genesis-sim-users — A list for users to discuss scripting and using the Genesis Neural Simulator

Re: [Genesis-sim-users] Testers needed for GENESIS 2.4 beta release

[Gilles D. <gr...@sc...>]

I've tested it briefly on Scientific Linux 5.10, an RHEL 5 clone 
system.  There's a slight bug in the Linux section of src/Makefile.dist: 
the XINCLUDE= line is missing the -I option argument, and instead just 
lists the include directory name.  This results in a bunch of spurious 
linker warnings like the following:

cc: /usr/include/X11: linker input file unused because linking not done

The fix is simple enough:

--- Makefile.dist.orig  2014-07-20 18:05:25.000000000 -0500
+++ Makefile.dist       2014-07-21 16:11:00.000000000 -0500
@@ -836,7 +836,7 @@
  # MACHINE=Linux
  # OS=BSD

-# XINCLUDE=/usr/include/X11
+# XINCLUDE=-I/usr/include/X11

  ## Choose ONE XLIB line to uncomment:
  ## For 32-bit architectures

(Note that this is a capital "i" option, not a lower-case "L".  It's 
hard to tell with some fonts.)

Another problem is that after running genesis, the ioctl/stty settings 
for the terminal window aren't properly restored.  It seems the "onlcr" 
mode is turned off and not turned back on after quitting.  I haven't 
looked at the code enough to find a fix for that problem.

I ran the Squid script as a test, and it seems to behave as it did under 
2.3.  I haven't tested any further yet.

Gilles

On 07/15/2014 02:56 PM, Dave Beeman wrote:
> I am preparing a beta release of GENESIS 2.4, in preparation
> for the tutorial that Hugo Corenelis will give at CNS 2014.
> There will be further additions in the final November release,
> but the present version is looking pretty good.
>
> However, compilation has only been tested on recent Fedora and Ubuntu
> Linux distribution.  It would be a big help to me if I could get a
> few volunteers to try an installation on other Linux versions,
> and MacOS in particular.
>
> If anyone is using GENESIS under Cygwin, it would be wonderful if
> someone would build a Cygwin binary.
>
> The files and installation instructions can be viewed and downloaded
> at https://github.com/dbeeman/genesis-2.4beta-files.
>
> I'm not asking for any extensive testing, but only for reports of any
> issues that may come up during installation. However, there are some
> worthwhile new features that you may want to look at.  By helping us
> testing, you will not only help make a better final release, but have
> a chance to preview these additions:
>
> * The new 'stdp_rules' object for efficiently implementing spike
>      timing dependent plasticity in large networks of hsolved
>      multicompartmental cells.
>
> * A new version of the chemesis library for modeling second messengers
>     and calcium dynamics is now installed by default.
>
> * New tutorial Scripts and Doc entries were added for:
>       o chemesis
>       o the gpython-tools Python utility collection
>       o An updated Purkinje tutorial
>       o stdp_rules, including 'NewPlasticityObjects' documentation for
>         implementing similar objects.
>
>       o An improved hsolved implementation of the dual exponential
>         conductance version of the Vogels-Abbott network model. It serves
>         as a tutorial on how to achieve a speed improvement of 10 to 20
>         times when using hsolve with network models.
>
> * Bug fixes and Makefile improvements to ease installation.
>
> Thanks for your help,
> Dave Beeman
>
> ----------------------------------------------------------------------------
> Prof. David Beeman, GENESIS Users Group
> Dept. of Electrical, Computer, and Energy Engineering
> University of Colorado, Boulder, CO 80309
> email: ge...@ge... - db...@co...
> GENESIS 2 WWW site: http://www.genesis-sim.org/GENESIS/
> ----------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------
> Want fast and easy access to all the code in your enterprise? Index and
> search up to 200,000 lines of code with a free copy of Black Duck
> Code Sight - the same software that powers the world's largest code
> search on Ohloh, the Black Duck Open Hub! Try it now.
> http://p.sf.net/sfu/bds
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

-- 
Gilles R. Detillieux              E-mail: <gr...@sc...>
Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
Dept. of Physiology and Pathophysiology, Faculty of Health Sciences,
Univ. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)

[Genesis-sim-users] Testers needed for GENESIS 2.4 beta release

[Dave B. <db...@Co...>]

I am preparing a beta release of GENESIS 2.4, in preparation
for the tutorial that Hugo Corenelis will give at CNS 2014.
There will be further additions in the final November release,
but the present version is looking pretty good.

However, compilation has only been tested on recent Fedora and Ubuntu
Linux distribution.  It would be a big help to me if I could get a
few volunteers to try an installation on other Linux versions,
and MacOS in particular.

If anyone is using GENESIS under Cygwin, it would be wonderful if
someone would build a Cygwin binary.

The files and installation instructions can be viewed and downloaded
at https://github.com/dbeeman/genesis-2.4beta-files.

I'm not asking for any extensive testing, but only for reports of any
issues that may come up during installation. However, there are some
worthwhile new features that you may want to look at.  By helping us
testing, you will not only help make a better final release, but have
a chance to preview these additions:

* The new 'stdp_rules' object for efficiently implementing spike
    timing dependent plasticity in large networks of hsolved
    multicompartmental cells.

* A new version of the chemesis library for modeling second messengers
   and calcium dynamics is now installed by default.

* New tutorial Scripts and Doc entries were added for:
     o chemesis
     o the gpython-tools Python utility collection
     o An updated Purkinje tutorial
     o stdp_rules, including 'NewPlasticityObjects' documentation for
       implementing similar objects.

     o An improved hsolved implementation of the dual exponential
       conductance version of the Vogels-Abbott network model. It serves
       as a tutorial on how to achieve a speed improvement of 10 to 20
       times when using hsolve with network models.

* Bug fixes and Makefile improvements to ease installation.

Thanks for your help,
Dave Beeman

----------------------------------------------------------------------------
Prof. David Beeman, GENESIS Users Group
Dept. of Electrical, Computer, and Energy Engineering
University of Colorado, Boulder, CO 80309
email: ge...@ge... - db...@co...
GENESIS 2 WWW site: http://www.genesis-sim.org/GENESIS/
----------------------------------------------------------------------------

Re: [Genesis-sim-users] getglobal bug in Genesis2.3

[Dave B. <db...@Co...>]

Thanks for pointing out the bug, which I hadn't known about.

GENESIS 2 is user-supported, rather than being being actively
developed or maintained. The best way to report bugs of this sort is
through the mailing list in the hopes that another user can provide a
fix, workaround, or suggestions for a solution. Often I, or someone
else, can provide some suggestions for where the bug might lie.  I will
incorporate any bug fixes that I receive in the November GENESIS 2.4
release, but I can't offer to track them down and fix them myself.

Here is what I can tell you about this particular problem.
I tested your example, and found that it works properly for
test = 1e-6, but gives 0 for 1e-7.  Not only that, but

  setglobal foo 0.123456e-3
  float a = {getglobal foo}
  echo {a}

gives 0.000123

This is similar to other problems that can arise when GENESIS converts
from floats (used in SLI shell commands), to doubles, which are used
in some of the more recent C code, particularly with time values.

In this case it appears that strings such as "0.123456e-3" are being
converted to a fixed point representation before being converted to a
float.  I took a brief look at the code for 'getglobal', but was not
able to identify the specific problem.  Here are some suggestions:

GENESIS shell commands (e.g. the math functions sin, cos, sqrt, etc.)
are defined in term of functions listed in
genesis/src/shell/shelllib.g.  This also includes the commands
addglobal, setglobal, and getglobal.  The getglobal command is
processed with 'do_getglobal', which is defined in
genesis/src/ss/eval.c along with the others. The return value is given
by another function char *CopyString(value) that is defined in
shell/shell_string.c. It may take some work to figure out how this
works, but I suspect that the answer lies there, and in the conversions
from character strings to floats.

I hope that this is helpful.

Dave Beeman

On Fri, 13 Jun 2014, Cengiz Günay wrote:

> Hi,
> 
> This may be a known issue, but I just realized that getglobal truncates float
> values. See the following example:
> 
> addglobal float test 1e-9
> float a = {getglobal test}
> echo {a}
> 
> Returns 0. Although listglobals shows the correct value, getglobal truncates
> it to 0.
> 
> Let me know if there is a better place to report bugs. I'm assuming there
> will be a 2.4 patch some time, but if there won't be none please let me know.
> 
> Thanks,
> -Cengiz
> 
> --
> Cengiz Gunay
> Postdoctoral Fellow, Dept. of Biology
> Visiting Faculty, Dept. of Math & CS
> Emory University
> cg...@em...  cen...@us...
> http://www.biology.emory.edu/research/Prinz/Cengiz/
> 
> 
>

Re: [Genesis-sim-users] Genesis2 Emacs mode for syntax highlighting and indentation

[Cengiz G. <cg...@em...>]

Thank you Dave for trying it and writing the nice message supporting our
tool. If you have downloaded it earlier than Friday, please get the updated
version because I submitted major bugfixes. I also added a "release" on
github, which makes it easier to download the package:
https://github.com/cengique/emacs-genesis-mode/releases

In general, one can download the whole project in Github by clicking the
"Download ZIP" button hidden at the bottom of the right hand side
navigation bar.

I'm surprised and embarrassed to hear that Hugo's code was available
onlline and as part of the Genesis 2.3 distribution. :) In my defense, I
searched online before I started with the keywords "genesis emacs", but
apparently this missed "xemacs". Thankfully we have attacked different
features with Hugo, so the combined package is still relevant.

Best,

-Cengiz


On Sat, Jun 14, 2014 at 7:00 PM, Dave Beeman <db...@co...> wrote:

>
> Thanks to Cengiz and Hugo for putting together this useful macro for
> editing GENESIS SLI scripts. I gave it a try, and it makes editing
> a lot easier, with highlighted GENESIS object names and all that.
> The Index/Function menu is a nice way to locate SLI function definitions
> in a file.
>
> For those of you who don't use github, here are easy installation
> instructions.
>
>   1. Use a web browser to go to https://github.com/cengique/
> emacs-genesis-mode
>   2. click on genesis-mode.el
>   3. click the Raw button to see it in raw text mode
>   4. use your browser "Save page" to save the file.
>   5. copy it into your ~/.emacs.d directory
>
>   If it is not autoloaded when Emacs starts, place the following lines
>   in your ~/.emacs file:
>
>
>   (add-to-list 'load-path "~/.emacs.d/")
>   (require 'genesis-mode)
>
> If the '.emacs' file does't exist, create one containing just these two
> lines.
>
> To my surprise, I discovered that Hugo's original files, which Cengiz
> used when creating his single file for emacs or xemacs, exist in the
> directory
>
>   genesis-2.3/genesis/contrib/xemacs-mode
>
> The 'contrib' directory was added to GENESIS 2.3 just before release,
> and was meant to contain user-contributed GENESIS add-ons, tool, etc.
>
> When I put together the November GENESIS 2.4 release, I will update it
> with the latest version of Cengiz' macros. Please give him your feedback
> if you use them.
>
> If other GENESIS users have some favorite example scripts, tools, bug
> fixes or new objects or commands, please send them to me, and I
> will try to incorporate them in the 'contrib' directory or elsewhere.
>
> I'll have more to say about GENESIS 2.4 later, but you can read something
> about the plans at http://genesis-sim.org/GENESIS/
>
> Dave Beeman
>
>
>
> On Thu, 5 Jun 2014, Cengiz Günay wrote:
>
>  Thanks all for the feedback and patches. An updated version now works in
>> both
>> Emacs and Xemacs with better keyword coverage and function menu (only in
>> Emacs).
>>
>> Best,
>>
>> -Cengiz
>>
>>
>> On Tue, Jun 3, 2014 at 1:57 PM, Cengiz Günay <cg...@em...> wrote:
>>       Hi,
>>
>> I authored an Emacs major mode customized for Genesis2 scripts:
>> https://github.com/cengique/emacs-genesis-mode
>>
>> The keyword/object support is nowhere near complete, but I mainly
>> wanted it for automatic indentation. To run it, put it under your
>> ~/.emacs.d/ directory.
>>
>> If somebody has a full list of Genesis2 functions and objects in an
>> easy format (CSV or space-separated) I can easily add them.
>>
>> I hope you find it useful and please send me patches if you make
>> changes.
>>
>> Best,
>> -Cengiz
>>
>> --
>> Cengiz Gunay
>> Postdoctoral Fellow, Dept. of Biology
>> Visiting Faculty, Dept. of Math & CS
>> Emory University
>> cg...@em...  cen...@us...
>> Home/Cell: +1-678-559-8694
>> http://www.biology.emory.edu/research/Prinz/Cengiz/
>>
>>
>>
>>

Re: [Genesis-sim-users] Genesis2 Emacs mode for syntax highlighting and indentation

[Dave B. <db...@Co...>]

Thanks to Cengiz and Hugo for putting together this useful macro for
editing GENESIS SLI scripts. I gave it a try, and it makes editing
a lot easier, with highlighted GENESIS object names and all that.
The Index/Function menu is a nice way to locate SLI function definitions
in a file.

For those of you who don't use github, here are easy installation
instructions.

   1. Use a web browser to go to https://github.com/cengique/emacs-genesis-mode
   2. click on genesis-mode.el
   3. click the Raw button to see it in raw text mode
   4. use your browser "Save page" to save the file.
   5. copy it into your ~/.emacs.d directory

   If it is not autoloaded when Emacs starts, place the following lines
   in your ~/.emacs file:

   (add-to-list 'load-path "~/.emacs.d/")
   (require 'genesis-mode)

If the '.emacs' file does't exist, create one containing just these two
lines.

To my surprise, I discovered that Hugo's original files, which Cengiz
used when creating his single file for emacs or xemacs, exist in the 
directory

   genesis-2.3/genesis/contrib/xemacs-mode

The 'contrib' directory was added to GENESIS 2.3 just before release,
and was meant to contain user-contributed GENESIS add-ons, tool, etc.

When I put together the November GENESIS 2.4 release, I will update it
with the latest version of Cengiz' macros. Please give him your feedback
if you use them.

If other GENESIS users have some favorite example scripts, tools, bug
fixes or new objects or commands, please send them to me, and I
will try to incorporate them in the 'contrib' directory or elsewhere.

I'll have more to say about GENESIS 2.4 later, but you can read something
about the plans at http://genesis-sim.org/GENESIS/

Dave Beeman


On Thu, 5 Jun 2014, Cengiz Günay wrote:

> Thanks all for the feedback and patches. An updated version now works in both
> Emacs and Xemacs with better keyword coverage and function menu (only in
> Emacs).
> 
> Best,
> 
> -Cengiz
> 
> 
> On Tue, Jun 3, 2014 at 1:57 PM, Cengiz Günay <cg...@em...> wrote:
>       Hi,
> 
> I authored an Emacs major mode customized for Genesis2 scripts:
> https://github.com/cengique/emacs-genesis-mode
> 
> The keyword/object support is nowhere near complete, but I mainly
> wanted it for automatic indentation. To run it, put it under your
> ~/.emacs.d/ directory.
> 
> If somebody has a full list of Genesis2 functions and objects in an
> easy format (CSV or space-separated) I can easily add them.
> 
> I hope you find it useful and please send me patches if you make
> changes.
> 
> Best,
> -Cengiz
> 
> --
> Cengiz Gunay
> Postdoctoral Fellow, Dept. of Biology
> Visiting Faculty, Dept. of Math & CS
> Emory University
> cg...@em...  cen...@us...
> Home/Cell: +1-678-559-8694
> http://www.biology.emory.edu/research/Prinz/Cengiz/
> 
> 
> 
>

[Genesis-sim-users] getglobal bug in Genesis2.3

[Cengiz G. <cg...@em...>]

Hi,

This may be a known issue, but I just realized that getglobal truncates
float values. See the following example:

addglobal float test 1e-9
float a = {getglobal test}
echo {a}

Returns 0. Although listglobals shows the correct value, getglobal
truncates it to 0.

Let me know if there is a better place to report bugs. I'm assuming there
will be a 2.4 patch some time, but if there won't be none please let me
know.

Thanks,
-Cengiz

--
Cengiz Gunay
Postdoctoral Fellow, Dept. of Biology
Visiting Faculty, Dept. of Math & CS
Emory University
cg...@em...  cen...@us...
http://www.biology.emory.edu/research/Prinz/Cengiz/

Re: [Genesis-sim-users] Genesis2 Emacs mode for syntax highlighting and indentation

[Cengiz G. <cg...@em...>]

Thanks all for the feedback and patches. An updated version now works in
both Emacs and Xemacs with better keyword coverage and function menu (only
in Emacs).

Best,

-Cengiz


On Tue, Jun 3, 2014 at 1:57 PM, Cengiz Günay <cg...@em...> wrote:

> Hi,
>
> I authored an Emacs major mode customized for Genesis2 scripts:
> https://github.com/cengique/emacs-genesis-mode
>
> The keyword/object support is nowhere near complete, but I mainly wanted
> it for automatic indentation. To run it, put it under your ~/.emacs.d/
> directory.
>
> If somebody has a full list of Genesis2 functions and objects in an easy
> format (CSV or space-separated) I can easily add them.
>
> I hope you find it useful and please send me patches if you make changes.
>
> Best,
> -Cengiz
>
> --
> Cengiz Gunay
> Postdoctoral Fellow, Dept. of Biology
> Visiting Faculty, Dept. of Math & CS
> Emory University
> cg...@em...  cen...@us...
> Home/Cell: +1-678-559-8694
> http://www.biology.emory.edu/research/Prinz/Cengiz/
>
>

[Genesis-sim-users] v5.7 of NeuroMorpho.Org released on 30 May, 2014

[NeuroMorpho.Org Admin. <neu...@gm...>]

Version 5.7 of NeuroMorpho.Org was released on 30 May, 2014.

 The release included 29 new data sets (1341 reconstructions), including
from three new animal species (dragonfly, moth, and sheep). The database
now contains 11,335 reconstructions from 144 contributing labs. More than
3.2 million reconstructions were downloaded in over 130,000 unique visits
from 146 countries.

 Please visit the What’s new <http://neuromorpho.org/neuroMorpho/WIN.jsp>
page for details on data included in this release, including new species
strains, brain regions, cell types, and experimental conditions. The
Acknowledgements
<http://neuromorpho.org/neuroMorpho/acknowl.jsp>include details on
contributing labs, and the About
<http://neuromorpho.org/neuroMorpho/about.jsp> page provides an updated
overview of the repository content.

 A new user-friendly functionality, OntoSearch
<http://neuromorpho.org/neuroMorpho/OntoSearch.jsp>, was introduced in this
release, enabling more powerful searches of species and strains with
automated synonym translation, taxonomical relations, and keyword
auto-completion. The literature coverage database was also updated to
include publications through March 2014.

 We are continuously grateful to all the data owners who freely share their
data with the community.

 We always appreciate any and all feedback and comments.

 Sincerely,

The NeuroMorpho.Org team



-- 
Ruchi Parekh, Ph.D.
NeuroMorpho.Org Project Lead
Postdoctoral Research Fellow
Center for Neural Informatics, Structures, and Plasticity
Krasnow Institute for Advanced Study
MS2A1, George Mason University
Fairfax, VA 22030 (USA)
Ph - +1-703-993-4382

www.neuromorpho.org
nm...@gm...

[Genesis-sim-users] v5.7 of NeuroMorpho.Org released on 30 May, 2014

[NeuroMorpho A. <nm...@gm...>]

Version 5.7 of NeuroMorpho.Org was released on 30 May, 2014.

The release included 29 new data sets (1341 reconstructions), including from three new animal species (dragonfly, moth, and sheep). The database now contains 11,335 reconstructions from 144 contributing labs. More than 3.2 million reconstructions were downloaded in over 130,000 unique visits from 146 countries.

Please visit the What's new<http://neuromorpho.org/neuroMorpho/WIN.jsp> page for details on data included in this release, including new species strains, brain regions, cell types, and experimental conditions. The Acknowledgements <http://neuromorpho.org/neuroMorpho/acknowl.jsp> include details on contributing labs, and the About<http://neuromorpho.org/neuroMorpho/about.jsp> page provides an updated overview of the repository content.

A new user-friendly functionality, OntoSearch<http://neuromorpho.org/neuroMorpho/OntoSearch.jsp>, was introduced in this release, enabling more powerful searches of species and strains with automated synonym translation, taxonomical relations, and keyword auto-completion. The literature coverage database was also updated to include publications through March 2014.

We are continuously grateful to all the data owners who freely share their data with the community.

We always appreciate any and all feedback and comments.

Sincerely,

The NeuroMorpho.Org team


--
Ruchi Parekh, Ph.D.
NeuroMorpho.Org Project Lead
Postdoctoral Research Fellow
Center for Neural Informatics, Structures, and Plasticity
Krasnow Institute for Advanced Study
MS2A1, George Mason University
Fairfax, VA 22030 (USA)
Ph - +1-703-993-4382<tel:%2B1-703-993-4382>

www.neuromorpho.org<http://www.neuromorpho.org/>
nm...@gm...<mailto:nm...@gm...>?

[Genesis-sim-users] v5.7 of NeuroMorpho.Org released on 30 May, 2014

[NeuroMorpho.Org Admin. <neu...@gm...>]

Version 5.7 of NeuroMorpho.Org was released on 30 May, 2014.

 The release included 29 new data sets (1341 reconstructions), including
from three new animal species (dragonfly, moth, and sheep). The database
now contains 11,335 reconstructions from 144 contributing labs. More than
3.2 million reconstructions were downloaded in over 130,000 unique visits
from 146 countries.

 Please visit the What’s new <http://neuromorpho.org/neuroMorpho/WIN.jsp>
page for details on data included in this release, including new species
strains, brain regions, cell types, and experimental conditions. The
Acknowledgements
<http://neuromorpho.org/neuroMorpho/acknowl.jsp>include details on
contributing labs, and the About
<http://neuromorpho.org/neuroMorpho/about.jsp> page provides an updated
overview of the repository content.

 A new user-friendly functionality, OntoSearch
<http://neuromorpho.org/neuroMorpho/OntoSearch.jsp>, was introduced in this
release, enabling more powerful searches of species and strains with
automated synonym translation, taxonomical relations, and keyword
auto-completion. The literature coverage database was also updated to
include publications through March 2014.

 We are continuously grateful to all the data owners who freely share their
data with the community.

 We always appreciate any and all feedback and comments.

 Sincerely,

The NeuroMorpho.Org team

-- 
Ruchi Parekh, Ph.D.
NeuroMorpho.Org Project Lead
Postdoctoral Research Fellow
Center for Neural Informatics, Structures, and Plasticity
Krasnow Institute for Advanced Study
MS2A1, George Mason University
Fairfax, VA 22030 (USA)
Ph - +1-703-993-4382

www.neuromorpho.org
nm...@gm...

[Genesis-sim-users] Genesis2 Emacs mode for syntax highlighting and indentation

[Cengiz G. <cg...@em...>]

Hi,

I authored an Emacs major mode customized for Genesis2 scripts:
https://github.com/cengique/emacs-genesis-mode

The keyword/object support is nowhere near complete, but I mainly wanted it
for automatic indentation. To run it, put it under your ~/.emacs.d/
directory.

If somebody has a full list of Genesis2 functions and objects in an easy
format (CSV or space-separated) I can easily add them.

I hope you find it useful and please send me patches if you make changes.

Best,
-Cengiz

--
Cengiz Gunay
Postdoctoral Fellow, Dept. of Biology
Visiting Faculty, Dept. of Math & CS
Emory University
cg...@em...  cen...@us...
Home/Cell: +1-678-559-8694
http://www.biology.emory.edu/research/Prinz/Cengiz/

Re: [Genesis-sim-users] Genesis-2.3, Slackware 14.1, won't compile.

[Dave B. <db...@Co...>]

Not being able to find the basic math functions is a sure sign that
the math library is not being found.

Of course, you should be sure that the math library is installed.
But, as Gilles said, it is probably a path in the Makefile that
is the problem.

Also, please subscribe to the list, or edit your email address at
https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

Dave Beeman

On Fri, 2 May 2014, Gilles Detillieux wrote:

> You need to uncomment the lines...
> 
> # LEXLIB=-lfl
> 
> and
> 
> # LIBS= $(LEXLIB) -lm
> 
> in the Linux section of your Makefile, so that the cc command that does the
> linking knows were to find the math library for the exp, log, pow and sqrt
> functions (-lm) and the flex library for the yywrap function (-lfl).
> 
> On 05/01/2014 05:54 PM, TFstgStUPq Tabasco wrote:
>       Goes along ok until -o genesis, then breaks.
>
>       make[2]: Leaving directory
>       `/home/user/code/genesis-2.3/genesis/src/par'
>       All Libs Compiled
>       ./libsh < liblist > loadlib.c
>       cc -O2 -D__NO_MATH_INLINES -DLONGWORDS  -DINCSPRNG -DLinux -c 
>       loadlib.c
>       cc -O2 -D__NO_MATH_INLINES -DLONGWORDS  -DINCSPRNG -L/usr/lib64
>       sim/simlib.o sys/utillib.o ss/ss.o shell/shelllib.o
>       par/parlib.o buffer/buflib.o segment/seglib.o hh/hhlib.o
>       device/devlib.o out/outlib.o olf/olflib.o tools/toollib.o
>       concen/conclib.o hines/hineslib.o user/userlib.o
>       param/paramlib.o pore/porelib.o oldconn/axon/axonlib.o
>       oldconn/synapse/synlib.o oldconn/personal/perlib.o
>       oldconn/sim/simconnlib.o oldconn/tools/toolconnlib.o 
>       kinetics/kinlib.o newconn/newconnlib.o loadlib.o
>       Xodus/_xo/xolib.o Xodus/_widg/widglib.o Xodus/_draw/drawlib.o
>       Xodus/Draw/libDraw.a Xodus/Widg/libWidg.a Xodus/Xo/libXo.a
>       -L/usr/X11R6/lib64 -lXt -lX11  sprng/lib/liblfg.a -ltermcap -o
>       genesis
>       ss/ss.o: In function `PTEval':
>       (.text+0x2849): undefined reference to `pow'
>       ss/ss.o: In function `input':
>       y.tab.c:(.text+0x46a5): undefined reference to `yywrap'
>       ss/ss.o: In function `yylex':
>       (.text+0x5062): undefined reference to `yywrap'
>       sim/simlib.o: In function `IntegrateMethod':
>       (.text+0xd103): undefined reference to `exp'
>       shell/shelllib.o: In function `rangauss':
>       (.text+0x54c4): undefined reference to `log'
>       shell/shelllib.o: In function `rangauss':
>       (.text+0x5593): undefined reference to `sqrt'
> 
>
>       and so on until...
>
>       Xodus/Draw/libDraw.a(View.o): In function `DrawPoints':
>       View.c:(.text+0x1363): undefined reference to `sqrt'
>       Xodus/Draw/libDraw.a(Tree.o): In function `DrawPoints':
>       Tree.c:(.text+0x503): undefined reference to `sqrt'
>       Xodus/Draw/libDraw.a(Tree.o):Tree.c:(.text+0x1ce1): more
>       undefined references to `sqrt' follow
>       collect2: error: ld returned 1 exit status
>       make[1]: *** [genesis] Error 1
>       make[1]: Leaving directory
>       `/home/user/code/genesis-2.3/genesis/src'
>       make: *** [default] Error 2
>       ~/genesis-2.3/genesis/src $
> 
> 
> -- 
> Gilles R. Detillieux              E-mail: <gr...@sc...>
> Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
> Dept. Physiology, U. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)
> 
>

Re: [Genesis-sim-users] Genesis-2.3, Slackware 14.1, won't compile.

[Gilles D. <gr...@sc...>]

You need to uncomment the lines...

# LEXLIB=-lfl

and

# LIBS= $(LEXLIB) -lm

in the Linux section of your Makefile, so that the cc command that does 
the linking knows were to find the math library for the exp, log, pow 
and sqrt functions (-lm) and the flex library for the yywrap function 
(-lfl).

On 05/01/2014 05:54 PM, TFstgStUPq Tabasco wrote:
> Goes along ok until -o genesis, then breaks.
>
> make[2]: Leaving directory `/home/user/code/genesis-2.3/genesis/src/par'
> All Libs Compiled
> ./libsh < liblist > loadlib.c
> cc -O2 -D__NO_MATH_INLINES -DLONGWORDS  -DINCSPRNG -DLinux -c loadlib.c
> cc -O2 -D__NO_MATH_INLINES -DLONGWORDS  -DINCSPRNG -L/usr/lib64 
> sim/simlib.o sys/utillib.o ss/ss.o shell/shelllib.o par/parlib.o 
> buffer/buflib.o segment/seglib.o hh/hhlib.o device/devlib.o 
> out/outlib.o olf/olflib.o tools/toollib.o concen/conclib.o 
> hines/hineslib.o user/userlib.o param/paramlib.o pore/porelib.o 
> oldconn/axon/axonlib.o oldconn/synapse/synlib.o 
> oldconn/personal/perlib.o oldconn/sim/simconnlib.o 
> oldconn/tools/toolconnlib.o  kinetics/kinlib.o newconn/newconnlib.o 
> loadlib.o Xodus/_xo/xolib.o Xodus/_widg/widglib.o 
> Xodus/_draw/drawlib.o Xodus/Draw/libDraw.a Xodus/Widg/libWidg.a 
> Xodus/Xo/libXo.a -L/usr/X11R6/lib64 -lXt -lX11  sprng/lib/liblfg.a 
> -ltermcap *-o genesis*
> ss/ss.o: In function `PTEval':
> (.text+0x2849): undefined reference to `pow'
> ss/ss.o: In function `input':
> y.tab.c:(.text+0x46a5): undefined reference to `yywrap'
> ss/ss.o: In function `yylex':
> (.text+0x5062): undefined reference to `yywrap'
> sim/simlib.o: In function `IntegrateMethod':
> (.text+0xd103): undefined reference to `exp'
> shell/shelllib.o: In function `rangauss':
> (.text+0x54c4): undefined reference to `log'
> shell/shelllib.o: In function `rangauss':
> (.text+0x5593): undefined reference to `sqrt'
>
>
> and so on until...
>
> Xodus/Draw/libDraw.a(View.o): In function `DrawPoints':
> View.c:(.text+0x1363): undefined reference to `sqrt'
> Xodus/Draw/libDraw.a(Tree.o): In function `DrawPoints':
> Tree.c:(.text+0x503): undefined reference to `sqrt'
> Xodus/Draw/libDraw.a(Tree.o):Tree.c:(.text+0x1ce1): more undefined 
> references to `sqrt' follow
> collect2: error: ld returned 1 exit status
> make[1]: *** [genesis] Error 1
> make[1]: Leaving directory `/home/user/code/genesis-2.3/genesis/src'
> make: *** [default] Error 2
> ~/genesis-2.3/genesis/src $

-- 
Gilles R. Detillieux              E-mail: <gr...@sc...>
Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
Dept. Physiology, U. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)

[Genesis-sim-users] Genesis-2.3, Slackware 14.1, won't compile.

[TFstgStUPq T. <tfs...@gm...>]

Goes along ok until -o genesis, then breaks.

make[2]: Leaving directory `/home/user/code/genesis-2.3/genesis/src/par'
All Libs Compiled
./libsh < liblist > loadlib.c
cc -O2 -D__NO_MATH_INLINES -DLONGWORDS  -DINCSPRNG -DLinux -c  loadlib.c
cc -O2 -D__NO_MATH_INLINES -DLONGWORDS  -DINCSPRNG -L/usr/lib64
sim/simlib.o sys/utillib.o ss/ss.o shell/shelllib.o par/parlib.o
buffer/buflib.o segment/seglib.o hh/hhlib.o device/devlib.o out/outlib.o
olf/olflib.o tools/toollib.o concen/conclib.o hines/hineslib.o
user/userlib.o param/paramlib.o pore/porelib.o oldconn/axon/axonlib.o
oldconn/synapse/synlib.o oldconn/personal/perlib.o oldconn/sim/simconnlib.o
oldconn/tools/toolconnlib.o  kinetics/kinlib.o newconn/newconnlib.o
loadlib.o Xodus/_xo/xolib.o Xodus/_widg/widglib.o Xodus/_draw/drawlib.o
Xodus/Draw/libDraw.a Xodus/Widg/libWidg.a Xodus/Xo/libXo.a
-L/usr/X11R6/lib64 -lXt -lX11  sprng/lib/liblfg.a -ltermcap *-o genesis*
ss/ss.o: In function `PTEval':
(.text+0x2849): undefined reference to `pow'
ss/ss.o: In function `input':
y.tab.c:(.text+0x46a5): undefined reference to `yywrap'
ss/ss.o: In function `yylex':
(.text+0x5062): undefined reference to `yywrap'
sim/simlib.o: In function `IntegrateMethod':
(.text+0xd103): undefined reference to `exp'
shell/shelllib.o: In function `rangauss':
(.text+0x54c4): undefined reference to `log'
shell/shelllib.o: In function `rangauss':
(.text+0x5593): undefined reference to `sqrt'


and so on until...

Xodus/Draw/libDraw.a(View.o): In function `DrawPoints':
View.c:(.text+0x1363): undefined reference to `sqrt'
Xodus/Draw/libDraw.a(Tree.o): In function `DrawPoints':
Tree.c:(.text+0x503): undefined reference to `sqrt'
Xodus/Draw/libDraw.a(Tree.o):Tree.c:(.text+0x1ce1): more undefined
references to `sqrt' follow
collect2: error: ld returned 1 exit status
make[1]: *** [genesis] Error 1
make[1]: Leaving directory `/home/user/code/genesis-2.3/genesis/src'
make: *** [default] Error 2
~/genesis-2.3/genesis/src $

[Genesis-sim-users] Debian package in now ready

[Saeed <sa...@gn...>]

Dear all,

Debian based installation packages are provided at Files tab in the 
project page,
  for 64 bit 
<http://sourceforge.net/projects/genesis-sim/files/genesis_2.3-1_amd64.deb/download> 
and 32 bit 
<http://sourceforge.net/projects/genesis-sim/files/genesis_2.3-1_i386.deb/download> 
architectures. It can install via *dpkg* or *Ubuntu Software Center*.

In the case of any problem, please inform us.

Best Regards,
Saeed

Re: [Genesis-sim-users] running genesis2.3 under Cygwin64?

[james b. <bo...@ut...>]

Thanks Gilles and Dave

Jim


On Apr 17, 2014, at 8:16 PM, Jaeger, Dieter <dj...@em...> wrote:

> Thanks Gilles!  This easily qualifies as the 'most useful' answer to my question.  I like Cygwin b/c I can install it in 10 minutes while drinking coffee, and I used it for years on several machines, and it works smoothly, and it just integrates within the ordinary Windows file system so I can easily see / edit / copy files across the whole file system.  Maybe VBox does that, too, and I will look into it, but for now I will uninstall the 64 bit version on my new desktop, and replace it with the 32 bit version.  If that runs on my 64 bit Windows OS, I am just fine.  This is about teaching Genesis in class along with powerpoints etc, not about running research grade speeds / performance. We have a cluster for that.
> 
> -Dieter
> 
> -----Original Message-----
> From: Gilles Detillieux [mailto:gr...@sc...] 
> Sent: Thursday, April 17, 2014 2:24 PM
> To: gen...@li...
> Subject: Re: [Genesis-sim-users] running genesis2.3 under Cygwin64?
> 
> Yes, Cygwin is still being actively developed, and quite widely used. 
> It's a more lightweight method of running UNIX code under Windows than running a virtual machine, and so it's still quite popular as a result. 
> The 32-bit version has been around for quite some time and is quite stable, though still regularly updated.
> 
> The 64-bit version is quite new by comparison, and my own impression of it is that it's still a work in progress and not-quite-ready for prime time. They seem to be going with a different set of packages under the 64-bit version, so there isn't a one-for-one correspondence between the packages in the two versions. In particular, many of the libraries in the 32-bit version simply aren't available in the 64-bit version. It does make porting applications from one version to the other less than straightforward.
> 
> Dieter, if you need 64-bit support, you may do better with a virtual environment as Dave suggested. If you don't, then you may find that the 32-bit version of Cygwin will serve you well. It does run fine on 64-bit versions of Windows.
> 
> Gilles
> 
> On 04/17/2014 01:08 PM, Dave Beeman wrote:
>> 
>> I think that Cygwin has been pretty much replaced by modern virtual 
>> environments for running Linux under Windows. I haven't tried 
>> compiling GENESIS under Cygwin for years.
>> 
>> Some students at the LASCON course had good experiences running 
>> GENESIS with Ubuntu under something called VirtualBox. Mando has used 
>> Fedora with VMware. Perhaps other GENESIS users can report their 
>> favorites. But, I think it is time say goodbye to Cygwin and use real 
>> Linux under a virtual environment.
>> 
>> Is Cygwin still being developed?
>> 
>> Dave Beeman
>> 
>> On Wed, 16 Apr 2014, Jaeger, Dieter wrote:
>> 
>>> 
>>> Hello - has anyone installed genesis 2.3 under 64 bit Cygwin? For me 
>>> the Cygwin.bindist files don't work (genesis is not recognized as an 
>>> executable - I assume b/c it is a 32 bit executable), and when I try 
>>> to compile from src by using Makefile.cygwin (renamed to Makefile, 
>>> and executing 'make
>>> genesis'.) the compilation just shoots back 'All libs compiled' (not 
>>> true), and 'make: *** No rule to make target 'liblist', needed by 
>>> 'loadlib.c'. Stop.'. This is pretty little to sink ones teeth into. 
>>> Any insights and genesis2.3 for 64 bit Cygwin is much welcome. 
>>> -Dieter
>>> 
> 
> -- 
> Gilles R. Detillieux              E-mail: <gr...@sc...>
> Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
> Dept. Physiology, U. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)
> 
> 
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
> 
> 
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

Re: [Genesis-sim-users] running genesis2.3 under Cygwin64?

[Jaeger, D. <dj...@em...>]

Thanks Gilles!  This easily qualifies as the 'most useful' answer to my question.  I like Cygwin b/c I can install it in 10 minutes while drinking coffee, and I used it for years on several machines, and it works smoothly, and it just integrates within the ordinary Windows file system so I can easily see / edit / copy files across the whole file system.  Maybe VBox does that, too, and I will look into it, but for now I will uninstall the 64 bit version on my new desktop, and replace it with the 32 bit version.  If that runs on my 64 bit Windows OS, I am just fine.  This is about teaching Genesis in class along with powerpoints etc, not about running research grade speeds / performance. We have a cluster for that.

-Dieter

-----Original Message-----
From: Gilles Detillieux [mailto:gr...@sc...] 
Sent: Thursday, April 17, 2014 2:24 PM
To: gen...@li...
Subject: Re: [Genesis-sim-users] running genesis2.3 under Cygwin64?

Yes, Cygwin is still being actively developed, and quite widely used. 
It's a more lightweight method of running UNIX code under Windows than running a virtual machine, and so it's still quite popular as a result. 
The 32-bit version has been around for quite some time and is quite stable, though still regularly updated.

The 64-bit version is quite new by comparison, and my own impression of it is that it's still a work in progress and not-quite-ready for prime time. They seem to be going with a different set of packages under the 64-bit version, so there isn't a one-for-one correspondence between the packages in the two versions. In particular, many of the libraries in the 32-bit version simply aren't available in the 64-bit version. It does make porting applications from one version to the other less than straightforward.

Dieter, if you need 64-bit support, you may do better with a virtual environment as Dave suggested. If you don't, then you may find that the 32-bit version of Cygwin will serve you well. It does run fine on 64-bit versions of Windows.

Gilles

On 04/17/2014 01:08 PM, Dave Beeman wrote:
>
> I think that Cygwin has been pretty much replaced by modern virtual 
> environments for running Linux under Windows. I haven't tried 
> compiling GENESIS under Cygwin for years.
>
> Some students at the LASCON course had good experiences running 
> GENESIS with Ubuntu under something called VirtualBox. Mando has used 
> Fedora with VMware. Perhaps other GENESIS users can report their 
> favorites. But, I think it is time say goodbye to Cygwin and use real 
> Linux under a virtual environment.
>
> Is Cygwin still being developed?
>
> Dave Beeman
>
> On Wed, 16 Apr 2014, Jaeger, Dieter wrote:
>
>>
>> Hello - has anyone installed genesis 2.3 under 64 bit Cygwin? For me 
>> the Cygwin.bindist files don't work (genesis is not recognized as an 
>> executable - I assume b/c it is a 32 bit executable), and when I try 
>> to compile from src by using Makefile.cygwin (renamed to Makefile, 
>> and executing 'make
>> genesis'.) the compilation just shoots back 'All libs compiled' (not 
>> true), and 'make: *** No rule to make target 'liblist', needed by 
>> 'loadlib.c'. Stop.'. This is pretty little to sink ones teeth into. 
>> Any insights and genesis2.3 for 64 bit Cygwin is much welcome. 
>> -Dieter
>>

-- 
Gilles R. Detillieux              E-mail: <gr...@sc...>
Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
Dept. Physiology, U. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)


------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Genesis-sim-users mailing list
Gen...@li...
https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

Re: [Genesis-sim-users] running genesis2.3 under Cygwin64?

[Hugo C. <hug...@gm...>]

I don't like Cygwin, I don't care if we drop supporting it for the planned
2.4 release.


On Thu, Apr 17, 2014 at 8:08 PM, Dave Beeman <db...@co...> wrote:

> Is Cygwin still being developed?



Yes, it is.  It has a large install base for software developers in the
industry.


Hugo




> Dave Beeman
>
>
> On Wed, 16 Apr 2014, Jaeger, Dieter wrote:
>
>
>> Hello -  has anyone installed genesis 2.3 under 64 bit Cygwin?   For me
>> the
>> Cygwin.bindist files don’t work (genesis is not recognized as an
>> executable
>> – I assume b/c it is a 32 bit executable), and when I try to compile from
>> src by using Makefile.cygwin (renamed to Makefile, and executing ‘make
>> genesis’.)   the compilation just shoots back ‘All libs compiled’ (not
>> true),  and ‘make: *** No rule to make target 'liblist', needed by
>> 'loadlib.c'.  Stop.’.   This is pretty little to sink ones teeth into.
>> Any
>> insights and genesis2.3 for 64 bit Cygwin is much welcome. -Dieter
>>
>>
>>
>> --
>> Dieter Jaeger
>> Professor
>> Department of Biology, Emory University
>> 1510 Clifton Rd., Atlanta, GA 30322
>> 404 727 8139, e-mail: dj...@em...
>>
>> http://www.biology.emory.edu/research/Jaeger
>>
>>
>>
>>
>>
>
> ------------------------------------------------------------------------------
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
>
>


-- 
Hugo



--

                  Hugo Cornelis Ph.D.

            GENESIS-3 -- lead architect
              http://www.genesis-sim.org/

            Neurospaces Project Architect
              http://www.neurospaces.org/

Re: [Genesis-sim-users] running genesis2.3 under Cygwin64?

[Gilles D. <gr...@sc...>]

Yes, Cygwin is still being actively developed, and quite widely used. 
It's a more lightweight method of running UNIX code under Windows than 
running a virtual machine, and so it's still quite popular as a result. 
The 32-bit version has been around for quite some time and is quite 
stable, though still regularly updated.

The 64-bit version is quite new by comparison, and my own impression of 
it is that it's still a work in progress and not-quite-ready for prime 
time. They seem to be going with a different set of packages under the 
64-bit version, so there isn't a one-for-one correspondence between the 
packages in the two versions. In particular, many of the libraries in 
the 32-bit version simply aren't available in the 64-bit version. It 
does make porting applications from one version to the other less than 
straightforward.

Dieter, if you need 64-bit support, you may do better with a virtual 
environment as Dave suggested. If you don't, then you may find that the 
32-bit version of Cygwin will serve you well. It does run fine on 64-bit 
versions of Windows.

Gilles

On 04/17/2014 01:08 PM, Dave Beeman wrote:
>
> I think that Cygwin has been pretty much replaced by modern virtual
> environments for running Linux under Windows. I haven't tried compiling
> GENESIS under Cygwin for years.
>
> Some students at the LASCON course had good experiences running
> GENESIS with Ubuntu under something called VirtualBox. Mando has
> used Fedora with VMware. Perhaps other GENESIS users can report
> their favorites. But, I think it is time say goodbye to Cygwin
> and use real Linux under a virtual environment.
>
> Is Cygwin still being developed?
>
> Dave Beeman
>
> On Wed, 16 Apr 2014, Jaeger, Dieter wrote:
>
>>
>> Hello - has anyone installed genesis 2.3 under 64 bit Cygwin? For me the
>> Cygwin.bindist files don’t work (genesis is not recognized as an 
>> executable
>> – I assume b/c it is a 32 bit executable), and when I try to compile 
>> from
>> src by using Makefile.cygwin (renamed to Makefile, and executing ‘make
>> genesis’.) the compilation just shoots back ‘All libs compiled’ (not
>> true), and ‘make: *** No rule to make target 'liblist', needed by
>> 'loadlib.c'. Stop.’. This is pretty little to sink ones teeth into. Any
>> insights and genesis2.3 for 64 bit Cygwin is much welcome. -Dieter
>>

-- 
Gilles R. Detillieux              E-mail: <gr...@sc...>
Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
Dept. Physiology, U. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)

Re: [Genesis-sim-users] running genesis2.3 under Cygwin64?

[Dave B. <db...@Co...>]

I think that Cygwin has been pretty much replaced by modern virtual
environments for running Linux under Windows.  I haven't tried compiling
GENESIS under Cygwin for years.

Some students at the LASCON course had good experiences running
GENESIS with Ubuntu under something called VirtualBox.  Mando has
used Fedora with VMware.  Perhaps other GENESIS users can report
their favorites.  But, I think it is time say goodbye to Cygwin
and use real Linux under a virtual environment.

Is Cygwin still being developed?

Dave Beeman

On Wed, 16 Apr 2014, Jaeger, Dieter wrote:

> 
> Hello -  has anyone installed genesis 2.3 under 64 bit Cygwin?   For me the
> Cygwin.bindist files don’t work (genesis is not recognized as an executable
> – I assume b/c it is a 32 bit executable), and when I try to compile from
> src by using Makefile.cygwin (renamed to Makefile, and executing ‘make
> genesis’.)   the compilation just shoots back ‘All libs compiled’ (not
> true),  and ‘make: *** No rule to make target 'liblist', needed by
> 'loadlib.c'.  Stop.’.   This is pretty little to sink ones teeth into.  Any
> insights and genesis2.3 for 64 bit Cygwin is much welcome. -Dieter
> 
>  
> 
> --
> Dieter Jaeger
> Professor
> Department of Biology, Emory University
> 1510 Clifton Rd., Atlanta, GA 30322
> 404 727 8139, e-mail: dj...@em...
> 
> http://www.biology.emory.edu/research/Jaeger
> 
>  
> 
> 
>

[Genesis-sim-users] running genesis2.3 under Cygwin64?

[Jaeger, D. <dj...@em...>]

Hello -  has anyone installed genesis 2.3 under 64 bit Cygwin?   For me the Cygwin.bindist files don't work (genesis is not recognized as an executable - I assume b/c it is a 32 bit executable), and when I try to compile from src by using Makefile.cygwin (renamed to Makefile, and executing 'make genesis'.)   the compilation just shoots back 'All libs compiled' (not true),  and 'make: *** No rule to make target 'liblist', needed by 'loadlib.c'.  Stop.'.   This is pretty little to sink ones teeth into.  Any insights and genesis2.3 for 64 bit Cygwin is much welcome. -Dieter

--
Dieter Jaeger
Professor
Department of Biology, Emory University
1510 Clifton Rd., Atlanta, GA 30322
404 727 8139, e-mail: dj...@em...<mailto:dj...@em...>

http://www.biology.emory.edu/research/Jaeger

[Genesis-sim-users] Run parallel GENESIS simulations on supercomputers free of charge using the NSG

[Dave B. <db...@Co...>]

The Neuroscience Gateway, NSG (http://www.nsgportal.org) allows
computational neuroscientists to run parallel simulations,
free of charge, on supercomputers using tools like GENESIS, NEURON, NEST,
Brian, and PyNN. Other tools will be added
based on users' request.

NSG provides a simple web-based interface that makes it quick and easy to
create an account, upload model code, run
simulations, and get back results. To get started, go to
http://www.nsgportal.org , click on the "Go to the NSG Portal"
button, and follow the instructions in the sentence:

"New users who are interested in getting an account should fill out the form
and email it to ns...@sd..."

For any questions or suggestions related to the NSG portal, please contact
us at ns...@sd...

The NSG developers team

Re: [Genesis-sim-users] change gmax during simulation

[Dave B. <db...@Co...>]

Hi Howard,

This is a common problem when you want to make some changes to an element
of an object type that doesn't accept a message to change a field.
For example, the synchan can't receive a message to change the gmax.

In cases like this, you can use a script_out object to execute a
function that is defined in the GENESIS SLI language.  For example,
as Hugo suggested:

function set_gmax
    float new_gmax = <your new gmax value, calculated from [Ca] or Ik>
    setfield {cellpath}/input_name gmax {new_gmax}
end

Then have a command:

create script_out /gmax_setter
setfield /gmax_setter command set_gmax
// optionally, use a step that is larger than the simulation clock
useclock /gmax_setter 1
setclock 1 {out_dt}

The function 'set_gmax' will now be called at intervals of {out_dt}.
Use these last statements if you don't need to update gmax at every
simulation time step with clock 0.  The function that you define will
have to be interpreted by the SLI each time that it is called, so you
want to make it as efficient as possible, and call at as large an interval
as you can.

You can find other examples in the description of my November SfN poster
at http://genesis-sim.org/GENESIS/fMRInet/

Here, I needed to either provide an injection current or a membrane
potential shift to every compartment in the pyramidal cells of
a network.  These depend on compartment dimensions and on an
applied electrical field.

The script_out object is a very versatile one that GENESIS modelers
can use to avoid making custom objects that will not be hsolvable.

Dave Beeman

On Wed, 12 Feb 2014, Huo Lu wrote:

> Hi, Dave,
> Normally, we set the gmax in following way as a fixed value:
> 
> copy non_NMDA {cellpath}/input_name
> setfield {cellpath}/input_name gmax {Gbar*surf}
> 
> If I want to have a variable gmax following either [Ca] or the current from
> certain channel, how can I do that?
> 
> Howard
> 
>

[Genesis-sim-users] change gmax during simulation

[Huo Lu <how...@gm...>]

Hi, Dave,

Normally, we set the gmax in following way as a fixed value:

copy non_NMDA {cellpath}/input_name
setfield {cellpath}/input_name gmax {Gbar*surf}

If I want to have a variable gmax following either [Ca] or the current from
certain channel, how can I do that?

Howard

[Genesis-sim-users] solution for multi task of writing data to disk?

[Kai Du <kai...@gm...>]

Hi All,

I am running GENESIS on Fedora 14 (X86-64) and my CPU is Xeon X5675 (6
cores). I noticed a problem:  when I run several (>4) GENESIS tasks, each
of them requiring heavy load of writing  data to the disk, the *actual*
simulation speed drops dramatically. Accordingly,   If I *shut down* data
writing, the simulation speed would maintain.

I am wondering if I use RAID10+SSD could solve this problem, i.e. the
bottom-neck of multi-task data writing?

-- 
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden