Users list for the GNU MCSim modeling and simulation program

headers Lisa Lowe | 8 Jun 2012 16:16 · /local/

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Help-mcsim mailing list
Help-mcsim <at> gnu.org
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Hi,

It says on the website that gsl is not required with the latest mcsim,
but I get the following error when doing "make check":
  -Testing mod on perc.model
  --PASSED-
  -Testing makemcsim on perc.model
  -Compiling mcsim.perc...
  -/usr/bin/ld: cannot find -lgsl
  -collect2: ld returned 1 exit status
  --FAILED-

Also, gsl is installed on the cluster where I am working, and I added
its path to LD_LIBRARY_PATH (/usr/local/gsl/lib).  The compiler still
doesn't find it.  As per the archived emails about this problem, I
tried the command : /sbin/ldconfig -p | grep gsl, and it comes up with
nothing.  Are there other system variables I should be setting so it
can find this library?  Should the latest version need the gsl library
to do the samples?

Thanks!
Lisa

In case anyone else here runs Debian, I created a Debian package that
may be of help.  It's the first time I have shared one, so there may be
all sorts of problems.

I created it using ./configure, make, checkinstall on a Debian Squeeze
(6.0.3) amd64 architecture system.  libsbml 5.4.0 had been installed
previously.  I presume (and Frederic seems to agree) that the
./configure is general enough so that specifics besides being a 64-bit
system may not be an issue.

While I think I'm trustworthy, use it at your own risk.  It's not much
easier to use this than to build it locally, but it does save a few
minutes.

While I don't have much spare time, I do welcome your feedback.  If I
did something strange that's preventing it from being useful, perhaps I
can learn and then improve it to make it more generally useful.

You can find the download on the main MCSim page at
http://www.gnu.org/software/mcsim/.  

Bill

PS: If anyone has a foolproof installation for Windows (in particular,
for XP Pro or XP 64), I'm still interested.  I did that once years ago
with an earlier version of MCSim, but my recent attempts have failed.
An msi or the like would be great, if anyone is _really_ dedicated. 
--

-- 
Bill Harris                  
Facilitated Systems
http://makingsense.facilitatedsystems.com/

Has anyone here used MCSim to model a hysteresis process?  Think of the
energy used by a building as a control system (thermostat) turns on and
off.  Instead of a 0.25-0.5 degree C hysteresis band, as you might see
in a home system, think of a significant band -- perhaps a 5-10 degree
hysteresis band.  That's not quite the problem, but I hope it makes it
understandable. 

What I'd want is something like two linear (or perhaps nonlinear)
equations describing energy use per unit time as a function of outdoor
air temperature, one for each state of the system (there could be more
than two states, of course).  The model would need to estimate the
temperatures at which the system switched between the states, and I'd
want to be able to feed it a new path of temperatures and have it
calculate the distribution of predicted energy use per unit time for
that path.

I've looked at hidden Markov models, but I'm not sure the assumptions of
HMMs quite fit, and I've not made it work (R's depmixS4, for example).
It does nicely separate the observations and transitions, though.

I've looked at R's cusp, but I don't yet understand how to model the
observations and their uncertainty.

I've considered relearning Kalman filtering but haven't yet.

Any ideas on how to set up the model in MCSim?  Any examples?

Thanks,

Bill
--

-- 
Bill Harris                  http://makingsense.facilitatedsystems.com/
Facilitated Systems                              Everett, WA 98208 USA
http://www.facilitatedsystems.com/               phone: +1 425 374-1845

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Help-mcsim mailing list
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_______________________________________________
Help-mcsim mailing list
Help-mcsim <at> gnu.org
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Hi Rudy,

I cc this to the help mcsim list, as it is of general interest...

Yes, the easy way to do this is to us the SetPoint() simulations. You can actually take an MCMC output file
straight as a SetPoint input parameters' file.
You can also create such a file yourself to have a grid sampling, or a specific need (like sensitivity
analysis: you can use Simlab (from A. Saltelli) to generate
parameter vectors and then input them in MCSim to run your model, the output can them be further processed by Simlab).

Frederic

>>> "Gunawan, Rudy" 19/10/2010 19:35 >>>

...

I have a small question, may be trivial for you. I would like to know how I can run a MCSim simulation if one or
more of the parameters has an array of values ? Preferably, if I can automate parameter assignment by
reading the values from .txt file, for example. The idea is I would like to make a simulation out of the MCMC
MCSim outputs. It's quite like Monte Carlo runs, but it is not. I hope it is not confusing. Thank you very
much for all your help.

Regards,

Rudy

__________________________________________________
Rudy Gunawan, Ph. D
Post Doctoral Research Associate
Biological Monitoring/Modeling
Pacific Northwest National Laboratory

New code (available on Savannah) allows you to perform stochastic optimization
with GNU MCSim. The MCMC simulation type flag needs to be set to value "4"...

This is mildly embarrassing, for I think I should know what to do.  I'm
coming back to MCSim for some work I need to do -- work I intended to do
tonight -- and I'm stuck.

I'm running Ubuntu 9.10 (32-bit), and I just installed MCSim v5.3.1.  I
first tried from CVS, but I couldn't find configure, so I grabbed the
tarball, and that worked.

Then I tried configure and got

I found http://osdir.com/ml/help-mcsim-gnu/2009-08/msg00001.html and
http://osdir.com/ml/help-mcsim-gnu/2009-08/msg00002.html.  Running
sudo ldconfig -v didn't help.  I gather you only need to set
LD_LIBRARY_PATH if libgsl isn't in /usr/lib, but

,----
|   /usr/lib:
|   total used in directory 488844 available 15233936
|   .
|   .
|   .
|   lrwxrwxrwx   1 root root       20 2009-11-29 18:04 libgslcblas.so.0 -> libgslcblas.so.0.0.0
|   -rw-r--r--   1 root root   226580 2008-12-22 05:28 libgslcblas.so.0.0.0
|   lrwxrwxrwx   1 root root       16 2009-11-29 18:04 libgsl.so.0 -> libgsl.so.0.13.0
|   -rw-r--r--   1 root root  1964616 2008-12-22 05:28 libgsl.so.0.13.0
|   .
|   .
|   .
`----

I did try 

,----
| ~/bin/mcsim-v5.3.1/mcsim$ export LD_LIBRARY_PATH=/usr/lib
| ~/bin/mcsim-v5.3.1/mcsim$ echo $LD_LIBRARY_PATH
`----

but ./configure still failed in the same way.

Finally, I found an old email from Frédéric suggesting to use 

,----
| gcc *.c -lm -lgsl -lgslcblas 
`----

instead of make.  I tried running find to find *.c files and pass them
to gcc, but that failed with lots of 

,----
| /usr/bin/ld: cannot find -lgsl
| collect2: ld returned 1 exit status
`----

and other errors.

I did have 5.2.beta working sometime in late 2008 / early 2009, but I've
been away from it since then.  Can anyone point out the obvious error in
my ways?  I now have a real need for MCMC applied to a dynamic model.

Thanks,

Bill
--

-- 
Bill Harris                  http://makingsense.facilitatedsystems.com/
Facilitated Systems                              Everett, WA 98208 USA
http://www.facilitatedsystems.com/               phone: +1 425 374-1845

Hi,

I have been trying to install MCSim on Windows XP. I have already had C 
compilers, both gcc and lcc. 'Mod' has already worked properly (I guess). When 
I did 'mod perc.model', it gives me 'model.c' as expected. Nevertheless, the 
problem arises when I attempt to compile 'model.c', it gave me there errors:

"... undefined reference to _vbModelReinitd"
"... undefined reference to CalcInputs"
"... undefined WinMain <at> 16"

While the last error can be fixed by adding 

int main(int argc, char *argv[]) {
    return 0;
}

into model.c, I have no clue for the first two errors. I have followed the 
aforementioned steps. I put 'mod.exe' into the 'sim' folder. Moreover, I 
move 'perc.model' into the 'sim' folder in order to link it with the other sim 
files. 

So if anybody has some suggestions, please share. Thank you very much.

Hi,

I am trying to install McSim to run it on a cluster and can therefore
not use the standard installation (/usr/local/..).  When trying to
configure I get this:

h18n01$ ./configure --prefix=$HOME
LDFLAGS=-L/afs/pdc.kth.se/home/a/akmork/lib       

checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... yes
checking for gzip... yes
checking for gnuplot... no
checking for wish... no
checking for info... yesI have installed the GSL library in my home
directory $HOME/lib.
checking for install-info... no
checking for makeinfo... yes
checking for gv... no
checking for touch... yes
checking for date... yes
checking for tex... no
postscript not generated
checking for dvi2ps... no
checking for texi2html... no
checking for main in -lm... yes
checking for main in -lgslcblas... no
configure: error: You first need to install the 'gslcblas' library to
build MCSim

h18n01$ cd ~/lib
h18n01$ ls
libgsl.a   libgsl.so.0      libgslcblas.la    libgslcblas.so.0.0.0
libgsl.la  libgsl.so.0.8.0  libgslcblas.so    pkgconfig
libgsl.so  libgslcblas.a    libgslcblas.so.0

What am I doing wrong?

Thanks!
Anna-Karin

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mcsim.perc: command not found

gsl problems

Debian package availability

MCSim and hysteresis?

problems: make[1]: ***[libmcsim.a] error 1

problems: make[1]: ***[libmcsim.a] error 1

Rép. : MCSim questions

Stochastic optimization with MCSim

configure: error: You first need to install the 'gslcblas' library to build MCSim

MCSIM installation

Configure problems

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