libroadrunner-devel — development mailing list

[Libroadrunner-devel] New beta8

[Andy S. <and...@gm...>]

Uploaded new beta8 to SF, binaries for Linux64 and Win32.

This version has the newest libsbml 5.11 — no problems found yet. 

Adds reading matrix rows via row/column name:

In [2]: r=RoadRunner("feedback.xml")
Notice: Using LLVM symbol/value cache

In [3]: mat = r.getFullStoichiometryMatrix()

# print the mat
In [4]: mat
Out[4]:
    J0, J1, J2, J3, J4
S1 [[  1, -1,  0,  0,  0],
S2  [  0,  1, -1,  0,  0],
S3  [  0,  0,  1, -1,  0],
S4  [  0,  0,  0,  1, -1]]


# can look up by either row or col name, use a col name here
In [5]: mat['J0']
Out[5]: array([ 1.,  0.,  0.,  0.])

# row name here
In [6]: mat['S4']
Out[6]: array([ 0.,  0.,  0.,  1., -1.])

# if the arg does not match either the row or col names, it falls through to the Numpy mp_subscript function.
# here bumpy pulls the 2nd row
In [7]: mat[2]
Out[7]: [ 0.  0.  1. -1.  0.]

# standard bumpy error message if invalid subscript arg. 
In [8]: mat['xxx']
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-8-1d4dda1fffaf> in <module>()
----> 1 mat['xxx']

ValueError: field named xxx not found.

[Libroadrunner-devel] new beta

[Andy S. <and...@gm...>]

New beta is up, beta 7 (just Linux now, will get a Windows one in the morning). This build adds enhancements to event handling with variable time steps, some general improvements and specifically adds output points on each side of the event boundary separated by 1 machine epsilon. 

Some examples of the updated behavior are attached. The top plot is the before behavior, below is new. 

Note, this only works with variable time stepping, the fixed time steps will always produce a result like the top plot, as by definition it is on a fixed time points. 

Note, with variable time stepping, it is easy to skip over events, make sure you are setting your SimulateOptions.maximumTimeStep to a sane value to avoid too long time steps that might miss event triggers. 

[Libroadrunner-devel] New beta6

[Andy S. <and...@gm...>]

Hi Guys, 

The new beta6 is up on source forge. 

All of the performance enhancements from the symcache branch have been merged into the main develop branch, and there is the same build on all platforms. 

The main thing this build does is add support for a wider range range of compilers / platforms. The #ifdef zoo has been cleaned up and RR now builds on the following platforms:

1: RedHat Enterprise >= 6.5 with gcc >= 4.4
2: SUSE Linux Enterprise Server >= 11 with gcc >= 4.4
3: Ubuntu >= 12.04 with either clang or gcc
4: Mac OSX 10.6 - 10.9 with either clang or gcc
5: Win32, MSVC 2010 or 2012

Also, roadrunner should now compile in either C++ 03 or C++11 mode, but only C++03 has been extensively tested.  

Binaries are up for Linux (Ubuntu >= 12.04, but should work with any newer distro), Mac OSX >= 10.7 and Win32. 

A lot of HPC clusters use RHEL 6.5 or Suse 11, so these have to be supported for a while. 

[Libroadrunner-devel] New build

[Andy S. <and...@gm...>]

New beta5 was pushed to SF. 

This build corrects a bug that was introduced with nested conditionals.

[Libroadrunner-devel] test

[Andy S. <and...@gm...>]

test