Activity for AUTO-07P
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Anuj Pradhan posted a comment on discussion Help
Hi, I'm new to auto-07p. I was trying to run a continuation on a system of 2 ODEs but keep getting a MX error. I've tried adjusting the step size, the NTST and the tolerance values but the issue is still there. I've attached the .f90 file and .c file for reference.
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Przemyslaw Perlkowski posted a comment on discussion Help
Is it possible to follow in Auto the periodic solutions of the integrodifferential equations? Przemyslaw
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Neil M Ribe posted a comment on discussion Help
I have AUTO-07p installed on Mac OSX 11.6, and all my existing AUTO programs run fine. However, when I try to run a new code (in this case "capgeneral.f") I get the following: neilmribe% @r capgeneral c1 gfortran -fopenmp -O -c capgeneral.f -o capgeneral.o gfortran -fopenmp -O capgeneral.o -o capgeneral.exe /Users/neilmribe/auto/07p/lib/.o Starting capgeneral ... make: ** [run] Segmentation fault: 11 capgeneral ... done The .o and .exe are thus being created, but I am prevented from running the code...
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Chiraprabha Bhattacharyya posted a comment on discussion Help
I am having problems checking stability of a solution branch in boundary value problems. For stationary solutions of ODEs (IPS=1), stability of a branch is indicated by the sign of PT in the fort.7 file. But for boundary value problems (IPS=4), there is no such stability indicator. How do I examine stability of branches for BVPs? (eg. a transcritical bifurcation problem with some boundary conditions and integral conditions) Can someone help me out?
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Karishma created ticket #11
digifil header error
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lanast posted a comment on discussion Help
Hi community, I am using AUTO-07p on Windows 10 and have successfully run the enz demo from the manual. However, at the lrz demo, which involves a 2nd run, I am getting this error: AUTO> run(lrz('HB1'),IPS=2,ICP=['rho','PERIOD'],NMX=35,NPR=2,DS=0.5) Starting lrz ... Traceback (most recent call last): File "<console>", line 1, in <module> File "c:\AUTO\auto\07p\python\AUTOCommands.py", line 1585, in run res = runner.run() File "c:\AUTO\auto\07p\python\runAUTO.py", line 377, in run self.runCommand(command,...
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Thanks Javier, this was the issue
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Javier Perez modified a comment on discussion Help
I don't sure if in linux environment work it, but you could try typing: source $HOME/auto/07p/cmds/auto.env.sh
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I don't sure if in linux environment work it, but you could try typing source $HOME/auto/07p/cmds/auto.env.sh
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Got it, it was that the PATH was not set yet. So when typing which auto it did not know where the software path is. Nevertheless I would like to ask whether someone has encountered the error /users/.../auto/07p/python/interactiveBindings.py: No such file or directory when simply entering auto in the terminal. The file is actually there and the python module is loaded, but it seems it is not recognized by the computer (?)
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Hi community I have unpacked the software on linux machine according to the manual and set the environmental variable $HOME/auto/07p/cmds/auto.env.sh. However typing "auto" inside the command window in order to start the command line interface leads to auto: command not found. Is it possible that there is no command line interface on linux? Or do I have to change my current directory somehow, so that is recognized as a program? Many thanks! lanast
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baudelaire31 created ticket #3
Exporting output data
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Bart Oldeman created a blog post
Migrated to GitHub
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Maurizio De Pitta' posted a comment on discussion Help
Hello everyone, how can I run AUTO 07p given an ODE system defined in C file where I have several #include directives of other header H files (associated with C sources) that define some of the functions that I call in the RHS of my system?
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Divide by zero error and crash
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Maureen Chou posted a comment on discussion Help
I encountered the same results. I guess this may be caused by the version of numpy or other depended python packages. But I do not have time to figure out which package play the role. I changed the version of python, matplotlib on my mac. Nothing helps. It seems that the newer version of python modules are using different logics from the older ones, so I think one possible way to takcle this problem may be installing all the modules used by the source code developers of AUTO 07p
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Woo Seok Jung posted a comment on discussion Help
Hi, I recently downloaded auto-07p in ubuntu 16.04, and I'm practicing it with the provided documentation. But I have a problem in generating every plot when I run any demo codes (demo2, demo3, userScript, etc) I keep getting RuntimeError: maximum recursion depth exceeded while calling a Python object So I changed the recursion limit by using sys.setrecursionlimit, but then I got an error message Segmentation fault (core dumped) I think there is no problem in installation of auto files because all...
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system does not have required compilers and libraries
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Not able to see all the results in the bifurcation diagram (8 dim ODE)
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There are two workarounds: 1. set NPR=1 and use the values in the solution file; for every line in the bifurcation diagram there is now a label with a corresponding solution. 2. or: use the PVLS subroutine (see demo pvl for examples) to put the values of U into unused parameter values (e.g PAR(21) to PAR(29)) and list those explicitly in the ICP list. All parameters that are listed in ICP are put in the bifurcation diagram file.
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Floating point number format
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This was done in 2013 in the SVN here and now at https://github.com/auto-07p
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problem in compiling fcon.c
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Install error: "No rule to make target `install'. Stop."
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There has never been a proper "make install". You compiled successfully and can now use AUTO by doing "source cmds/auto.env.sh" (you may need to edit that file to adjust AUTO_DIR if AUTO is not in $HOME/auto/07p).
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Error when trying to plot since instation of Matplotlib 2.0
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It's a combination of not overriding N.nonzero (because that is now used by matplotlib itself) but also explicitly using N.flatnonzero in the AUTO python code, as done here: https://github.com/auto-07p/auto-07p/commit/df84ddbc79ae86f13d5840f3c6cdfdfe56b7936a it's now fixed in that github repository.
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fix auto-07p for newer numpy
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Please try: https://github.com/auto-07p/auto-07p it's fixed there and the plotter tested with Python 3, numpy and matplotlib.
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E for exponent dropped in solution file
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Fails to build with GCC/ gfortran 8: "Error: Actual argument contains too few elements for dummy argument ‘angle’ (3/4) at (1)".
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I fixed it here: https://github.com/auto-07p/auto-07p/commit/4d22983d627762fc2d6e763796668e6ea4f7a783 just replace ANGLE(3) with ANGLE(4) and it will compile.
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Minor compile fix
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fcon.c
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I L created ticket #8
Install error: "No rule to make target `install'. Stop."
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D A posted a comment on ticket #7
This patch seems to fix that particular issue, it looks as though parseB.py expects numpy to concatenate to an empty array which fails. There's definitely a better way to do this, but as a quick and dirty fix we can just catch the error and return the expected result. 371c371,372 < stab = N.concatenate((N.nonzero(N.less(points[:-1]*points[1:],0)), --- > try: > stab = N.concatenate((N.nonzero(N.less(points[:-1]*points[1:],0)), 372a374,375 > except ValueError: > stab = N.array([len(points)-1])
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Drei Eck posted a comment on ticket #9
Using the old g95-compiler seems to be a workaround, but not a proper solution, though.
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Jose Manuel Montilla García posted a comment on ticket #9
I'm having the very same problem. I'm trying to install in Manjaro 18.0.2 and can't have a succesfull instalation. I have tried the solution of Carsten Bruns but the result is a corrupted instalation that does't work. Any news?
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Carsten Bruns posted a comment on ticket #9
As a temporary workaround, -std=legacy can be added to the compiler flags, e.g. in the FFLAGS variable in the Makefile of plaut (07p/plaut/Makefile.in). This changes the error message into a warning, the same way as older version of gfortran behaved.
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Omer Tzuk posted a comment on ticket #7
Hello Sergey, I've recently tried to use the patch (commenting out the line you've mentioned), but I get an error message like this: ValueError: all the input arrays must have same number of dimensions
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I have commented out the line N.nonzero = N.flatnonzero, however, I still get an error message when I try to plot something using Python 3: $ auto Python 3.7.0 (default, Oct 9 2018, 10:31:47) [GCC 7.3.0] on linux Type "help", "copyright", "credits" or "license" for more information. (AUTOInteractiveConsole) AUTO> from autoutilities import plotCont AUTO> bif,ps=plotCont() ... Using plain TkInter for plotting. You can obtain better quality graphics using matplotlib (http://matplotlib.sf.net). Traceback...
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Fails to build with GCC/ gfortran 8: "Error: Actual argument contains too few elements for dummy argument ‘angle’ (3/4) at (1)".
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kumara posted a comment on ticket #6
Not really. But the work around is you can access the info of the states using python commands. Been more than two years I stopped working on bifurcation analysis, don't exactly remember the commands. Regards, Kumara On Fri, Oct 12, 2018 at 6:02 AM Parul Verma parulv1@users.sourceforge.net wrote: Hi, I have the same problem. I have a system of 9 ODEs. Was this problem solved? Regards, Parul [support-requests:#6] https://sourceforge.net/p/auto-07p/support-requests/6/ Not able to see all the results...
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Parul Verma posted a comment on ticket #6
Hi, I have the same problem. I have a system of 9 ODEs. Was this problem solved? Regards, Parul
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Hello, I am also facing matplotlib related errors. When I try using PyPlaut, I get the following: Traceback (most recent call last): File "/home/parul/Software/AutoForLinux/auto/07p/python/graphics/pyplaut.py", line 605, in <module> runner = PyPlautInteractiveConsole(exportFunctions(), b, s) File "/home/parul/Software/AutoForLinux/auto/07p/python/graphics/pyplaut.py", line 82, in __init__ self.handle.config(**dict) File "/home/parul/Software/AutoForLinux/auto/07p/python/graphics/windowPlotter.py",...
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I think you need to source auto.env.sh first, so that the path to AUTO is added in your bash profile.
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Sergey Kirpichev posted a comment on ticket #7
Could you try https://sourceforge.net/p/auto-07p/patches/2/ ? I have managed to make auto-07p & matplotlib v2.2.3 working with this little patch.
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fix auto-07p for newer numpy
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Dap Eu posted a comment on discussion Help
Dear Maia, I have encountered exactly the same problem. May I know whether you have get it solved? Thanks! Dap
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Mary posted a comment on discussion Help
Hi After I have installed Auto-07p, I have run an AUTO demo by typing (cd auto/07p/demos/abc), then typing (@r abc), I received an error message (sh: @r: command not found) . Please, could any one hel me?
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dch posted a comment on discussion Help
I have some code that uses some lapack libraries, and I am able to compile it with the auto libraries from the command line. However when I use the python utility AUTO, and try and run this code of mine, AUTO tries to recompile it. However, it is unable to find the lapack libraries, and compilation fails. Is there a way to add the lapack library call to the makefile (or the compile command that AUTO) uses it? Also, is it possible to just compile once, and not every time? Thanks. David Halpern
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Dear Laurien, Sorry for the late response. I just returned from vacation. I could not get solution to that problem. But we can access the data of all the states printed using some 'python' language commands. Regards, Kumara On Thu, Jun 1, 2017 at 9:38 AM, Laurien Vandewalle lavdwall@users.sf.net wrote: I have the same problem... Did you find a solution? AUTO-07P - Not able to see results for more than 6 states in the bifurcation diagram. Problem is solved without errors though? https://sourceforge.net/p/auto-07p/discussion/68848/thread/894d200c/?limit=25#680a...
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Laurien Vandewalle posted a comment on discussion Help
I have the same problem... Did you find a solution?
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Leonardo Gordillo posted a comment on ticket #7
Thanks for your answer Omer. I spent a few days trying to install AUTO in Mac OS X Sierra. Typical errors I bumped into after plotting in AUTO were: > Exception in Tkinter callback > Traceback (most recent call last): > File "/anaconda/lib/python2.7/lib-tk/Tkinter.py", line 1536, in __call__ > return self.func(*args) or //anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2507: VisibleDeprecationWarning: `rank` is deprecated; use the `ndim` attribute or function instead. To find the rank...
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No...I reinstalled python with Matplotlib 1.5, and auto again and it works as previously, but I did not manage to make auto work with Matplotlib 2.0
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Have you solved the problem? I also have it. I tried to downgrade the matplotlib but it did not work either. Any progress?
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I have the same error when trying to parse bifdiag object: assert isUniqueSeq(self.coordnames),...
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Error when trying to plot since instation of Matplotlib 2.0
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Jarek Glowacki modified a comment on discussion Open Discussion
In the course of my PhD reserch I have faced a problem that for my particular 26-D...
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In the course of my PhD reserch I have faced a problem that for my particular 26-D...
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Hi, I've a dynamical systsem (Aircraft) with 8 state variables (U1,U2,U3..U8) (and...
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Hi, I've a dynamical systsem (Aircraft) with 8 state variables (U1,U2,U3..U8) (and...
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Not able to see all the results in the bifurcation diagram (8 dim ODE)
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Hi, I've a dynamical systsem (Aircraft) with 8 state variables (U1,U2,U3..U8) (and...
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Parallellize part of fort.8 I/O (FP to string c...
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Call STUPBV in parallel for OpenMP.
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Make sure FUNI does not overflow on U/UOLD in c...
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Store UOLD vector into U past NDIM. This allows...
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Correct NTSTNA in LCSPBV subroutine call.
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Integrate master and worker code more in LCSPBV...
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Simplify MPI logic in CNRLBV, moving it to LCSP...
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More CNRLBV merging for master and workers. Bot...
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Eliminate LCSPBV_NOT_CONVERGED and make worker ...
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Further merge master/workers in CNRLBV
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Merge MPI_CNRLBV_WORKER back into CNRLBV to sav...
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Call PVLI at a higher level, moves all test fun...
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Call MPIGAT/PVLS from STEPBV instead of NEWTONB...
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Eliminate use of QT3_SUPPORT methods for pulldo...
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Qt4 compat for file dialog windows.
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Replace insertItem with addItem for lists for Q...
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Use toLocal8Bit() instead of implicit QString->...
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Call constructors for QComboBox, QSpinBox, QDia...
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Create a seperate method for every pulldown men...
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Workaround for the menu bar in newer Mac OS X v...
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Optimize INTWTS so it is around 4-5x faster.
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Scatter adapted TM,UPS,UOLDPS to workers as soo...
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Let INTERP work on two solutions in one loop, t...
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Simplify INTWTS interface/implementation to rem...
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Do UPS output in WRTBV9 in partly in parallel a...
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Make mpigats subroutine more general so it work...
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Add dummy mpigats for nompi.f90
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Make writing to text strings for solution files...
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Centralize computation of counts and displaceme...
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In MPI communication send TM instead of DTM, an...
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Fix uninitialized ISTOP in MPI worker code from...
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Compute maxima of solution components for fort....
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Call STPLBV from MPI workers, with most measure...
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Use parallel scaling for periodic solutions com...
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Introduce RMXUPSP/RMNUPSP to calculate minimum/...
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Run STDRBV in parallel, including the scaling, ...
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