Anna-Karin Mork | 4 Aug 16:32 2009

Configure problems


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

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
(Continue reading)

Frederic Y. Bois | 8 Jun 12:41 2009

New patch for Windows installation

A new patch has just been posted for installing version 5.3.1 under Windows

MCSim on Cygwin

Attached is a listing from a build attempt on Cygwin on Windows XP

There are errors in the creation of

What am I doing wrong ?

cd ./mod; make
make[1]: Entering directory `/usr/local/src/mcsim/mod'
make[1]: Nothing to be done for `one'.
make[1]: Leaving directory `/usr/local/src/mcsim/mod'
cd ./sim; make lib
make[1]: Entering directory `/usr/local/src/mcsim/sim'
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/cc7g5Fz1.o:lsodes1.c:(.text+0x956): undefined
reference to `_CalcDeriv'
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/cc7g5Fz1.o:lsodes1.c:(.text+0x2b9c): undefined
reference to `_CalcDeriv'
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/cc7g5Fz1.o:lsodes1.c:(.text+0x2ed9): undefined
reference to `_CalcDeriv'
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/cc7g5Fz1.o:lsodes1.c:(.text+0x387d): undefined
reference to `_CalcDeriv'
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/cc7g5Fz1.o:lsodes1.c:(.text+0x3b83): undefined
reference to `_CalcDeriv'
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/cc7g5Fz1.o:lsodes1.c:(.text+0x4212): more undefined
references to `_CalcDeriv' follow
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/ccGXujfI.o:mh.c:(.text+0x2bbb): undefined reference to `_InitModel'
/cygdrive/c/DOCUME~1/Tim/LOCALS~1/Temp/ccGXujfI.o:mh.c:(.text+0x3474): undefined reference to `_InitModel'
(Continue reading)


"Standard Platform" ?

Ive been trying to use MCSim on both windows and Mac OS (Leopard), and have run in to quirks related to the compilation that prompt the following question:

What is thestandard platform that MCSim development is being done on ? Im assuming by posing this question that the build scripts and tools are all designed for a certain Linux or Unix platform and that a build will run clean on such a platform.

Ive been unsuccessful at finding good help in build MCSim for Mac OS, and am attempting to create a virtual machine running a linux distro, so that I can at least have a reference installation to refer to as I work through what it takes to build for Mac.

Thanks in advance for any help you can give me.

Tim Hansell

Henry M. Jackson Foundation


2729 R St, Bldg 837

Wright-Patterson AFB, OH 45433-5707

Phone: (937) 255-4332

E-Mail: Timothy.Hansell <at> WPAFB.AF.MIL

Attachment (smime.p7s): application/x-pkcs7-signature, 7003 bytes
Help-mcsim mailing list
Help-mcsim <at>
Bill Harris | 12 May 04:12 2009

Re: Fwd: questions about MCSim


It's good to see another MCSim user in the Pacific Northwest!  Enjoy
your modeling!

If it's of any use, I created a quick reference card for MCSim that
includes some of its newer features.  You can find it along with a
presentation I made two and a half years ago in Portland at

As to your question, I use J ( as my scripting
language, and I've written J scripts to assemble simulation files
programmatically, run the model, and produce graphs.  That worked quite

For a simple example, see  While
that article doesn't contain the scripts, it does show the results.  For
example (as I recall), I had a script that picked percentage ranges for
the three key parameters, assembled a simulation file, ran the
simulation, and plotted and saved the table of eight graphs or the stick
plot you can see.


Bill Harris            
Facilitated Systems                              Everett, WA 98208 USA                  phone: +1 425 337-5541
Zhenhong Li | 14 Apr 21:26 2009

Fwd: questions about MCSim


I am a PhD student at Oregon Health & Science University. I am using MCSim to do my modeling work for hormone
profiles in Fathead Minnows. The question I would like to ask is about "vectors". 

According to MCSim manual, vectors should be defined as <variable-name>'['<integer>']'. Can I define
the <integer> as a variable? I mean, for example, I would like to use a 'n' to replace the <integer>; then in
the first run, I define n=10 (the vector has a length of 10), and in the second run I define n=7 (the vector has
a length of 7), as so on. Then, for different runs, the length of the vector varies.

I tried several times, it seems that the present program does not accept it. Would you please give me any
suggestion? Can I modify the program a little bit to add this function in? and how? Thank you very much!


Frederic Y. Bois | 3 Mar 09:32 2009

GNU MCSim version 5.3.1 release

Version 5.3.1 of GNU MCSim is now available from
It fixes some problems with OptimalDesign();

Frederic Bois
Frédéric BOIS | 12 Jan 09:16 2009

GNU MCSim version 5.3.0 release

Version 5.3.0 of GNU MCSim is now available from

Frederic Bois
Frederic Y. Bois | 8 Sep 10:10 2008

new mcsim users list : mcsim-info

A new public list "Info-mcsim" has been set up to provide general announcements
on MCSim.
Frederic Y. Bois | 25 Mar 15:02 2008

The official MCSim web page can now be found at
The old page point to there now.

F. Bois
Frederic Bois | 3 Mar 17:53 2008

MCSim source code is now under CVS access on GNU Savannah

All the source code of MCSim is now accessible online via CVS on GNU Savannah.
You can fetch the latest code (almost!) as well as past versions.
You can also envision contributing to the project ;^)...
Just go to
(for help go to
From now on maintenance an diffusion of the software will be made via Savannah.

F. Bois