http://permalink.gmane.org/gmane.comp.gnu.mcsim hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.comp.gnu.mcsim/6906 <pre>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</pre> Bill Harris 2012-02-25T16:39:45 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6902 <pre> Oh, nevermind. I realized that all I have to do is program a model as if it were a system dynamics model (http://www.facilitatedsystems.com/mcsimqrc.pdf) and then use MCMC to produce the distributions. Now I've discovered that my data isn't showing the behavior I thought it was, so it's a mute point, at least for a bit. Thanks anyway. Bill </pre> Bill Harris 2011-09-23T03:23:44 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6901 <pre>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 nice</pre> Bill Harris 2011-09-22T02:35:30 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6900 <pre> Bin, I'm curious, too. I have run an earlier version under XP, but I can't make the current one work on XP64. When I get time, I want to try to document what I did and what didn't work to see if I'm missing something. Perhaps the answer to your question will help me. I do run it on Linux just fine. Bill </pre> Bill Harris 2011-08-09T03:36:23 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6899 <pre>Hi Sir, I am trying to install McSim to run it under Windows 7 system according to the instructions as follows: http://www.gnu.org/s/mcsim/WindowsInstall.html I did one step by step until 11. Type 'make' at the command prompt. When I type 'make', it reported that : make[1]: *** [libmcsim.a] Error 1 make[1]: leaving directory '/cygdrive/c/mcsim/mcsim/sim' make: [one] Error 2 ,ignored. Would you help me to see what the problem is ? I have another question is that I have full understood this paragraph:" libgsl: Get a binary distribution for Windows. This installation has been tested with the GnuWin32 distribution of libgsl version 1.8, available at http://gnuwin32.sourceforge.net as of 15 April 2008. There are two choices for download: an installer that installs all of the GnuWin32 packages in a common tree, or zip files for the 'bin' files (some sample executables and the dlls) and the 'lib' files (files for developing software). If you take the latter choice (the two zip files)</pre> Binnian Wei 2011-07-21T14:23:59 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6898 <pre>Hello, I am trying to install McSim to run it under Windows 7 system according to the instructions as follows: http://www.gnu.org/s/mcsim/WindowsInstall.html I did one step by step until 11. Type 'make' at the command prompt. When I type ‘make’, it reported that : make[1]: *** [libmcsim.a] Error 1 make[1]: leaving directory ‘/cygdrive/c/mcsim/mcsim/sim’ make: [one] Error 2 ,ignored. Would you help me to see what the problem is ? I have another question is that I have full understood this paragraph:” libgsl: Get a binary distribution for Windows. This installation has been tested with the GnuWin32 distribution of libgsl version 1.8, available at http://gnuwin32.sourceforge.net as of 15 April 2008. There are two choices for download: an installer that installs all of the GnuWin32 packages in a common tree, or zip files for the 'bin' files (some sample executables and the dlls) and the 'lib' files (files for developing software). If you take the latter choice (the two zip files)</pre> Binnian Wei 2011-07-21T17:50:08 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6895 <pre> Hi everyone, I find one free to download book about Modeling and simulation. Maybe you can find something useful for your research. It collects original and innovative research studies concerning modeling and simulation of physical systems in a very wide range of applications, encompassing micro-electric-mechanical systems, measurement instrumentation, catalytic reactors, bio mechanical applications, biological and chemical sensors, magneto-sensitive materials, silicon photonic devices, electronic devices, optical fibers, electro-microfluidic systems, composite materials, fuel cells, indoor air-conditioning systems, active magnetic levitation systems and more. You can find it here: http://www.intechopen.com/books/show/title/modelling_and_simulation </pre> Hopkins 2010-10-25T13:36:39 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6894 <pre>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 ... 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 ________________</pre> Frederic BOIS 2010-10-20T11:42:54 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6894 <pre>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 ... 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 ________________</pre> Frederic BOIS 2010-10-20T11:42:54 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6893 <pre>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"... </pre> Frederic Y. Bois 2010-06-18T21:49:13 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6892 <pre>It's easier than that. My offline source had the answer (thanks!): I hadn't installed the gsl header files. Now configure works; I'll have to try mcsim tonight. Bill </pre> Bill Harris 2010-05-04T13:09:50 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6891 <pre> $ sudo /sbin/ldconfig -v &gt; ldconfig.txt gives ~1K lines. figuring you just want the gsl part, I'll skip to your next question... $ /sbin/ldconfig -p | grep gsl libgslcblas.so.0 (libc6) =&gt; /usr/lib/libgslcblas.so.0 libgsl.so.0 (libc6) =&gt; /usr/lib/libgsl.so.0 Actually, it is in my PATH FWIW. Someone asked offline about config.log. Here's the pertinent part: configure:2856: checking for main in -lgslcblas configure:2880: gcc -o conftest -g -O2 conftest.c -lgslcblas -lm &gt;&amp;5 /usr/bin/ld: cannot find -lgslcblas collect2: ld returned 1 exit status configure:2886: $? = 1 configure: failed program was: | /* confdefs.h. */ | | #define PACKAGE_NAME "" | #define PACKAGE_TARNAME "" | #define PACKAGE_VERSION "" | #define PACKAGE_STRING "" | #define PACKAGE_BUGREPORT "" | #define HAVE_LIBM 1 | /* end confdefs.h. */ | | | int | main () | { | main (); | ; | return 0; | } configure:2912: result: no configure:2924: error: You first need to install the 'gslcblas' library to build MCSim ## ------------</pre> Bill Harris 2010-05-04T13:03:53 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6890 <pre>ldconfig should work. What was the output of "/sbin/ldconfig -v"? Can you do "/sbin/ldconfig -p | grep gsl" or "/sbin/ldconfig | more" to check the results of ldconfig? You may need to give ldconfig full path, as it is usually not in the PATH of standard user, as it sits in /sbin Frederic This is mildly embarrassing, for I think I should know what to do. I'm coming back to MCSim for some work I need to do -- work I intended to do tonight -- and I'm stuck. I'm running Ubuntu 9.10 (32-bit), and I just installed MCSim v5.3.1. I first tried from CVS, but I couldn't find configure, so I grabbed the tarball, and that worked. Then I tried configure and got ,---- | ~/bin/mcsim-v5.3.1/mcsim$ ./configure | 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 comp</pre> Frederic BOIS 2010-05-04T12:13:36 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6889 <pre>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 ,---- | ~/bin/mcsim-v5.3.1/mcsim$ ./configure | 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 $(MAKE)... yes | checking for gzip... yes | checking for gnuplot... yes | checking for wis</pre> Bill Harris 2010-05-04T05:28:43 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6888 <pre>Hi, I have been trying to install MCSim on Windows XP. I have already had C compilers, both gcc and lcc. 'Mod' has already worked properly (I guess). When I did 'mod perc.model', it gives me 'model.c' as expected. Nevertheless, the problem arises when I attempt to compile 'model.c', it gave me there errors: "... undefined reference to _vbModelReinitd" "... undefined reference to CalcInputs" "... undefined WinMain&lt; at &gt;16" While the last error can be fixed by adding int main(int argc, char *argv[]) { return 0; } into model.c, I have no clue for the first two errors. I have followed the aforementioned steps. I put 'mod.exe' into the 'sim' folder. Moreover, I move 'perc.model' into the 'sim' folder in order to link it with the other sim files. So if anybody has some suggestions, please share. Thank you very much. </pre> Rudy Gunawan 2010-01-18T23:10:05 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6887 <pre>Check also the ldconfig command (but you may need to have sysadmin privileges) Frederic Hi, I am trying to install McSim to run it on a cluster and can therefore not use the standard installation (/usr/local/..). When trying to configure I get this: h18n01$ ./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 $HOME/lib. che</pre> Frédéric BOIS 2009-08-12T14:41:44 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6886 <pre>You may need to include the path where you have installed libgsl, etc. in LD_LIBRARY_PATH, or otherwise tell the OS where to find the shared library. R. Woodrow Setzer, Ph. D. National Center for Computational Toxicology http://www.epa.gov/comptox US Environmental Protection Agency Mail Drop B205-01/US EPA/RTP, NC 27711 Ph: (919) 541-0128 Fax: (919) 541-1194 From: Anna-Karin Mork &lt;Anna-Karin.Mork&lt; at &gt;ki.se&gt; To: help-mcsim&lt; at &gt;gnu.org </pre> Setzer.Woodrow< at >epamail.epa.gov 2009-08-10T13:48:53 http://permalink.gmane.org/gmane.comp.gnu.mcsim/6885 <pre>Hi, I am trying to install McSim to run it on a cluster and can therefore not use the standard installation (/usr/local/..). When trying to configure I get this: h18n01$ ./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 $HOME/lib. checking for install-info... no checking for makeinfo... yes checking for gv... no checking f</pre> Anna-Karin Mork 2009-08-04T14:32:33 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.gnu.mcsim