Some experience of AUTO software on bifurcation analysis

mxlzhenzhu · 发表于 2019-1-3 10:06

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本帖最后由 mxlzhenzhu 于 2019-1-3 21:21 编辑

The AUTO software is  powerful in numerical computation and nonlinear analysis(eg. bifurcation analysis, plot the interested bifurcation diagram), further information about the software and the pakage can be referred to: http://cmvl.cs.concordia.ca/auto

This software is Unix or Linux based, for most users,  they may encounter so many tricks and difficulties, so I share some experience  here, hope you can enjoy it more easily.

1, It is strongly recommended to installl the VMware for new users, and you may install the Linux correctly.
[2 days]

2, Try to download the AUTO pakage and prepare some other  dependent compliers and softwares.
[Prepare some knowledge about numeric analysis, especially the numerical continuation theories, homotopy analysis, bifurcation theories, stability theory] [0.5 or 1 year ]

3, Read the software user mannual for intallation guides.
3.1 Gfortran is necessary.[0.5 or 1 day]
3.2 Gcc may be installed, the Internet connection is critical.( Some Linux system may have the built-in pakage, need no further installation, and easier updating) [0.5 day]
type ./configure in the terminal under the .../auto/07p  directory , now it looks  like

The configuration result after the gcc and gfortran installation

3.3 Now it is time to install the SoQt pakage.The SoQt installation guide:[1 or 2 days]
https://github.com/iat-cener/ton ... ling-SoQt-For-Linux

3.3.1 Coin3D can be downloaded from:
https://bitbucket.org/Coin3D/coin/downloads/
3.3.2 Qt can be downloaded from:
https://www.qt.io/download
https://github.com/iat-cener/ton ... alling-Qt-For-Linux

and the Anaconda from Tsinghua Mirror:
https://mirrors.tuna.tsinghua.edu.cn/anaconda/archive/

3.4 Now it is time to install the......[Not finished yet]

mxlzhenzhu · 发表于 2019-1-6 09:52

安装手册和使用说明，忘记从哪儿下载的了：

Auto07p-Continuation and Bifurcations Software for ODEs.pdf (2.14 MB, 下载次数: 2)

安装软件：

auto07p-0.9.1.tar.zip (4.7 MB, 下载次数: 1)

软件的格式需要将.tar.zip修改为.tar.gz

mxlzhenzhu · 发表于 2019-1-3 10:49

本帖最后由 mxlzhenzhu 于 2019-1-3 20:27 编辑

Then I encounter the following error:

Could not find any way to build against the Qt library. If you
are sure Qt is properly installed on your system, see the file
config.log to find out what went wrong.

One common way to solve this problem is to set up the environment
variable QTDIR to the base of the Qt installation directory. Or if it
was already set up, double check to see that it is pointing at the
correct directory.

Note that it is possible to override the combinations of Qt libraries
configure tries to link against by setting up the environment variable
CONFIG_QTLIBS. This might be necessary if you have installed the Qt
library in a manner that is not compatible with any of the known
configurations, for instance by changing the name of the library or
the Qt library having more dependencies on other libraries that we are
aware of.

If you for instance know the correct set of libraries to be qt304.lib,
qtmain.lib and gdi32.lib (this would be on an MSWindows system), then
set CONFIG_QTLIBS to the string ''-lqt304 -lqtmain -lgdi32'' before
re-running configure.

If you still can't get the configure script to detect the presence of
and how to use the Qt library, please mail the config.log file to
<coin-support@coin3d.org> and ask for help.

configure: error: aborting
======================================================
May be the QTDIR environment Var is not set properly.see more about how to set the environment Var on Linux:
http://www.cnblogs.com/blindwandering/p/3711643.html======================================================
Download the Qt from:
http://download.qt.io/archive/qt/4.7/
or
http://download.qt.io/archive/qt ... ce-src-4.7.0.tar.gz
https://mirrors.tuna.tsinghua.edu.cn/qt/archive/qt

Installation guide:
https://www.cnblogs.com/ljf181275034/articles/2875098.html

补充内容 (2019-1-5 09:42):
https://wiki.qt.io/Install_Qt_5_on_Ubuntu

mxlzhenzhu · 发表于 2019-1-3 12:05

本帖最后由 mxlzhenzhu 于 2019-1-3 23:17 编辑

I downloaded the
ipython-7.2.0.tar.gz
Extract the file, and type the command under the source code directory
$ python -m IPython
to find the error:

Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 163, in _run_module_as_main
mod_name, _Error)
  File "/usr/lib/python2.7/runpy.py", line 111, in _get_module_details
__import__(mod_name)  # Do not catch exceptions initializing package
  File "IPython/__init__.py", line 41, in <module>
""")
ImportError:
IPython 7.0+ supports Python 3.5 and above.
When using Python 2.7, please install IPython 5.x LTS Long Term Support version.
Python 3.3 and 3.4 were supported up to IPython 6.x.

See IPython `README.rst` file for more information:

https://github.com/ipython/ipython/blob/master/README.rst

=============================================================
Check the mentioned READE.rst to find:

Welcome to IPython.  Our full documentation is available on `ipython.readthedocs.io
<https://ipython.readthedocs.io/en/stable/>`_ and contains information on how to install, use, and
contribute to the project.

**IPython versions and Python Support**

**IPython 7.0** requires Python version 3.5 and above.

**IPython 6.x** requires Python version 3.3 and above.

**IPython 5.x LTS** is the compatible release for Python 2.7.
If you require Python 2 support, you **must** use IPython 5.x LTS. Please
update your project configurations and requirements as necessary.

The Notebook, Qt console and a number of other pieces are now parts of *Jupyter*.
See the `Jupyter installation docs <https://jupyter.readthedocs.io/en/latest/install.html>`__
if you want to use these.

================================================

Correct solution:

https://zhidao.baidu.com/question/205685363715017045

mxlzhenzhu · 发表于 2019-1-3 12:11

Further trial, type the command:

$ python3

it returns:

Python 3.6.5 (default, Apr 1 2018, 05:46:30)
[GCC 7.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.

mxlzhenzhu · 发表于 2019-1-3 23:44

本帖最后由 mxlzhenzhu 于 2019-1-4 10:30 编辑

Download the Qt from Tsinghua Mirror site:
https://mirrors.tuna.tsinghua.edu.cn/qt/archive/qt/5.0/5.0.0/

I downloaded it and saved in the /home/../Downloads

Then type the following command to run(for Ubuntu 18.04.1) the *.run file in the terminal(..../Downloads directory)
./qt-linux-opensource-5.0.0-x86_64-offline.run

Have fun.
================================================
Another error:

qmake: could not exec '/usr/lib/x86_64-linux-gnu/qt4/bin/qmake': No such file or directory

Try the following guide
https://blog.csdn.net/x356982611/article/details/71169940
and the VI command can be referred to:
https://blog.csdn.net/sunbo_csdn/article/details/81917214

mxlzhenzhu · 发表于 2019-1-5 11:18

本帖最后由 mxlzhenzhu 于 2019-1-5 21:17 编辑

下载SoQt：
https://pkgs.org/download/libsoqt4-dev

文件名like this
libsoqt4-dev-(version).deb
这个文件，安装过程中发现是支持Qt4的，而我去下载了一个Qt5，双击运行，看看能成否。

补充说明1，虽然安装了Qt5，但是这个.deb文件，会自动安装了Qt4，所以，最终并没有带来影响，可能Qt5安装多余了。补充说明2，后续修改了Python默认版本以后，即可正常运行AUTO了。

mxlzhenzhu · 发表于 2019-1-5 11:41

本帖最后由 mxlzhenzhu 于 2019-1-5 20:54 编辑

在../auto/07p下面，./configure以后，如果SoQt等安装正常，应该是这样的

然后执行两个命令：

make

make clean

如果make不成功，我就不知道了，你还是对照安装目录的建议搞吧。

接着设置环境变量，手册里都有命令的，不抄了。

修改Python默认版本，参考：https://blog.csdn.net/u014525760/article/details/79675469，也就两个命令：

sudo rm -rf /usr/bin/python
sudo ln -s /usr/bin/python3 /usr/bin/python

复制代码

mxlzhenzhu · 发表于 2019-1-5 21:07

按照手册的命令，第一个案例算通了：

First Demo

mxlzhenzhu · 发表于 2019-1-14 10:34

nvh@nvh-virtual-machine:~/Documents/2018-12-27 AUTO-07p pakage/auto07p-0.9.1/auto/07p$ auto

Command 'auto' not found, did you mean:

command 'uuto' from deb uucp

nvh@nvh-virtual-machine:~/Documents/2018-12-27 AUTO-07p pakage/auto07p-0.9.1/auto/07p$ cd
nvh@nvh-virtual-machine:~$ source $HOME/auto/07p/cmds/auto.env.sh

nvh@nvh-virtual-machine:~$ auto
Python 3.6.7 (default, Oct 22 2018, 11:32:17)
[GCC 8.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
(AUTOInteractiveConsole)
AUTO>

mxlzhenzhu · 发表于 2019-1-14 15:40

本帖最后由 mxlzhenzhu 于 2019-1-14 15:57 编辑

nvh@nvh-virtual-machine:~$ auto
Python 3.6.7 (default, Oct 22 2018, 11:32:17)
[GCC 8.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
(AUTOInteractiveConsole)
AUTO> mkdir ab
AUTO> cd ab
AUTO> demo('ab')
Copying demo ab ... done
Runner configured
AUTO> auto('ab.auto')

***Generate starting data***
gfortran -fopenmp -O -c ab.f90 -o ab.o
gfortran -fopenmp -O ab.o -o ab.exe /home/nvh/auto/07p/lib/*.o
Starting ab ...

  BR PT  TY  LAB PAR(2)       L2-NORM       U(1)       U(2)
1    1  EP 1 8.00000E+00 0.00000E+00 0.00000E+00 0.00000E+00
1 31  UZ 2 1.40000E+01 0.00000E+00 0.00000E+00 0.00000E+00
1 36  UZ 3 1.50000E+01 0.00000E+00 0.00000E+00 0.00000E+00
1 41  UZ 4 1.60000E+01 0.00000E+00 0.00000E+00 0.00000E+00
1 46  UZ 5 1.70000E+01 0.00000E+00 0.00000E+00 0.00000E+00
1 51  UZ 6 1.80000E+01 0.00000E+00 0.00000E+00 0.00000E+00

Total Time 0.572E-02
ab ... done

***Compute stationary solution families***
Starting ab ...
Traceback (most recent call last):
  File "/usr/lib/python3.6/code.py", line 91, in runcode
exec(code, self.locals)
  File "ab.auto", line 12, in <module>
ab = ab + run(solution,c='ab.2')
  File "/home/nvh/auto/07p/python/AUTOCommands.py", line 1585, in run
res = runner.run()
  File "/home/nvh/auto/07p/python/runAUTO.py", line 377, in run
self.runCommand(command, solution)
  File "/home/nvh/auto/07p/python/runAUTO.py", line 478, in runCommand
status = self.__runCommand_noredir(command, solution)
  File "/home/nvh/auto/07p/python/runAUTO.py", line 534, in __runCommand_noredir
self.__write_constants_solution(stdin, solution)
  File "/home/nvh/auto/07p/python/runAUTO.py", line 515, in __write_constants_solution
solution.write(f,mlab=True)
  File "/home/nvh/auto/07p/python/parseS.py", line 1066, in write
write_enc(line+os.linesep)
  File "/home/nvh/auto/07p/python/parseS.py", line 1032, in write_enc
output.write(s.encode("ascii"))
TypeError: write() argument must be str, not bytes
AUTO>

Does anyone know  how to deal with this error?

chaosy · 发表于 2019-8-21 10:53

楼主, 除了官方的算例()AUTO-07P: Continuation and bifurcation software for ordinary differential equations)之外还有其他的算例书或者文章吗, 靠上面这本书入门有点困难

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[应用数学] Some experience of AUTO software on bifurcation analysis

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