working fine in debug mood also working in mobile phone but when I make a build for distribution compiler send me error
I have used Wireguard vpn use and its integration in app.
Makefile:68: warning: overriding commands for target `/Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy'
Makefile:65: warning: ignoring old commands for target `/Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy'
Makefile:68: warning: overriding commands for target `of'
Makefile:65: warning: ignoring old commands for target `of'
Makefile:71: warning: overriding commands for target `/Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy'
Makefile:68: warning: ignoring old commands for target `/Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy'
Makefile:71: warning: overriding commands for target `of'
Makefile:68: warning: ignoring old commands for target `of'
make: Circular /Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy <- /Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy dependency dropped.
make: Circular of <- /Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy dependency dropped.
make: Circular of <- of dependency dropped.
go build -ldflags=-w -trimpath -v -o "/Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy of OortVPN/IntermediateBuildFilesPath/FriendsVPN.build/Debug-iphoneos/wireguard-go-bridge/libwg-go-arm64.a" -buildmode c-archive
runtime/cgo
net
golang.zx2c4.com/wireguard/apple
rm -f "/Users/fitoutfit/Library/Developer/Xcode/DerivedData/FriendsVPN-guiobyjdevstmafjlnlacycwutee/Build/Intermediates.noindex/ArchiveIntermediates/Copy of OortVPN/IntermediateBuildFilesPath/FriendsVPN.build/Debug-iphoneos/wireguard-go-bridge/libwg-go-arm64.h"
lipo -create -output "of" OortVPN/IntermediateBuildFilesPath/FriendsVPN.build/Debug-iphoneos/wireguard-go-bridge/libwg-go-arm64.a /usr/local/Cellar/go/1.17/libexec/.prepared go.mod
fatal error: lipo: can't open input file: OortVPN/IntermediateBuildFilesPath/FriendsVPN.build/Debug-iphoneos/wireguard-go-bridge/libwg-go-arm64.a (No such file or directory)
make: *** [of] Error 1
Command ExternalBuildToolExecution failed with a nonzero exit code

Cupy error installation

I tried to install cupy via pip install cupy. I get the following error:
Looking in links:
/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/avx2,
/cvmfs/soft.computecanada.ca/custom/python/wheelhouse/generic Collecting cupy
Using cached https://files.pythonhosted.org/packages/38/14/ddb1a13f77a50d721814e28181ae90e0d57c3f8d4faa9a7b2e028cfcc99a/cupy-4.0.0.tar.gz
Complete output from command python setup.py egg_info:
Options: {'profile': False, 'annotate': False, 'linetrace': False, 'wheel_libs': [], 'package_name': 'cupy', 'no_rpath': False, 'no_cuda': False, 'long_description': None}
**************************************************
*** WARNING: nvcc not in path.
*** WARNING: Please set path to nvcc.
**************************************************
**************************************************
*** WARNING: nvcc path != CUDA_PATH
*** WARNING: nvcc path: None
*** WARNING: CUDA_PATH: /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/cuda/8.0.44
**************************************************
-------- Configuring Module: cuda --------
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
gcc: warning: /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/cuda/8.0.44/include: linker input file unused because linking not done
/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/cuda/8.0.44/lib64: file not recognized: Is a directory
collect2: error: ld returned 1 exit status
Cannot build a stub file.
Original error: command 'g++' failed with exit status 1
************************************************************
* CuPy Configuration Summary *
************************************************************
Build Environment:
Include directories: ['/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/cuda/8.0.44/include']
Library directories: ['/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/cuda/8.0.44/lib64']
nvcc command : ['/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/cuda/8.0.44/bin/nvcc']
Environment Variables:
CFLAGS : /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/cuda/8.0.44/include
LDFLAGS : /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/gcc5.4/cuda/8.0.44/lib64
LIBRARY_PATH : /cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/python/2.7.14/lib:/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/CUDA/intel2016.4/cuda8.0/openmpi/2.1.1/lib:/cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/cuda/8.0.44/lib64:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/mkl/lib/intel64:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258/lib/intel64:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/ifort/2016.4.258/compilers_and_libraries_2016.4.258/linux/compiler/lib/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/lib64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/gcc-5.4.0/lib:/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/icc/2016.4.258/compilers_and_libraries_2016.4.258/linux/compiler/lib/intel64:/cvmfs/soft.computecanada.ca/nix/var/nix/profiles/16.09/lib
CUDA_PATH : /cvmfs/soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/cuda/8.0.44
NVCC : (none)
Modules:
cuda : No
-> Include files not found: ['cublas_v2.h', 'cuda.h', 'cuda_profiler_api.h', 'cuda_runtime.h', 'cufft.h', 'curand.h', 'cusparse.h', 'nvrtc.h', 'nvToolsExt.h']
-> Check your CFLAGS environment variable.
ERROR: CUDA could not be found on your system.
Please refer to the Installation Guide for details:
https://docs-cupy.chainer.org/en/stable/install.html
************************************************************
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/localscratch/tamouze.7243408.0/pip-install-_wUDId/cupy/setup.py", line 65, in <module>
ext_modules = cupy_setup_build.get_ext_modules()
File "cupy_setup_build.py", line 561, in get_ext_modules
extensions = make_extensions(arg_options, compiler, use_cython)
File "cupy_setup_build.py", line 374, in make_extensions
raise Exception('Your CUDA environment is invalid. '
Exception: Your CUDA environment is invalid. Please check above error log.
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /localscratch/tamouze.7243408.0/pip-install-_wUDId/cupy/
Im working on SSH linux server. Im not comfortable with linux environment. My problem looks like the environment is not ok, please how can setup correctly them? I want to use cupy with cahiner
for cuda 9.0:
pip install --pre cupy-cuda90
Or you may want to first do:
1. check you module list : module list
unload pgi module: module unload pgi/16.9

squid make error about libltdlc.la on compile

I encounter a error when I was execute make.
The environment is
1. OS X 10.10.5
2. compiler is gcc ( I am not sure and make command log shows gcc many times)
3. Squid source version 3.5.13
log as this:
./libtool: line 4228: cd: /Users/lorancechen/version: No such file or directory
libtool: link: (cd .libs/libltdlc.lax/dlopen.a && ar x "/Users/lorancechen/version control/_open_source/squid-3.5.13/libltdl/./.libs/dlopen.a")
./libtool: line 1085: cd: .libs/libltdlc.lax/dlopen.a: No such file or directory
make[2]: *** [libltdlc.la] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
===============================
Besides, I am not find .libs directory with log reminded.
UPDATE
with #Tibidabo help, I find the directory can't contains "." or "-".
Now, another error occurred, such as
basic_ldap_auth.cc:610:13: error: 'ldap_unbind' is deprecated: first deprecated
in OS X 10.10 - use ldap_unbind_ext [-Werror,-Wdeprecated-declarations]
ldap_unbind(ld);
^
I attempt change to ldap_unbind_ext, compiler tips with can't find it or no known.
Please check that the directory does not have any "funny" characters.
I have the same error, I renamed the directory to have only alphanumerical characters by removing ".","-" etc and after that the make worked just fine!

Qt Compilation with dbus

I am trying to compile qt with dbus but it gives me the following exception. I have installed the dbus version 1.3 in the system and I am using the following configure command.
Can someone point me as to what should be done.
configure -dbus -I/usr/include/dbus-1.0 -L/usr/local/dbus/lib -ldbus-1 -fast -prefix /home/thwijeth/Software/qt-4.8.1-com-debug -v
thank you in advance.
qdbus_symbols_p.h:39: fatal error: dbus/dbus.h: No such file or directory
compilation terminated.
In file included from qdbusconnection_p.h:51,
from qdbusconnection.cpp:33:
qdbus_symbols_p.h:39: fatal error: dbus/dbus.h: No such file or directory
compilation terminated.
make[1]: *** [qdbuserror.o] Error 1
make[1]: *** Waiting for unfinished jobs....
make[1]: *** [qdbusconnection.o] Error 1
In file included from qdbusconnectioninterface.cpp:33:
qdbus_symbols_p.h:39: fatal error: dbus/dbus.h: No such file or directory
compilation terminated.
make[1]: *** [qdbusconnectioninterface.o] Error 1
In file included from qdbusconnection_p.h:51,
from qdbusintegrator.cpp:33:
qdbus_symbols_p.h:39: fatal error: dbus/dbus.h: No such file or directory
compilation terminated.
make[1]: *** [qdbusintegrator.o] Error 1
make[1]: Leaving directory `/home/thwijeth/Software/qt-repo/qt-4.8.1-src/src/dbus'
make: *** [sub-dbus-make_default-ordered] Error 2
verify if /usr/include/dbus-1.0 contains a dbus directory, if it does not, verify whether /usr/include/dbus-1.0 contains dbus.h, if so you need to create a symbolic link to dbus-1.0 as dbus
ln -s dbus-1.0 /usr/include/dbus
and then try to rerun configure.
This solution worked fine for me for this missing header. However, I got then a different error fatal error: dbus/dbus-arch-deps.h: No such file. I worked around this error by copying this file from /usr/lib/x86_64-linux-gnu/dbus-1.0/include/dbus to /usr/include/dbus-1.0/dbus/. I don't know why this header was not in the /usr/include directory from the beginning. But this is my hack to the problem.
Regards

Can't build a qt project using qtservice

I'm trying to use QtService from QtSolution in a Qt project.
I've unzipped it and run:
configure.bat -library
qmake
mingw32-make
the debug and release dll were placed inside C:\Qt\2010.03\qt\bin\
Examples were correctly built .
I added this line at the bottom of my .pro file:
include(../QtSolutions/qtservice/src/qtservice.pri)
and I was able to browse the qtservice's sources from the project source tree.
When I try to build my project I get:
Running build steps for project EMCSolutionCrawler...
Configuration unchanged, skipping QMake step.
Starting: C:/Qt/2010.03/mingw/bin/mingw32-make.exe -w
mingw32-make: Entering directory `C:/Progetti/EMCSolutionCrawler'
c:\qt\2010.03\qt\bin\qmake.exe -spec ..\..\Qt\2010.03\qt\mkspecs\win32-g++ -win32 -o Makefile EMCSolutionCrawler.pro
mingw32-make: Leaving directory `C:/Progetti/EMCSolutionCrawler'
mingw32-make: Entering directory `C:/Progetti/EMCSolutionCrawler'
C:/Qt/2010.03/mingw/bin/mingw32-make -f Makefile.Debug
mingw32-make[1]: Entering directory `C:/Progetti/EMCSolutionCrawler'
g++ -g -frtti -fexceptions -mthreads -Wall -DUNICODE -DQT_LARGEFILE_SUPPORT -DQT_QTSERVICE_IMPORT -DQT_DLL -DQT_SQL_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_THREAD_SUPPORT ../QtSolutions/qtservice/src/QtService.cpp -o ../QtSolutions/qtservice/src/QtService
mingw32-make[1]: Leaving directory `C:/Progetti/EMCSolutionCrawler'
mingw32-make: Leaving directory `C:/Progetti/EMCSolutionCrawler'
In file included from ../QtSolutions/qtservice/src/QtService.cpp:47:
../QtSolutions/qtservice/src/qtservice.h:50:35: error: QtCore/QCoreApplication: No such file or directory
In file included from ../QtSolutions/qtservice/src/QtService.cpp:48:
../QtSolutions/qtservice/src/qtservice_p.h:50:30: error: QtCore/QStringList: No such file or directory
../QtSolutions/qtservice/src/QtService.cpp:51:25: error: QtCore/QTimer: No such file or directory
../QtSolutions/qtservice/src/QtService.cpp:52:26: error: QtCore/QVector: No such file or directory
../QtSolutions/qtservice/src/QtService.cpp:53:27: error: QtCore/QProcess: No such file or directory
../QtSolutions/qtservice/src/QtService.cpp:426:25: error: qtservice.moc: No such file or directory
In file included from ../QtSolutions/qtservice/src/QtService.cpp:47:
../QtSolutions/qtservice/src/qtservice.h:73: error: ISO C++ forbids declaration of 'Q_DECLARE_PRIVATE' with no type
../QtSolutions/qtservice/src/qtservice.h:74: error: expected ';' before 'public'
../QtSolutions/qtservice/src/qtservice.h:80: error: ISO C++ forbids declaration of 'QString' with no type
../QtSolutions/qtservice/src/qtservice.h:80: error: expected ',' or '...' before '&' token
../QtSolutions/qtservice/src/qtservice.h:86: error: 'QString' does not name a type
../QtSolutions/qtservice/src/qtservice.h:87: error: 'QString' does not name a type
../QtSolutions/qtservice/src/qtservice.h:88: error: 'StartupType' does not name a type
../QtSolutions/qtservice/src/qtservice.h:89: error: 'QString' does not name a type
../QtSolutions/qtservice/src/qtservice.h:91: error: ISO C++ forbids declaration of 'QString' with no type
../QtSolutions/qtservice/src/qtservice.h:91: error: expected ',' or '...' before '&' token
../QtSolutions/qtservice/src/qtservice.h:110: error: ISO C++ forbids declaration of 'Q_DECLARE_PRIVATE' with no type
../QtSolutions/qtservice/src/qtservice.h:111: error: expected ';' before 'public'
../QtSolutions/qtservice/src/qtservice.h:125: error: 'ServiceFlags' has not been declared
../QtSolutions/qtservice/src/qtservice.h:125: error: ISO C++ forbids declaration of 'Q_DECLARE_FLAGS' with no type
../QtSolutions/qtservice/src/qtservice.h:127: error: expected ';' before 'QtServiceBase'
../QtSolutions/qtservice/src/qtservice.h:130: error: 'QString' does not name a type
...
What am I missing?
Environment infomation:
Qt 4.6.3 (mingw - LGPL)
Windows XP SP3
QtService 2.6
Thank you for your time.
Just a guess: I don't see a include -IC:\Qt\2010.03\qt\include in your call of g++. So the compiler can't find the Qt Headers. I tink there is something wrong in your EMCSolutionCrawler.pro.

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