ecell-devel Mailing List for E-Cell System

Hi Tom,


Are you running your model on osogo (GUI) or ecell3-session (script)?

Are you using Loggers?

-sha


> I am trying to test some gene network inferencing algorithms and would
> like to use the output of an E-Cell model.  Is there any way I can
> specify how many samples or time points I can get?
> 
>  
> 
> Thank you!!
> 
>  
> 
> Sincerely,
> 
>  
> 
> Tom   
> 
>  
> 
> Thoughts for the day:
> 
>  
> 
> (1) "No matter where you go there you are" (B. Banzai)
> 
>  
> 
> (2) "Time exists so that everything doesn't occur at once" (B. Banzai)
> 
>  
> 
> (3) "The world is full of friends that we have not yet met" (T.Heiman)
> 
>  
> 
> (4) I live in my own little world, but it's OK,they know me
> there(T.Heiman)
> 
>  
> 
> 
>  
> 
> 

Hi,
 
I am trying to test some gene network inferencing algorithms and would
like to use the output of an E-Cell model.  Is there any way I can
specify how many samples or time points I can get?
 
Thank you!!
 
Sincerely,
 
Tom   
 
Thoughts for the day:
 
(1) "No matter where you go there you are" (B. Banzai)
 
(2) "Time exists so that everything doesn't occur at once" (B. Banzai) 
 
(3) "The world is full of friends that we have not yet met" (T.Heiman)
 
(4) I live in my own little world, but it's OK,they know me
there(T.Heiman)
 
 

Hi,
 
I am trying to test some gene network inferencing algorithms and would
like to use the output of an E-Cell model.  When I am running a model is
there any way I can specify how many samples or time points I can get?
 
Thank you!!
 
Sincerely,
 
Tom   
 
Thoughts for the day:
 
(1) "No matter where you go there you are" (B. Banzai)
 
(2) "Time exists so that everything doesn't occur at once" (B. Banzai) 
 
(3) "The world is full of friends that we have not yet met" (T.Heiman)
 
(4) I live in my own little world, but it's OK,they know me
there(T.Heiman)
 
 

Hi everyone,

Following Shafi's suggestion, we have created an IRC channel for E-Cell 
3 at irc://irc.freenode.net/#ecell
This is a public channel for general discussion related to E-Cell 3. You 
can join using Gaim, Xchat, Chatzilla, mIRC or any other IRC clients.

satya

Hi everyone,


We are pleased to announce the availability of E-Cell Simulation
Environment Version 3.1.99 (Hekkever).

Source code and binary packages for Linux/Windows are available at:
http://sourceforge.net/project/showfiles.php?group_id=72485&release_id=190942


Some prominent new features of this version, among others, are:

- New ExpressionFluxProcess class, which enables users to 
  use infix rate equations in model files, without creating
  a new class for each reaction mechanism.  (written by Ishida)
  The functionality is compatible with SBML level 2.
  Usage in the manual will follow.

- Parameter estimation toolkit using Generic Algorithm, that
  works on SessionManager distributed computation platform.
  (by Sugimoto)

- This is the first version of E-Cell 3 that can be built and
  installed on Windows 2000/XP. (by Satya)
 
  The binary installer package is available at the download page.

  Windows support is in beta.   The installer is about 60MB,
  and installation requires about 300MB HDD space.

  For those who want to build it from scratch, a detailed instruction on
  building ecell3 on Windows, written by Satya Arjunan, can be seen
  here:
  http://www2.e-cell.org/moin/moin.cgi/CreatingWindowsInstaller


-sha



Here goes the full list of changes from version 3.1.98.


* added ExpressionFluxProcess (tishida)
* added ConstantFluxProcess (tkitayama)
* Drosophila sample model is modified by using ExpressionFluxProcess
   instead of PythonFluxProcess (tishida)
* added DMInfo functionality to the core (shafi)
* changed logger mechanism (bgabor)
* added plotting history traces by min-max plotting (bgabor)
* fixed a serious undefined reference to my_open_to_read bug in Vvector (bgabor)
* StepperWindow property update strategy optimized. Properties consisting
   of tuples are not refreshed. (bgabor)
* When TracerWindow is created, loggers are created automatically and show
   history mode is default. (bgabor)
* Step button now doesn't overwrite the step size text input. (bgabor)
* Unit measure doesn't disappear when changing to strip mode. (bgabor)
* If user creates loggers while simulation is running, they get a warning
   poup message. (bgabor)
* Changes for MinGW compilation on MS-Windows environment (satyanandavel)
* enabled direct package installation in Windows (satyanandavel)
* added a parameter estimation toolkit using Genetic Algorithm and
   SessionManager (osugi)
* updated for deletion of some Loki files, comment update (shafi)
* MessageWindow now inserts new text at the end of text instead at
   cursor. (bgabor)
* Closing windows really close them not just iconify. buttons and
   menuitems for these windows are now togglebuttons and menus. (bgabor)
* gtk-preference menupoint taken out because it is not implemented (bgabor)
* Session loadscript now changes working directory to script's dir. (bgabor)
* ToggleWindow method added to GtkSessionMonitor (bgabor)
* Bug fix. Now destroying board window makes add to board button
   insensitive on entitylistwindows. (bgabor)
* fixed the mysterious time counter bug in osogo. (bgabor)
* fixed bugs of eri2eml (tsakurada)
* OSOGOPATH needs to be declared beforehand for gecell3-session
   since config.py no longer defines it (satyanandavel)
* updated users manual (shafi)

Satya-san,

Thank you for the error report.

I fixed ExpressionProcessBase.hpp now.
But it can not use the following functions.

{asech , acsch , acoth , csch , coth , asec , acsc
 acot , sec , csc , cot , fact} 

I defined those functions in Util.hpp,but  

I will add those functions later. 

> -----Original Message-----
> From: ece...@li... 
> [mailto:ece...@li...] On Behalf Of 
> Satya Arjunan
> Sent: Saturday, October 11, 2003 6:45 AM
> To: ti...@us...
> Cc: ece...@li...
> Subject: [Ecell-devel] ExpressionProcessBase.hpp
> 
> 
> Ishida-san,
> 
> I am getting the following error when I compile 
> ExpressionProcessBase.hpp in Linux (cacao). Can you find out 
> what could 
> be the problem?
> Thanks.
> 
> satya
> 
> Entering directory `/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell/dm'
> /bin/sh ../../bin/ecell3-dmc -v --dmcompile=../../dmtool 
> --no-stdinclude 
> --no-stdlibdir --ldflags=-L../libecs --cxxflags='-I../libecs -I../.. 
> -I.. -I/usr/include/python2.2 ' ExpressionFluxProcess.cpp 
> ../../dmtool/dmcompile ExpressionFluxProcess.cpp 
> -D_ECELL3_DM_CLASSNAME=ExpressionFluxProcess -I../libecs -I../.. -I.. 
> -I/usr/include/python2.2
> g++ -g -O2 -D_ECELL3_DM_CLASSNAME=ExpressionFluxProcess -I../libecs
> -I../.. -I.. -I/usr/include/python2.2 -fPIC -c 
> ExpressionFluxProcess.cpp In file included from 
> ExpressionFluxProcess.cpp:35:
> ExpressionProcessBase.hpp: In member function `void
>    libecs::ExpressionProcessBase::Compiler::setFunctionMap()':
> ExpressionProcessBase.hpp:610: `fact' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:610: (Each undeclared identifier is 
> reported only
>    once for each function it appears in.)
> ExpressionProcessBase.hpp:614: `asech' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:615: `acsch' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:616: `acoth' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:617: `sech' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:618: `csch' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:619: `coth' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:620: `asec' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:621: `acsc' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:622: `acot' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:623: `sec' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:624: `csc' undeclared (first use 
> this function)
> ExpressionProcessBase.hpp:625: `cot' undeclared (first use 
> this function)
> Error: dmcompile failed.
> make[4]: *** [ExpressionFluxProcess.so] Error 1
> make[4]: Leaving directory 
> `/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell/dm'
> make[3]: *** [all-recursive] Error 1
> make[3]: Leaving directory 
> `/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell'
> make[2]: *** [all] Error 2
> make[2]: Leaving directory 
> `/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell'
> make[1]: *** [all-recursive] Error 1
> make[1]: Leaving directory `/a/home0/satya/src/ecell/cvs/ori/ecell3'
> make: *** [all] Error 2
> 
> 
> 
> 
> -------------------------------------------------------
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> 

Ishida-san,

I am getting the following error when I compile 
ExpressionProcessBase.hpp in Linux (cacao). Can you find out what could 
be the problem?
Thanks.

satya

Entering directory `/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell/dm'
/bin/sh ../../bin/ecell3-dmc -v --dmcompile=../../dmtool --no-stdinclude 
--no-stdlibdir --ldflags=-L../libecs --cxxflags='-I../libecs -I../.. 
-I.. -I/usr/include/python2.2 ' ExpressionFluxProcess.cpp
../../dmtool/dmcompile ExpressionFluxProcess.cpp 
-D_ECELL3_DM_CLASSNAME=ExpressionFluxProcess -I../libecs -I../.. -I.. 
-I/usr/include/python2.2
g++ -g -O2 -D_ECELL3_DM_CLASSNAME=ExpressionFluxProcess -I../libecs 
-I../.. -I.. -I/usr/include/python2.2 -fPIC -c ExpressionFluxProcess.cpp
In file included from ExpressionFluxProcess.cpp:35:
ExpressionProcessBase.hpp: In member function `void
   libecs::ExpressionProcessBase::Compiler::setFunctionMap()':
ExpressionProcessBase.hpp:610: `fact' undeclared (first use this function)
ExpressionProcessBase.hpp:610: (Each undeclared identifier is reported only
   once for each function it appears in.)
ExpressionProcessBase.hpp:614: `asech' undeclared (first use this function)
ExpressionProcessBase.hpp:615: `acsch' undeclared (first use this function)
ExpressionProcessBase.hpp:616: `acoth' undeclared (first use this function)
ExpressionProcessBase.hpp:617: `sech' undeclared (first use this function)
ExpressionProcessBase.hpp:618: `csch' undeclared (first use this function)
ExpressionProcessBase.hpp:619: `coth' undeclared (first use this function)
ExpressionProcessBase.hpp:620: `asec' undeclared (first use this function)
ExpressionProcessBase.hpp:621: `acsc' undeclared (first use this function)
ExpressionProcessBase.hpp:622: `acot' undeclared (first use this function)
ExpressionProcessBase.hpp:623: `sec' undeclared (first use this function)
ExpressionProcessBase.hpp:624: `csc' undeclared (first use this function)
ExpressionProcessBase.hpp:625: `cot' undeclared (first use this function)
Error: dmcompile failed.
make[4]: *** [ExpressionFluxProcess.so] Error 1
make[4]: Leaving directory 
`/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell/dm'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/a/home0/satya/src/ecell/cvs/ori/ecell3/ecell'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/a/home0/satya/src/ecell/cvs/ori/ecell3'
make: *** [all] Error 2

Dear Satya,

Thank you for your replay and checking the programs on Linux.
And please send me the latest binary package until next morning.
If any problem, please contact me.

Seiji Ota
Mitsui Knowledge Industry Co.,Ltd.

----- Original Message ----- 
From: "Satya Arjunan" <sa...@tt...>
To: "Seiji Ota" <ot...@hy...>
Cc: <ece...@li...>; <ece...@eg...>
Sent: Thursday, October 09, 2003 9:11 PM
Subject: Re: [ecell3-pkg] Fw: installer etc


> Dear Seiji Ota-san,
>
> Thank you for the changes that you have made. I will commit them to cvs
> after checking it on linux. After that I will submit the latest binaries
> in the ecell3winDistribution.
>
> satya
>
> >Dare Satya and Sakurada
> >
> >Thank you for preparation of package.
> >But these following programs have problem on the windows version
> >which are not considered blank in input paths.
> >(Cf. "C:\Documents and Settings" or so)
> >
> >/bin/dmcompile
> >/bin/ecell3-dmc
> >
> >We performed easy repair about attached files.
> >We want to ask you for the check of the repair parts,
> >and want to get permission of the inclusion to the installer of windows.
> >Your cooperation is greatly appreciated.
> >
> >Seiji Ota
> >Mitsui Knowledge Industry Co.,Ltd.
> >
> >------------------------------------------------------------------------
> >
> >import sys
> >import os
> >import glob
> >import string
> >import getopt
> >
> >prefix=os.environ['ecell3_prefix']
> >exec_prefix=prefix
> >libdir=exec_prefix + os.sep + 'lib'
> >CXX='g++'
> >ORIG_CXXFLAGS="-g -O2"
> >LDADD='-lstdc++'
> >SHLEXT='.dll'
> >CXXSUFFIX='.cpp'
> >CXXFLAGS = os.environ.get('CXXFLAGS','')
> >VERBOSE = False
> >
> >def help():
> >    ext = os.path.basename( sys.argv[0] )
> >    aProgramName, ext = os.path.splitext( ext )
> >    print '''
> >%s -- Compile dynamic modules for E-Cell Simulation Environment Version 3
> >
> >Usage:
> >       %s [-v|--verbose] <source.cpp> [compile options]
> >       %s [-h|--help]
> >    '''% ( aProgramName, aProgramName, aProgramName )
> >
> >def msg( outstr ):
> >    print "E-Cell3 dmcompile: " + outstr
> >
> >def execute( cmdstr ):
> > if VERBOSE:
> > print cmdstr
> >
> > return os.system( cmdstr )
> >
> >def compile( CXX, CXXCOMPILEFLAGS, SRC ):
> >    return execute( CXX + ' ' + CXXCOMPILEFLAGS + ' -fPIC -c ' + SRC )
> >
> >def link( CXX, OBJ, SOBJ, LDFLAGS ):
> >    return execute( CXX + ' -shared ' + OBJ + ' -o ' + SOBJ + ' ' +
LDFLAGS )
> >
> >def cleanup( OBJ ):
> >    if os.path.isfile( OBJ ):
> > os.remove( OBJ )
> >
> >def main():
> >    opts , args = getopt.getopt( sys.argv[1:], "hv", ["help", "verbose"])
> >    global VERBOSE
> >
> >    for anOption, anArg in opts:
> >
> > # print help message
> >        if anOption in ( "-h", '--help' ):
> >            help()
> >            sys.exit(0)
> >
> > # be verbose
> >        if anOption in ( "-v", '--verbose'):
> >     VERBOSE = True
> >
> >    # check if source file is given
> >    if len( args ) < 1:
> > help()
> > msg( "Error: source file was not given." )
> > sys.exit(1)
> >
> >    # check if source file is valid
> >    if len( glob.glob ( args[0] ) ) < 1:
> > msg( "Error: source file "+ args[0] + " was not found." )
> > sys.exit(1)
> >
> >    SRC = args[0]
> >    ext = os.path.basename(SRC)
> >    CLASSNAME, ext = os.path.splitext(ext)
> >    OBJ = CLASSNAME + '.o'
> >    SOBJ = CLASSNAME + SHLEXT
> >    LDFLAGS =  os.environ.get('LDFLAGS','')
> >    LDFLAGS = '-Wl,-rpath=' + libdir + ',-soname=' + SOBJ + ' ' + LDFLAGS
> >    if CXXFLAGS != '':
> > CXXCOMPILEFLAGS = CXXFLAGS + ' ' + string.join( args[1:] )
> >    else:
> > CXXCOMPILEFLAGS = ORIG_CXXFLAGS + ' ' + string.join( args[1:] )
> >
> >    if compile( CXX, CXXCOMPILEFLAGS, "\""+SRC+"\"" ) or not
os.path.isfile( OBJ ):
> > msg( "Error: The compiler failed to create " + OBJ )
> > sys.exit(1)
> >
> >    if link( CXX, OBJ, SOBJ, LDFLAGS ) or not os.path.isfile( SOBJ ):
> > msg( "Error: The compiler failed to create " + SOBJ )
> > sys.exit(1)
> >
> >    msg( 'generated ' + SOBJ )
> >    cleanup( OBJ )
> >
> >if __name__ == '__main__':
> > main()
> >
> >
> >
> >
> >------------------------------------------------------------------------
> >
> >import sys
> >import os
> >import glob
> >import getopt
> >
> >def usage():
> >    ext = os.path.basename( sys.argv[0] )
> >    aProgramName, ext = os.path.splitext( ext )
> >    print '''
> >%s -- Compile dynamic modules for E-Cell Simulation Environment Version
3.
> >
> >Usage:
> >       %s [options] [sourcefile(s)]
> >       %s [-h] or [--help]
> >    '''% ( aProgramName, aProgramName, aProgramName )
> >
> >def help():
> >    usage()
> >    ext = os.path.basename( sys.argv[0] )
> >    aProgramName, ext = os.path.splitext( ext )
> >    print '''
> >%s options:
> >        --no-stdinclude          Don't set standard include file path.
> >        --no-stdlibdir           Don't set standard library directory
path.
> >        --ldflags=[ldflags]      Specify options to the linker.
> >        --cxxflags=[cxxflags]    Add compiler options.
> >        --no-define-cxxflags=[cxxflags]
> >                                 Override the default compiler options.
> >        --dmcompile=[path]       Specify dmcompile path.
> >        -v or --verbose   Be verbose.
> >        -h or --help Print this message.
> >
> >
> >This program is part of E-Cell Simulation Environment Version 3.
> >Written by:
> >    Tomoya Kitayama <to...@e-...>
> >    Satya Arjunan <sa...@tt...>
> >    '''% ( aProgramName )
> >
> >def msg( outstr ):
> >    print "E-Cell3 ecell3-dmc: " + outstr
> >
> >def main():
> >
> >    # -------------------------------------
> >    # initialize file names
> >    # -------------------------------------
> >    prefix = os.environ['ecell3_prefix']
> >    exec_prefix = prefix
> >    BINDIR = exec_prefix + os.sep + 'bin'
> >    STDLIBDIR = '-L' + exec_prefix + os.sep + 'lib'
> >    ECELL_INCLUDE = prefix + os.sep + 'include' + os.sep + 'ecell'
> >    LIBECS_INCLUDE = ECELL_INCLUDE + os.sep + 'libecs'
> >    STDINCLUDE = '-I' + prefix + os.sep + 'include' + ' -I' +
ECELL_INCLUDE + \
> >    ' ' + '-I' + LIBECS_INCLUDE + ' -I.'
> >    DMCOMPILE = '\"'+BINDIR + os.sep + 'dmcompile\"'
> >    SRC = None
> >
> >
> >    # -------------------------------------
> >    # get options and arguments
> >    # -------------------------------------
> >    try:
> > opts , args = getopt.getopt( sys.argv[1:], "hv",
> > ["help", "verbose", "no-stdinclude","no-stdlibdir", "ldflags=",
"cxxflags=", "no-define-cxxflags=", "dmcompile="])
> >    except:
> >        help()
> >        sys.exit(1)
> >
> >    VERBOSE = False
> >    NO_STDINCLUDE = False
> >    NO_STDLIBDIR = False
> >    NO_DEFINE_CXXFLAGS = False
> >    LDFLAGS = ''
> >    CXXFLAGS = ''
> >    CXXCOMPILEFLAGS = ''
> >
> >    # -------------------------------------
> >    # check argument
> >    # -------------------------------------
> >    for anOption, anArg in opts:
> >
> >        # print help message
> >        if anOption in ( "-h", '--help' ):
> >            help()
> >            sys.exit(0)
> >
> >  # be verbose
> >        if anOption in ( "-v", '--verbose'):
> >     VERBOSE = True
> >
> > # without stdinclude
> >        if anOption == "--no-stdinclude":
> >     NO_STDINCLUDE = True
> >
> > # without stdlibdir
> >        if anOption == "--no-stdlibdir":
> >     NO_STDLIBDIR = True
> >
> > # set ldflags
> >        if anOption == "--ldflags":
> >            LDFLAGS = LDFLAGS + ' ' + anArg
> >
> > # set no-define-cxxflags
> >        if anOption == "--no-define-cxxflags":
> >            NO_DEFINE_CXXFLAGS = True
> >     CXXFLAGS = anArg
> >
> > # set cxxflags
> >        if anOption == "--cxxflags":
> >     CXXCOMPILEFLAGS = CXXFLAGS + ' ' + anArg
> >
> > # set cxxflags
> >        if anOption == "--dmcompile":
> >     DMCOMPILE = anArg + os.sep + 'dmcompile'
> >
> >    # check if source file is given
> >    if len( args ) < 1:
> > help()
> > msg( "Error: source file was not given." )
> > sys.exit(1)
> >
> >    # check if source file is valid
> >    if len( glob.glob ( args[0] ) ) < 1:
> > msg( "Error: source file "+ args[0] + " was not found." )
> > sys.exit(1)
> >
> >    if NO_STDINCLUDE:
> > INCLUDE = ""
> >    else:
> > INCLUDE = STDINCLUDE
> >
> >    if not NO_STDLIBDIR:
> > LDFLAGS = LDFLAGS + ' ' + STDLIBDIR
> >    LDFLAGS = LDFLAGS + " -Wl,--enable-runtime-pseudo-reloc -lecs -lgsl \
> >    -lpython22 -lboost_python"
> >    os.environ['LDFLAGS'] = LDFLAGS
> >
> >    if NO_DEFINE_CXXFLAGS:
> > os.environ['CXXFLAGS'] = CXXFLAGS
> >
> >    for SRC in glob.glob( args[0] ):
> > ext = os.path.basename(SRC)
> > CLASSNAME, ext = os.path.splitext(ext)
> > CLASSNAMEDEFINE = '-D_ECELL3_DM_CLASSNAME=' + CLASSNAME
> > cmdstr = '\"'+SRC + '\" \"' + INCLUDE + '\" \"' + CLASSNAMEDEFINE + '\"
\"' + CXXCOMPILEFLAGS+'\"'
> >
> > if VERBOSE:
> >     cmdstr = 'python ' + DMCOMPILE + ' -v ' + cmdstr
> >     print cmdstr
> >     os.system( cmdstr )
> > else:
> >     cmdstr = 'python ' + DMCOMPILE + ' ' + cmdstr
> >     print cmdstr
> >     os.system( cmdstr )
> >
> >if __name__ == '__main__':
> > main()
> >
> >
> >
> >
> >------------------------------------------------------------------------
> >
> >
> >56c56
> ><     DMCOMPILE = '\"'+BINDIR + os.sep + 'dmcompile\"'
> >---
> >
> >
> >>    DMCOMPILE = BINDIR + os.sep + 'dmcompile'
> >>
> >>
> >146,147c146
> ><       cmdstr = '\"'+SRC + '\" \"' + INCLUDE + '\" \"' + CLASSNAMEDEFINE
+ '\" \"' + CXXCOMPILEFLAGS+'\"'
> ><
> >---
> >
> >
> >>      cmdstr = SRC + ' ' + INCLUDE + ' ' + CLASSNAMEDEFINE + ' ' +
CXXCOMPILEFLAGS
> >>
> >>
> >154d152
> ><           print cmdstr
> >rune%
> >
> >------------------------------------------------------------------------
> >
> >
> >33,34c33,35
> ><       if VERBOSE:
> ><               print cmdstr
> >---
> >
> >
> >>    if VERBOSE:
> >>      print cmdstr
> >>    return os.system( cmdstr )
> >>
> >>
> >36,37d36
> ><       return os.system( cmdstr )
> ><
> >59c58
> ><       # be verbose
> >---
> >
> >
> >>      # be verbose
> >>
> >>
> >86c85
> ><     if compile( CXX, CXXCOMPILEFLAGS, "\""+SRC+"\"" ) or not
os.path.isfile( OBJ ):
> >---
> >
> >
> >>    if compile( CXX, CXXCOMPILEFLAGS, SRC ) or not os.path.isfile(
OBJ ):
> >>
> >>
> >rune%
> >
>
>
>
>

Dear Seiji Ota-san,

Thank you for the changes that you have made. I will commit them to cvs
after checking it on linux. After that I will submit the latest binaries
in the ecell3winDistribution.

satya

>Dare Satya and Sakurada
>
>Thank you for preparation of package.
>But these following programs have problem on the windows version
>which are not considered blank in input paths.
>(Cf. "C:\Documents and Settings" or so)
>
>/bin/dmcompile
>/bin/ecell3-dmc
>
>We performed easy repair about attached files.
>We want to ask you for the check of the repair parts, 
>and want to get permission of the inclusion to the installer of windows.
>Your cooperation is greatly appreciated.
>
>Seiji Ota
>Mitsui Knowledge Industry Co.,Ltd.
>
>------------------------------------------------------------------------
>
>import sys
>import os
>import glob
>import string
>import getopt
>
>prefix=os.environ['ecell3_prefix']
>exec_prefix=prefix
>libdir=exec_prefix + os.sep + 'lib'
>CXX='g++'
>ORIG_CXXFLAGS="-g -O2"
>LDADD='-lstdc++'
>SHLEXT='.dll'
>CXXSUFFIX='.cpp'
>CXXFLAGS = os.environ.get('CXXFLAGS','')
>VERBOSE = False
>
>def help():
>    ext = os.path.basename( sys.argv[0] )
>    aProgramName, ext = os.path.splitext( ext )
>    print '''
>%s -- Compile dynamic modules for E-Cell Simulation Environment Version 3
>
>Usage:
>       %s [-v|--verbose] <source.cpp> [compile options]
>       %s [-h|--help]
>    '''% ( aProgramName, aProgramName, aProgramName )
>
>def msg( outstr ):
>    print "E-Cell3 dmcompile: " + outstr
>
>def execute( cmdstr ):
>	if VERBOSE:
>		print cmdstr
>
>	return os.system( cmdstr )
>
>def compile( CXX, CXXCOMPILEFLAGS, SRC ):
>    return execute( CXX + ' ' + CXXCOMPILEFLAGS + ' -fPIC -c ' + SRC )
>
>def link( CXX, OBJ, SOBJ, LDFLAGS ):
>    return execute( CXX + ' -shared ' + OBJ + ' -o ' + SOBJ + ' ' + LDFLAGS )
>
>def cleanup( OBJ ):
>    if os.path.isfile( OBJ ):
>	os.remove( OBJ )
>    
>def main():
>    opts , args = getopt.getopt( sys.argv[1:], "hv", ["help", "verbose"])   
>    global VERBOSE
>    
>    for anOption, anArg in opts:
>
>	# print help message
>        if anOption in ( "-h", '--help' ):
>            help()
>            sys.exit(0)
>      
>	# be verbose
>        if anOption in ( "-v", '--verbose'):
>	    VERBOSE = True 
>
>    # check if source file is given
>    if len( args ) < 1:
>	help()
>	msg( "Error: source file was not given." )
>	sys.exit(1)
>
>    # check if source file is valid
>    if len( glob.glob ( args[0] ) ) < 1:
>	msg( "Error: source file "+ args[0] + " was not found." )
>	sys.exit(1)
>		
>    SRC = args[0]
>    ext = os.path.basename(SRC)
>    CLASSNAME, ext = os.path.splitext(ext)
>    OBJ = CLASSNAME + '.o'
>    SOBJ = CLASSNAME + SHLEXT
>    LDFLAGS =  os.environ.get('LDFLAGS','')
>    LDFLAGS = '-Wl,-rpath=' + libdir + ',-soname=' + SOBJ + ' ' + LDFLAGS 
>    if CXXFLAGS != '':
>	CXXCOMPILEFLAGS = CXXFLAGS + ' ' + string.join( args[1:] )
>    else:
>	CXXCOMPILEFLAGS = ORIG_CXXFLAGS + ' ' + string.join( args[1:] )
>
>    if compile( CXX, CXXCOMPILEFLAGS, "\""+SRC+"\"" ) or not os.path.isfile( OBJ ):
>	msg( "Error: The compiler failed to create " + OBJ )
>	sys.exit(1)
>	
>    if link( CXX, OBJ, SOBJ, LDFLAGS ) or not os.path.isfile( SOBJ ):
>	msg( "Error: The compiler failed to create " + SOBJ )
>	sys.exit(1)
>    
>    msg( 'generated ' + SOBJ )
>    cleanup( OBJ )
>
>if __name__ == '__main__':
>	main()
>	
>
>  
>
>------------------------------------------------------------------------
>
>import sys
>import os
>import glob
>import getopt
>
>def usage():
>    ext = os.path.basename( sys.argv[0] )
>    aProgramName, ext = os.path.splitext( ext )
>    print '''
>%s -- Compile dynamic modules for E-Cell Simulation Environment Version 3.
>
>Usage:
>       %s [options] [sourcefile(s)]
>       %s [-h] or [--help]
>    '''% ( aProgramName, aProgramName, aProgramName )
>
>def help():
>    usage()
>    ext = os.path.basename( sys.argv[0] )
>    aProgramName, ext = os.path.splitext( ext )
>    print '''
>%s options:
>        --no-stdinclude          Don't set standard include file path.
>        --no-stdlibdir           Don't set standard library directory path.
>        --ldflags=[ldflags]      Specify options to the linker.
>        --cxxflags=[cxxflags]    Add compiler options.
>        --no-define-cxxflags=[cxxflags]
>                                 Override the default compiler options.
>        --dmcompile=[path]       Specify dmcompile path.
>        -v or --verbose   	 Be verbose.
>        -h or --help		 Print this message.
>
>
>This program is part of E-Cell Simulation Environment Version 3.
>Written by:
>    Tomoya Kitayama <to...@e-...>
>    Satya Arjunan <sa...@tt...>
>    '''% ( aProgramName )
>
>def msg( outstr ):
>    print "E-Cell3 ecell3-dmc: " + outstr
>
>def main():
>
>    # -------------------------------------
>    # initialize file names
>    # -------------------------------------
>    prefix = os.environ['ecell3_prefix']
>    exec_prefix = prefix
>    BINDIR = exec_prefix + os.sep + 'bin'
>    STDLIBDIR = '-L' + exec_prefix + os.sep + 'lib'
>    ECELL_INCLUDE = prefix + os.sep + 'include' + os.sep + 'ecell'
>    LIBECS_INCLUDE = ECELL_INCLUDE + os.sep + 'libecs'
>    STDINCLUDE = '-I' + prefix + os.sep + 'include' + ' -I' + ECELL_INCLUDE + \
>    		' ' + '-I' + LIBECS_INCLUDE + ' -I.'
>    DMCOMPILE = '\"'+BINDIR + os.sep + 'dmcompile\"'
>    SRC = None
>
>
>    # -------------------------------------
>    # get options and arguments
>    # -------------------------------------
>    try:
>	opts , args = getopt.getopt( sys.argv[1:], "hv",
>			["help", "verbose", "no-stdinclude","no-stdlibdir", "ldflags=", "cxxflags=", "no-define-cxxflags=", "dmcompile="])
>    except:
>        help()
>        sys.exit(1)
>	
>    VERBOSE = False
>    NO_STDINCLUDE = False
>    NO_STDLIBDIR = False
>    NO_DEFINE_CXXFLAGS = False
>    LDFLAGS = ''
>    CXXFLAGS = ''
>    CXXCOMPILEFLAGS = ''
>
>    # -------------------------------------
>    # check argument
>    # -------------------------------------
>    for anOption, anArg in opts:
>
>        # print help message
>        if anOption in ( "-h", '--help' ):
>            help()
>            sys.exit(0)
>      
>  	# be verbose
>        if anOption in ( "-v", '--verbose'):
>	    VERBOSE = True            
>            
>	# without stdinclude            
>        if anOption == "--no-stdinclude":
>	    NO_STDINCLUDE = True
>
>	# without stdlibdir            
>        if anOption == "--no-stdlibdir":
>	    NO_STDLIBDIR = True
>
>	# set ldflags
>        if anOption == "--ldflags":
>            LDFLAGS = LDFLAGS + ' ' + anArg
>
>	# set no-define-cxxflags
>        if anOption == "--no-define-cxxflags":
>            NO_DEFINE_CXXFLAGS = True
>	    CXXFLAGS = anArg
>
>	# set cxxflags
>        if anOption == "--cxxflags":
>	    CXXCOMPILEFLAGS = CXXFLAGS + ' ' + anArg
>
>	# set cxxflags
>        if anOption == "--dmcompile":
>	    DMCOMPILE = anArg + os.sep + 'dmcompile'
>
>    # check if source file is given
>    if len( args ) < 1:
>	help()
>	msg( "Error: source file was not given." )
>	sys.exit(1)
>
>    # check if source file is valid
>    if len( glob.glob ( args[0] ) ) < 1:
>	msg( "Error: source file "+ args[0] + " was not found." )
>	sys.exit(1)
>
>    if NO_STDINCLUDE:
>	INCLUDE = ""
>    else:
>	INCLUDE = STDINCLUDE
>
>    if not NO_STDLIBDIR:
>	LDFLAGS = LDFLAGS + ' ' + STDLIBDIR
>    LDFLAGS = LDFLAGS + " -Wl,--enable-runtime-pseudo-reloc -lecs -lgsl \
>    			-lpython22 -lboost_python"
>    os.environ['LDFLAGS'] = LDFLAGS
>    
>    if NO_DEFINE_CXXFLAGS:
>	os.environ['CXXFLAGS'] = CXXFLAGS
>
>    for SRC in glob.glob( args[0] ):
>	ext = os.path.basename(SRC)
>	CLASSNAME, ext = os.path.splitext(ext)
>	CLASSNAMEDEFINE = '-D_ECELL3_DM_CLASSNAME=' + CLASSNAME
>	cmdstr = '\"'+SRC + '\" \"' + INCLUDE + '\" \"' + CLASSNAMEDEFINE + '\" \"' + CXXCOMPILEFLAGS+'\"'
>
>	if VERBOSE:
>	    cmdstr = 'python ' + DMCOMPILE + ' -v ' + cmdstr
>	    print cmdstr
>	    os.system( cmdstr )
>	else:
>	    cmdstr = 'python ' + DMCOMPILE + ' ' + cmdstr	
>	    print cmdstr
>	    os.system( cmdstr )
>
>if __name__ == '__main__':
>	main()
>
>
>  
>
>------------------------------------------------------------------------
>
>
>56c56
><     DMCOMPILE = '\"'+BINDIR + os.sep + 'dmcompile\"'
>---
>  
>
>>    DMCOMPILE = BINDIR + os.sep + 'dmcompile'
>>    
>>
>146,147c146
><       cmdstr = '\"'+SRC + '\" \"' + INCLUDE + '\" \"' + CLASSNAMEDEFINE + '\" \"' + CXXCOMPILEFLAGS+'\"'
>< 
>---
>  
>
>>      cmdstr = SRC + ' ' + INCLUDE + ' ' + CLASSNAMEDEFINE + ' ' + CXXCOMPILEFLAGS
>>    
>>
>154d152
><           print cmdstr
>rune% 
>
>------------------------------------------------------------------------
>
>
>33,34c33,35
><       if VERBOSE:
><               print cmdstr
>---
>  
>
>>    if VERBOSE:
>>      print cmdstr
>>    return os.system( cmdstr )
>>    
>>
>36,37d36
><       return os.system( cmdstr )
>< 
>59c58
><       # be verbose
>---
>  
>
>>      # be verbose
>>    
>>
>86c85
><     if compile( CXX, CXXCOMPILEFLAGS, "\""+SRC+"\"" ) or not os.path.isfile( OBJ ):
>---
>  
>
>>    if compile( CXX, CXXCOMPILEFLAGS, SRC ) or not os.path.isfile( OBJ ):
>>    
>>
>rune% 
>

Dare Satya and Sakurada

Thank you for preparation of package.
But these following programs have problem on the windows version
which are not considered blank in input paths.
(Cf. "C:\Documents and Settings" or so)

/bin/dmcompile
/bin/ecell3-dmc

We performed easy repair about attached files.
We want to ask you for the check of the repair parts, 
and want to get permission of the inclusion to the installer of windows.
Your cooperation is greatly appreciated.

Seiji Ota
Mitsui Knowledge Industry Co.,Ltd.

Hi ecell-devel members,

I would like to make the next release of the E-Cell System, version 3.1.99
(hekkever) will be out on this Friday, 10th October. So, everyone, please
commit and check your outcome of the development for the hekkever by the day
after.


-zak

Gabor,

> > Okay, btw, Should we put the machine requirement onto the packgage? and
What
> > do you think that apropriate specs for the Windows version.
>
>
> I think it depends on testing. If you still see problems after the
> bugfix then you could set a recommended machine and OS config. But here
> we have limited windows resources so we probably cannot scale it on
> windows.
> Gabor

yes, you're right. I think if we would like to set the requirement of the
machine specs, we have to check the software on various machines (such as
PentiumIII 300MHz with Win2000 box). and it is not so reasonable for our
resources (of the human and machines).

Hi Tom,

Thanks for your interest. If you are in a hurry, you can compile E-Cell 
3 directly on Windows 2000/XP using the current cvs version with MinGW 
and MSYS. Detailed instructions on how to go about this is available at
http://www2.e-cell.org/moin/moin.cgi/CreatingWindowsInstaller

You can also choose to wait for awhile longer (a week or so) for the 
setup file to be released. Please let me know if you run into any trouble.

satya

>Hello, Satya.
>
>My name is Tom Koehnle. I'm a graduate student in Animal Behavior at the
>University of California, at Davis. My present work requires me to do some
>fairly simple cell simulations, and I saw your name on the E-Cell page as
>having ported E-Cell to Cygwin. I was wondering if you had yet released
>the binary, or even the source, for public use.
>
>Any information you might have would be helpful,
>-Tom
>tjk...@uc...
>
>--
>---------------------------------------------------------
>----------This Space Intentionally Left Blank------------
>---------------------------------------------------------
>
>
>
>  
>

> Generally, in GUI mode, it should put higher priority on screen
>  redrawing than other tasks such as simulation stepping.
yes I believe so, but apparently Gtk does otherway and I have no way to interfere with it.

> Maybe related is the update interval of osogo should specify
> the interval between the end of the last screen updating and the
> beginning of the next updating, not between the beginnings.
> Or, the redrawing would never finish.   I believe it is implemented
> so, but just checking.
yes it was implemented that way, but gtk apparently inserts timeout
events before redraw events in the event queue, so it doesnt behaves the
way you'd expect.

> 
> One portion I could not understand well in osogo code is this:
> In GtkSessionMonitor.__updateByTimeout():
> 
>     if not gtk.events_pending():
>          self.updateWindows()
>     self.theTimer = gtk.timeout_add( self.theUpdateInterval, self.__updateByTimeOut, 0 )
> 
> I guess this 'if' is to assure that the updateWindows() is called
> after all the pending gtk events are handled, but should it set the
> timeout by the same self.theUpdateInterval even in this case?
> 
Maybe if updateWindow was not called timeout should be set to a smaller
delay, so as to tap the point more closely when redraw events are
finished. . I dont' know however it makes any change on a Windows
machine.
Gabor

> -sha
> 
> 
> > 
> > Regarding the 'ga' and 'sessionmanager' updates by Sugimoto-san, I have 
> > run into another problem. I will wait for them to be fixed by Sugimoto-san.
> > 
> > The latest ecell3win with the bugfix is available as 
> > /home/satya/zak/ecell-3.2beta-Oct-7-2003.exe
> > Please try to verify if the bug has been fixed.
> > 
> > I have also attached the screenshot that you requested. The typeface 
> > maybe too small because of the high resolution. If you want bigger 
> > typeface (in lower resolution), I will need to reduce the number of 
> > windows displayed, so let me know the critical windows which you need.
> > 
> > satya
> > 
> > >I think that bug was fixed by sugimoto-san. did you try new one?
> > >
> > >  
> > >
> > >>- I am also not including the 'ga' sample because it uses sh scripts
> > >>which needs to be converted to python first.
> > >>    
> > >>
> > >
> > >this issue was also solved by sugimoto-san.
> > >
> > >
> > >  
> > >
> > >>Zak, as usual the files are in /home/satya/zak. Please update the new
> > >>Inno script files as well because it implements the new shortcuts in the
> > >>Start menu.
> > >>    
> > >>
> > >
> > >Sure.
> > >
> > >  
> > >
> > >>For the last bug that you have mentioned, I followed exactly as you have
> > >>described but I could not reproduce it, probably because it is my
> > >>development machine. To verify this, in the computer that is causing the
> > >>bug:
> > >>
> > >>1. can you first install the GTK-Runtime-Environment-2.2.1.2.exe
> > >>available in my home directory and check if the bug persists.
> > >>2. if the bug persists, can you check again after installing
> > >>pygtk-1.99.14.win32-py2.2.exe (also from my home directory) if it still
> > >>exists.
> > >>    
> > >>
> > >
> > >Okay, I tried to install and run the simulation on both of cases. First I
> > >installed GTK-Runtime-Environment as a default option, but I got same
> > >problem at run. Additionally, I also set up pygtk and tried the simulation,
> > >but the problem issue was still on going..
> > >
> > >Do you have any other idea to dig this issue?
> > >
> > >BTW: could you make some cool screenshot(.png) of E-Cell3 on Windows?
> > >because, we would like to use it with the software description on the CD-ROM
> > >package. And it is prefer to a English environment (such as locale..) but I
> > >don't have it.
> > >
> > >
> > >-zak
> > >
> > >
> > >
> > >
> > >  
> > >
> > 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Ecell-devel mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-devel
> 

Generally, in GUI mode, it should put higher priority on screen
 redrawing than other tasks such as simulation stepping.


> It seems that the bug is related to the CPU clock speed. It is not 
> visible in my computer because it is fast enough. Presumably, the bug 
> only appears on slow machines, in which gtk is not able to update 
> redrawing on time.

Maybe related is the update interval of osogo should specify
the interval between the end of the last screen updating and the
beginning of the next updating, not between the beginnings.
Or, the redrawing would never finish.   I believe it is implemented
so, but just checking.

One portion I could not understand well in osogo code is this:
In GtkSessionMonitor.__updateByTimeout():

    if not gtk.events_pending():
         self.updateWindows()
    self.theTimer = gtk.timeout_add( self.theUpdateInterval, self.__updateByTimeOut, 0 )

I guess this 'if' is to assure that the updateWindows() is called
after all the pending gtk events are handled, but should it set the
timeout by the same self.theUpdateInterval even in this case?

-sha


> 
> Regarding the 'ga' and 'sessionmanager' updates by Sugimoto-san, I have 
> run into another problem. I will wait for them to be fixed by Sugimoto-san.
> 
> The latest ecell3win with the bugfix is available as 
> /home/satya/zak/ecell-3.2beta-Oct-7-2003.exe
> Please try to verify if the bug has been fixed.
> 
> I have also attached the screenshot that you requested. The typeface 
> maybe too small because of the high resolution. If you want bigger 
> typeface (in lower resolution), I will need to reduce the number of 
> windows displayed, so let me know the critical windows which you need.
> 
> satya
> 
> >I think that bug was fixed by sugimoto-san. did you try new one?
> >
> >  
> >
> >>- I am also not including the 'ga' sample because it uses sh scripts
> >>which needs to be converted to python first.
> >>    
> >>
> >
> >this issue was also solved by sugimoto-san.
> >
> >
> >  
> >
> >>Zak, as usual the files are in /home/satya/zak. Please update the new
> >>Inno script files as well because it implements the new shortcuts in the
> >>Start menu.
> >>    
> >>
> >
> >Sure.
> >
> >  
> >
> >>For the last bug that you have mentioned, I followed exactly as you have
> >>described but I could not reproduce it, probably because it is my
> >>development machine. To verify this, in the computer that is causing the
> >>bug:
> >>
> >>1. can you first install the GTK-Runtime-Environment-2.2.1.2.exe
> >>available in my home directory and check if the bug persists.
> >>2. if the bug persists, can you check again after installing
> >>pygtk-1.99.14.win32-py2.2.exe (also from my home directory) if it still
> >>exists.
> >>    
> >>
> >
> >Okay, I tried to install and run the simulation on both of cases. First I
> >installed GTK-Runtime-Environment as a default option, but I got same
> >problem at run. Additionally, I also set up pygtk and tried the simulation,
> >but the problem issue was still on going..
> >
> >Do you have any other idea to dig this issue?
> >
> >BTW: could you make some cool screenshot(.png) of E-Cell3 on Windows?
> >because, we would like to use it with the software description on the CD-ROM
> >package. And it is prefer to a English environment (such as locale..) but I
> >don't have it.
> >
> >
> >-zak
> >
> >
> >
> >
> >  
> >
> 

Hi Zak,
> Okay, btw, Should we put the machine requirement onto the packgage? and What
> do you think that apropriate specs for the Windows version.


I think it depends on testing. If you still see problems after the
bugfix then you could set a recommended machine and OS config. But here
we have limited windows resources so we probably cannot scale it on
windows.
Gabor

Hi, Satya and Gabor,


> OK we have found the bug.
> the problem is that gtk.timeout seems to have higher priority than
> redrawing screen widgets.
> I am working around the problem
> Gabor
>

Excellent!. I've confirmed the latest package made by Satya today.

> It seems that the bug is related to the CPU clock speed. It is not
> visible in my computer because it is fast enough. Presumably, the bug
> only appears on slow machines, in which gtk is not able to update
> redrawing on time.

Okay, btw, Should we put the machine requirement onto the packgage? and What
do you think that apropriate specs for the Windows version.



>
> Regarding the 'ga' and 'sessionmanager' updates by Sugimoto-san, I have
> run into another problem. I will wait for them to be fixed by
Sugimoto-san.
>
> The latest ecell3win with the bugfix is available as
> /home/satya/zak/ecell-3.2beta-Oct-7-2003.exe
> Please try to verify if the bug has been fixed.
>
> I have also attached the screenshot that you requested. The typeface
> maybe too small because of the high resolution. If you want bigger
> typeface (in lower resolution), I will need to reduce the number of
> windows displayed, so let me know the critical windows which you need.

Thanks, It seems good.

-zak



>
> satya
>
> >I think that bug was fixed by sugimoto-san. did you try new one?
> >
> >
> >
> >>- I am also not including the 'ga' sample because it uses sh scripts
> >>which needs to be converted to python first.
> >>
> >>
> >
> >this issue was also solved by sugimoto-san.
> >
> >
> >
> >
> >>Zak, as usual the files are in /home/satya/zak. Please update the new
> >>Inno script files as well because it implements the new shortcuts in the
> >>Start menu.
> >>
> >>
> >
> >Sure.
> >
> >
> >
> >>For the last bug that you have mentioned, I followed exactly as you have
> >>described but I could not reproduce it, probably because it is my
> >>development machine. To verify this, in the computer that is causing the
> >>bug:
> >>
> >>1. can you first install the GTK-Runtime-Environment-2.2.1.2.exe
> >>available in my home directory and check if the bug persists.
> >>2. if the bug persists, can you check again after installing
> >>pygtk-1.99.14.win32-py2.2.exe (also from my home directory) if it still
> >>exists.
> >>
> >>
> >
> >Okay, I tried to install and run the simulation on both of cases. First I
> >installed GTK-Runtime-Environment as a default option, but I got same
> >problem at run. Additionally, I also set up pygtk and tried the
simulation,
> >but the problem issue was still on going..
> >
> >Do you have any other idea to dig this issue?
> >
> >BTW: could you make some cool screenshot(.png) of E-Cell3 on Windows?
> >because, we would like to use it with the software description on the
CD-ROM
> >package. And it is prefer to a English environment (such as locale..) but
I
> >don't have it.
> >
> >
> >-zak
> >
> >
> >
> >
> >
> >
>
>


----------------------------------------------------------------------------
----

Hi, 
 
I have a dumb question and I wonder if anybody has an idea on how to do
it: I'd like to run the cell cycle model 1,000,000 times for a 
specified amount of time and tweak the starting parameters of several 
of the "genes" and then I would like to sum for each time point all of 
the model runs for that time point to simulate the aggregated data 
resulting from an mRNA expression experiment.  Any ideas on how to do 
that?  I'd greatly appreciate it!  Thank you!
 
Sincerely,
 
 
Tom
 
Thoughts for the day:
 
(1) "No matter where you go there you are" (B. Banzai)
 
(2) "Time exists so that everything doesn't occur at once" (B. Banzai) 
 
(3) "The world is full of friends that we have not yet met" (T.Heiman)
 
(4) I live in my own little world, but it's OK,they know me
there(T.Heiman)
 
 
 

Dear Satya

Thank you for your reports again.

>both ga and sessionmanager, which I suspect are related to windows 
>specific python:

You are right. I found that 'signal.SIGALRM' could be used on only unix.
I try to change design.
Thank you,

sugi

Satya Arjunan wrote:
>Dear Sugimoto-san,
>
>Thank you for your quick action. I have updated the createsampledata.py 
>in ga to let it run on windows. How I still get the following errors in 
>both ga and sessionmanager, which I suspect are related to windows 
>specific python:
>
>C:\satya\ecell3winDistribution\share\doc\sample\ga>ecell3 
>ecell3-session-manager ga.esm
>GA on E-Cell3 ........ start
>Traceback (most recent call last):
>  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
>159, in
> ?
>    main()
>  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
>153, in
> main
>    aSessionManager.loadScript( anEsmFile, aParameters  )
>  File 
>"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
>anager.py", line 292, in loadScript
>    execfile( esmfile, aContext )
>  File "ga.esm", line 2025, in ?
>    main()
>  File "ga.esm", line 2018, in main
>    anEstimator.run()
>  File "ga.esm", line 150, in run
>    self.__executeEvaluateStrategy()
>  File "ga.esm", line 237, in __executeEvaluateStrategy
>    run(block=False)
>  File 
>"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
>anager.py", line 661, in run
>    signal.signal(signal.SIGALRM, self.__timeout)
>AttributeError: 'module' object has no attribute 'SIGALRM'
>
>
>
>C:\satya\ecell3winDistribution\share\doc\sample\sessionmanager>ecell3 
>ecell3-session-manager sample.esm
>---- sample.esm ------------> start
>current environment = Local
>current concurrency = 1
>current temporary root dir = workingdir
>current temporary dir = workingdir\736
>run --> start
>Traceback (most recent call last):
>  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
>159, in
> ?
>    main()
>  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
>153, in
> main
>    aSessionManager.loadScript( anEsmFile, aParameters  )
>  File 
>"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
>anager.py", line 292, in loadScript
>    execfile( esmfile, aContext )
>  File "sample.esm", line 48, in ?
>    run(block=True)
>  File 
>"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
>anager.py", line 661, in run
>    signal.signal(signal.SIGALRM, self.__timeout)
>AttributeError: 'module' object has no attribute 'SIGALRM'
>
>
>satya
>
>>Dear Satya
>>
>>Thank you for your reports about error of 'sessionmanager' and 'ga'.
>>I fixed some bugs of the sample.esm in sessionmanager module.
>>I replaced a script file in ga module with a python script one.
>>
>>sugi
>>
>>  
>>
>
>
>

Zak,

It seems that the bug is related to the CPU clock speed. It is not 
visible in my computer because it is fast enough. Presumably, the bug 
only appears on slow machines, in which gtk is not able to update 
redrawing on time.

Regarding the 'ga' and 'sessionmanager' updates by Sugimoto-san, I have 
run into another problem. I will wait for them to be fixed by Sugimoto-san.

The latest ecell3win with the bugfix is available as 
/home/satya/zak/ecell-3.2beta-Oct-7-2003.exe
Please try to verify if the bug has been fixed.

I have also attached the screenshot that you requested. The typeface 
maybe too small because of the high resolution. If you want bigger 
typeface (in lower resolution), I will need to reduce the number of 
windows displayed, so let me know the critical windows which you need.

satya

>I think that bug was fixed by sugimoto-san. did you try new one?
>
>  
>
>>- I am also not including the 'ga' sample because it uses sh scripts
>>which needs to be converted to python first.
>>    
>>
>
>this issue was also solved by sugimoto-san.
>
>
>  
>
>>Zak, as usual the files are in /home/satya/zak. Please update the new
>>Inno script files as well because it implements the new shortcuts in the
>>Start menu.
>>    
>>
>
>Sure.
>
>  
>
>>For the last bug that you have mentioned, I followed exactly as you have
>>described but I could not reproduce it, probably because it is my
>>development machine. To verify this, in the computer that is causing the
>>bug:
>>
>>1. can you first install the GTK-Runtime-Environment-2.2.1.2.exe
>>available in my home directory and check if the bug persists.
>>2. if the bug persists, can you check again after installing
>>pygtk-1.99.14.win32-py2.2.exe (also from my home directory) if it still
>>exists.
>>    
>>
>
>Okay, I tried to install and run the simulation on both of cases. First I
>installed GTK-Runtime-Environment as a default option, but I got same
>problem at run. Additionally, I also set up pygtk and tried the simulation,
>but the problem issue was still on going..
>
>Do you have any other idea to dig this issue?
>
>BTW: could you make some cool screenshot(.png) of E-Cell3 on Windows?
>because, we would like to use it with the software description on the CD-ROM
>package. And it is prefer to a English environment (such as locale..) but I
>don't have it.
>
>
>-zak
>
>
>
>
>  
>

Dear Sugimoto-san,

Thank you for your quick action. I have updated the createsampledata.py 
in ga to let it run on windows. How I still get the following errors in 
both ga and sessionmanager, which I suspect are related to windows 
specific python:

C:\satya\ecell3winDistribution\share\doc\sample\ga>ecell3 
ecell3-session-manager ga.esm
GA on E-Cell3 ........ start
Traceback (most recent call last):
  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
159, in
 ?
    main()
  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
153, in
 main
    aSessionManager.loadScript( anEsmFile, aParameters  )
  File 
"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
anager.py", line 292, in loadScript
    execfile( esmfile, aContext )
  File "ga.esm", line 2025, in ?
    main()
  File "ga.esm", line 2018, in main
    anEstimator.run()
  File "ga.esm", line 150, in run
    self.__executeEvaluateStrategy()
  File "ga.esm", line 237, in __executeEvaluateStrategy
    run(block=False)
  File 
"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
anager.py", line 661, in run
    signal.signal(signal.SIGALRM, self.__timeout)
AttributeError: 'module' object has no attribute 'SIGALRM'



C:\satya\ecell3winDistribution\share\doc\sample\sessionmanager>ecell3 
ecell3-session-manager sample.esm
---- sample.esm ------------> start
current environment = Local
current concurrency = 1
current temporary root dir = workingdir
current temporary dir = workingdir\736
run --> start
Traceback (most recent call last):
  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
159, in
 ?
    main()
  File "C:\satya\ecell3winDistribution\bin\ecell3-session-manager", line 
153, in
 main
    aSessionManager.loadScript( anEsmFile, aParameters  )
  File 
"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
anager.py", line 292, in loadScript
    execfile( esmfile, aContext )
  File "sample.esm", line 48, in ?
    run(block=True)
  File 
"C:\satya\ecell3winDistribution\python22\lib\site-packages\ecell\SessionM
anager.py", line 661, in run
    signal.signal(signal.SIGALRM, self.__timeout)
AttributeError: 'module' object has no attribute 'SIGALRM'


satya

>Dear Satya
>
>Thank you for your reports about error of 'sessionmanager' and 'ga'.
>I fixed some bugs of the sample.esm in sessionmanager module.
>I replaced a script file in ga module with a python script one.
>
>sugi
>
>  
>

Another thing about timeout is: (This might be related to this bug...)
Currently emc.Simulator checks given event checker (gtk event
checker when it runs with osogo) once in several steps (this number is
currently hard-coded: 20).     That is, the real-time interval between
event checking varies according to the 'weight' of the running model.

I want to change this to be able to specify this interval also in
milli-second.    Specifying the number of steps between event checking
should be preserved, though, because in some use cases it is useful.
One possibility could be to allow frontends to specify in both manners
(ms and num steps), and the simulator checks if at least either of
these is met.   


-sha


> OK we have found the bug.
> the problem is that gtk.timeout seems to have higher priority than
> redrawing screen widgets.
> I am working around the problem
> Gabor
> 
> On Mon, 2003-10-06 at 18:09, Takeshi Sakurada wrote:
> > Gabor,
> > 
> > > did you have the problem with the time counter too? this would be
> > > important to know.
> > 
> > yes, I got time counter(indicator) problem(doesn't work) at the same time.
> > 
> > I added the line before "return return_list" as following.
> > 
> > ---------------------
> >   if value_from<value_to:
> >       a=self.theSession.theSimulator.getLoggerData(aFullPNString,
> >      value_from,
> >      value_to,interval)
> >       dimension = shape(a)[1]
> >       for t in range(size(a,0)):
> >    if dimension==2:
> >     return_list.append([ a[t,0], a[t,1], a[t,1], a[t,1], a[t,1] ])
> > 
> >    else:
> >     return_list.append([ a[t,0], a[t,1], a[t,2], a[t,3], a[t,4] ])
> > 
> > 
> >    print "data from logger", len(return_list), " from ", return_list[0][0],
> > "to", return_list[len(return_list)-1][0]
> >   return return_list
> > 
> > ---------------------
> > 
> > and then, loaded Drosophila-cpp model and run.
> > 
> > [first run]
> > ....
> > data from logger 455  from  0.0 to 165.963333469
> > data from logger 456  from  0.0 to 166.329546141
> > data from logger 457  from  0.0 to 166.695758813
> > data from logger 458  from  0.0 to 167.061971485
> > data from logger 459  from  0.0 to 167.428184156
> > data from logger 460  from  0.0 to 167.794396828
> > data from logger 461  from  0.0 to 168.115943817
> > data from logger 462  from  0.0 to 168.437490806
> > data from logger 463  from  0.0 to 168.711786363
> > data from logger 464  from  0.0 to 169.260377478
> > data from logger 465  from  0.0 to 169.492579162
> > data from logger 466  from  0.0 to 169.956982531
> > data from logger 467  from  0.0 to 170.189184215
> > data from logger 468  from  0.0 to 170.595171793
> > data from logger 469  from  0.0 to 171.00115937
> > data from logger 470  from  0.0 to 171.407146948
> > data from logger 471  from  0.0 to 171.610140736
> > gtk update
> > gtk update
> > gtk update
> > ...
> > 
> > Once 'gtk update' strings appeared, the graph was drawn and time indicator
> > was changed at same time. but after the once drawing and time changing,
> > tracer and time indicator didn't work and the 'gtk update' strings still was
> > putting on the console.
> > 
> > then, I pushed 'stop' and restarted the simulation, I got following
> > messages.
> > ...
> > data from logger 267  from  387.494631285 to 607.012101224
> > data from logger 268  from  387.494631285 to 607.852425257
> > data from logger 269  from  387.494631285 to 608.69274929
> > data from logger 270  from  387.494631285 to 609.533073323
> > data from logger 271  from  387.494631285 to 610.373397356
> > data from logger 272  from  387.494631285 to 610.933613378
> > data from logger 273  from  387.494631285 to 611.777677214
> > data from logger 274  from  387.494631285 to 612.656568537
> > data from logger 275  from  387.494631285 to 613.579061856
> > data from logger 276  from  387.494631285 to 614.542745114
> > data from logger 277  from  387.494631285 to 615.200759063
> > data from logger 278  from  387.494631285 to 616.207180944
> > data from logger 279  from  387.494631285 to 616.883601093
> > data from logger 280  from  387.494631285 to 617.567267887
> > data from logger 281  from  387.494631285 to 618.599860585
> > data from logger 282  from  387.494631285 to 619.303467052
> > data from logger 283  from  387.494631285 to 620.030078248
> > data from logger 284  from  387.494631285 to 621.130772295
> > gtk update
> > gtk update
> > gtk update
> > gtk update
> > gtk update
> > gtk update
> > gtk update
> > gtk update
> > gtk update
> > 
> > after the 'logger 284', the 'gtk update' strings added on the console, at
> > the same time I got same behavior (graph and time changed)
> > 
> > 
> > btw;
> > I found that similar behavior in the EntryListWindow. If some variables were
> > selected and checked the value in the window, I got similar behavior ( time
> > counter doesn't work ). and in the console window, only the 'gtk update'
> > strings still were putting.
> > And once all variables was hidden, there are no problem (including time
> > counter) but the 'gtk update' strings were still putting.
> > 
> > 
> > -zak
> > 
> > ----- Original Message ----- 
> > From: "Gabor Bereczki" <ga...@e-...>
> > To: "Takeshi Sakurada" <sak...@sf...>
> > Cc: "Satya Arjunan" <sa...@tt...>;
> > <ece...@li...>
> > Sent: Monday, October 06, 2003 5:13 PM
> > Subject: Re: [Ecell-devel] Re: [Koyurugi] Re: ecell3 bugs
> > 
> > 
> > > Hi,
> > > did you have the problem with the time counter too? this would be
> > > important to know.
> > > have you tried the other suggestion (just creating loggers not
> > > tracerwindows)
> > >
> > > also I think we have to go one step forward.
> > > please insert the following code into TracerWindow:
> > > from line 180 in function recache, right before line "return
> > > return_list"
> > >
> > > print "data from logger", len(return_list), " from ",
> > > return_list[0][0], "to", return_list[len(return_list)-1][0]
> > > return return_list
> > >
> > > Gabor
> > >
> > > On Mon, 2003-10-06 at 16:54, Takeshi Sakurada wrote:
> > > > Hi gabor, sorry the delay.
> > > > I tried your suggestion.
> > > >
> > > > I put 'print gtk update' into beginning __updateByTimeOut function.
> > > >  #
> > > >
> > ==========================================================================
> > > >  def __updateByTimeOut( self, arg ):
> > > >   """when time out, calls updates method()
> > > >   Returns None
> > > >   """
> > > >   print "gtk update"
> > > >   self.updateWindows()
> > > >   self.theTimer = gtk.timeout_add( self.theUpdateInterval,
> > > > self.__updateByTimeOut, 0 )
> > > >
> > > >
> > > > then try the Drosophila-cpp model, and got same problem. The string 'gtk
> > > > update' were still written on E-Cell3 console windows(over 10 times),
> > but
> > > > the graph drawing didn't work. and I restart run, I got same behavior.
> > > > -zak
> > > >
> > > > ----- Original Message ----- 
> > > > From: "Gabor Bereczki" <ga...@e-...>
> > > > To: "Takeshi Sakurada" <sak...@sf...>
> > > > Cc: "Satya Arjunan" <sa...@tt...>;
> > > > <ece...@li...>
> > > > Sent: Monday, October 06, 2003 9:52 AM
> > > > Subject: Re: [Ecell-devel] Re: [Koyurugi] Re: ecell3 bugs
> > > >
> > > >
> > > > > Hi,
> > > > >
> > > > > Unforunatelly we still couldnt reproduce the BUG, I would like to
> > > > > suggest two possible investigations so that we could find out at least
> > > > > which software part misbehaves (gtk, osogo, logger).
> > > > > Please try to do the following:
> > > > > do everything as you described below, but dont create TracerWindow
> > from
> > > > > the 3 traces. instead of that please create just loggers for them on
> > the
> > > > > EntityWindow.
> > > > > then try to push start and watch if the time counter gets blocked
> > again.
> > > > > Second investigation
> > > > > please insert a new line into GtkSessionMonitor.py line 327 at the
> > > > > beginnning of function __updateByTimeOut. insert some tracer line like
> > > > > 'print "gtk update"'
> > > > > run simulation normally. watch how many "gtk update" was written on
> > the
> > > > > screen.
> > > > > then restart osogo and try to reproduce the BUG and count how many
> > times
> > > > > the "gtk update" appears on the screen.
> > > > > this would take us closer to some solution.
> > > > > Gabor
> > > > >
> > > > > On Sun, 2003-10-05 at 19:41, Takeshi Sakurada wrote:
> > > > > > hi Satya,
> > > > > >
> > > > > > > As Gabor mentioned, he could not reproduce the last bug. Could you
> > > > > > > explain in more detail in what situation the bug appears? Eg. with
> > > > what
> > > > > > > E-Cell model, OS, does it happen in all tested computers? If I am
> > not
> > > > > > > mistaken you had the same problem the last time.
> > > > > >
> > > > > > hmm, yes. Although that issue was same as the last version which was
> > > > caught
> > > > > > by me, but this issue was reported from other tester with other
> > machine.
> > > > I'm
> > > > > > going to check the environment which is used for last week's testing
> > at
> > > > the
> > > > > > next morning.
> > > > > >
> > > > > > Anyway, I tried this issue on my laptop (usually I use it) and got
> > same
> > > > > > behavior. My environment is follow,
> > > > > > * Celeron 600MHz, 500MB physical memory, 40GB HDD
> > > > > > * MS-Windows XP Home edition [Japanese]
> > > > > > * Many software's is installed.
> > > > > >
> > > > > > And I got one solution which enables the drawing and changing the
> > time
> > > > > > indicator. It is that the "EntryListWindow" must not be invoked on
> > the
> > > > same
> > > > > > time of run the simulation with drawing graph. I don't know why that
> > > > > > interferes this behavior, but I wonder this is caused from the low
> > spec
> > > > > > machine. do you catch the point?
> > > > > >
> > > > > >
> > > > > > The behavior is follow,
> > > > > > 1. Invoke E-Cell3 from Start menu.
> > > > > > 2. load sample("simple") model on the osogo.
> > > > > > 3. Push Entry List panel
> > > > > > 4. Select 'S', 'P', and 'E'. and push 'Create with Tracer'
> > > > > > 5. Run the simulator (push run)
> > > > > >
> > > > > > then,  I got these messages
> > > > > >
> > > > > > > Loading Model file C:\E-Cell3\work\simple\simple.eml
> > > > > > >
> > > > > > > There is no osogo.ini file in this directory.
> > > > > > >  Falling back to system defauls.
> > > > > > >
> > > > > > > Logger created for Variable:/:E:Value
> > > > > > > Logger created for Variable:/:P:Value
> > > > > > > Logger created for Variable:/:S:Value
> > > > > > >             0.0:Start
> > > > > > >
> > > > > >
> > > > > > so, The drawing graph was stopped at about 20 seconds and the time
> > box
> > > > was
> > > > > > still indicate zero "0". But once I pushed "stop" button and The
> > time
> > > > was
> > > > > > changed and following message was put on the MessageWindow
> > > > > >
> > > > > > >         22.919:Stop
> > > > > >
> > > > > > and I put "start"
> > > > > >
> > > > > > >         22.919:Start
> > > > > >
> > > > > > time was changed to 45.059 and also graph was drawn at about same
> > time,
> > > > but
> > > > > > didn't work anymore. and the I pushed "stop" button , I got similar
> > > > > > behavior.
> > > > > >
> > > > > > But once I closed EntryWindow before or after run the simulation,
> > the
> > > > time
> > > > > > indicator and drawing graph did work.
> > > > > >
> > > > > > -Zak
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > -------------------------------------------------------
> > > > > > This sf.net email is sponsored by:ThinkGeek
> > > > > > Welcome to geek heaven.
> > > > > > http://thinkgeek.com/sf
> > > > > > _______________________________________________
> > > > > > Ecell-devel mailing list
> > > > > > Ece...@li...
> > > > > > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> > > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This sf.net email is sponsored by:ThinkGeek
> > > Welcome to geek heaven.
> > > http://thinkgeek.com/sf
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> > > Ece...@li...
> > > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> > >
> > 
> > 
> > 
> > 
> > -------------------------------------------------------
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> > Welcome to geek heaven.
> > http://thinkgeek.com/sf
> > _______________________________________________
> > Ecell-devel mailing list
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> > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> > 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Ecell-devel mailing list
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> https://lists.sourceforge.net/lists/listinfo/ecell-devel
> 

OK we have found the bug.
the problem is that gtk.timeout seems to have higher priority than
redrawing screen widgets.
I am working around the problem
Gabor

On Mon, 2003-10-06 at 18:09, Takeshi Sakurada wrote:
> Gabor,
> 
> > did you have the problem with the time counter too? this would be
> > important to know.
> 
> yes, I got time counter(indicator) problem(doesn't work) at the same time.
> 
> I added the line before "return return_list" as following.
> 
> ---------------------
>   if value_from<value_to:
>       a=self.theSession.theSimulator.getLoggerData(aFullPNString,
>      value_from,
>      value_to,interval)
>       dimension = shape(a)[1]
>       for t in range(size(a,0)):
>    if dimension==2:
>     return_list.append([ a[t,0], a[t,1], a[t,1], a[t,1], a[t,1] ])
> 
>    else:
>     return_list.append([ a[t,0], a[t,1], a[t,2], a[t,3], a[t,4] ])
> 
> 
>    print "data from logger", len(return_list), " from ", return_list[0][0],
> "to", return_list[len(return_list)-1][0]
>   return return_list
> 
> ---------------------
> 
> and then, loaded Drosophila-cpp model and run.
> 
> [first run]
> ....
> data from logger 455  from  0.0 to 165.963333469
> data from logger 456  from  0.0 to 166.329546141
> data from logger 457  from  0.0 to 166.695758813
> data from logger 458  from  0.0 to 167.061971485
> data from logger 459  from  0.0 to 167.428184156
> data from logger 460  from  0.0 to 167.794396828
> data from logger 461  from  0.0 to 168.115943817
> data from logger 462  from  0.0 to 168.437490806
> data from logger 463  from  0.0 to 168.711786363
> data from logger 464  from  0.0 to 169.260377478
> data from logger 465  from  0.0 to 169.492579162
> data from logger 466  from  0.0 to 169.956982531
> data from logger 467  from  0.0 to 170.189184215
> data from logger 468  from  0.0 to 170.595171793
> data from logger 469  from  0.0 to 171.00115937
> data from logger 470  from  0.0 to 171.407146948
> data from logger 471  from  0.0 to 171.610140736
> gtk update
> gtk update
> gtk update
> ...
> 
> Once 'gtk update' strings appeared, the graph was drawn and time indicator
> was changed at same time. but after the once drawing and time changing,
> tracer and time indicator didn't work and the 'gtk update' strings still was
> putting on the console.
> 
> then, I pushed 'stop' and restarted the simulation, I got following
> messages.
> ...
> data from logger 267  from  387.494631285 to 607.012101224
> data from logger 268  from  387.494631285 to 607.852425257
> data from logger 269  from  387.494631285 to 608.69274929
> data from logger 270  from  387.494631285 to 609.533073323
> data from logger 271  from  387.494631285 to 610.373397356
> data from logger 272  from  387.494631285 to 610.933613378
> data from logger 273  from  387.494631285 to 611.777677214
> data from logger 274  from  387.494631285 to 612.656568537
> data from logger 275  from  387.494631285 to 613.579061856
> data from logger 276  from  387.494631285 to 614.542745114
> data from logger 277  from  387.494631285 to 615.200759063
> data from logger 278  from  387.494631285 to 616.207180944
> data from logger 279  from  387.494631285 to 616.883601093
> data from logger 280  from  387.494631285 to 617.567267887
> data from logger 281  from  387.494631285 to 618.599860585
> data from logger 282  from  387.494631285 to 619.303467052
> data from logger 283  from  387.494631285 to 620.030078248
> data from logger 284  from  387.494631285 to 621.130772295
> gtk update
> gtk update
> gtk update
> gtk update
> gtk update
> gtk update
> gtk update
> gtk update
> gtk update
> 
> after the 'logger 284', the 'gtk update' strings added on the console, at
> the same time I got same behavior (graph and time changed)
> 
> 
> btw;
> I found that similar behavior in the EntryListWindow. If some variables were
> selected and checked the value in the window, I got similar behavior ( time
> counter doesn't work ). and in the console window, only the 'gtk update'
> strings still were putting.
> And once all variables was hidden, there are no problem (including time
> counter) but the 'gtk update' strings were still putting.
> 
> 
> -zak
> 
> ----- Original Message ----- 
> From: "Gabor Bereczki" <ga...@e-...>
> To: "Takeshi Sakurada" <sak...@sf...>
> Cc: "Satya Arjunan" <sa...@tt...>;
> <ece...@li...>
> Sent: Monday, October 06, 2003 5:13 PM
> Subject: Re: [Ecell-devel] Re: [Koyurugi] Re: ecell3 bugs
> 
> 
> > Hi,
> > did you have the problem with the time counter too? this would be
> > important to know.
> > have you tried the other suggestion (just creating loggers not
> > tracerwindows)
> >
> > also I think we have to go one step forward.
> > please insert the following code into TracerWindow:
> > from line 180 in function recache, right before line "return
> > return_list"
> >
> > print "data from logger", len(return_list), " from ",
> > return_list[0][0], "to", return_list[len(return_list)-1][0]
> > return return_list
> >
> > Gabor
> >
> > On Mon, 2003-10-06 at 16:54, Takeshi Sakurada wrote:
> > > Hi gabor, sorry the delay.
> > > I tried your suggestion.
> > >
> > > I put 'print gtk update' into beginning __updateByTimeOut function.
> > >  #
> > >
> ==========================================================================
> > >  def __updateByTimeOut( self, arg ):
> > >   """when time out, calls updates method()
> > >   Returns None
> > >   """
> > >   print "gtk update"
> > >   self.updateWindows()
> > >   self.theTimer = gtk.timeout_add( self.theUpdateInterval,
> > > self.__updateByTimeOut, 0 )
> > >
> > >
> > > then try the Drosophila-cpp model, and got same problem. The string 'gtk
> > > update' were still written on E-Cell3 console windows(over 10 times),
> but
> > > the graph drawing didn't work. and I restart run, I got same behavior.
> > > -zak
> > >
> > > ----- Original Message ----- 
> > > From: "Gabor Bereczki" <ga...@e-...>
> > > To: "Takeshi Sakurada" <sak...@sf...>
> > > Cc: "Satya Arjunan" <sa...@tt...>;
> > > <ece...@li...>
> > > Sent: Monday, October 06, 2003 9:52 AM
> > > Subject: Re: [Ecell-devel] Re: [Koyurugi] Re: ecell3 bugs
> > >
> > >
> > > > Hi,
> > > >
> > > > Unforunatelly we still couldnt reproduce the BUG, I would like to
> > > > suggest two possible investigations so that we could find out at least
> > > > which software part misbehaves (gtk, osogo, logger).
> > > > Please try to do the following:
> > > > do everything as you described below, but dont create TracerWindow
> from
> > > > the 3 traces. instead of that please create just loggers for them on
> the
> > > > EntityWindow.
> > > > then try to push start and watch if the time counter gets blocked
> again.
> > > > Second investigation
> > > > please insert a new line into GtkSessionMonitor.py line 327 at the
> > > > beginnning of function __updateByTimeOut. insert some tracer line like
> > > > 'print "gtk update"'
> > > > run simulation normally. watch how many "gtk update" was written on
> the
> > > > screen.
> > > > then restart osogo and try to reproduce the BUG and count how many
> times
> > > > the "gtk update" appears on the screen.
> > > > this would take us closer to some solution.
> > > > Gabor
> > > >
> > > > On Sun, 2003-10-05 at 19:41, Takeshi Sakurada wrote:
> > > > > hi Satya,
> > > > >
> > > > > > As Gabor mentioned, he could not reproduce the last bug. Could you
> > > > > > explain in more detail in what situation the bug appears? Eg. with
> > > what
> > > > > > E-Cell model, OS, does it happen in all tested computers? If I am
> not
> > > > > > mistaken you had the same problem the last time.
> > > > >
> > > > > hmm, yes. Although that issue was same as the last version which was
> > > caught
> > > > > by me, but this issue was reported from other tester with other
> machine.
> > > I'm
> > > > > going to check the environment which is used for last week's testing
> at
> > > the
> > > > > next morning.
> > > > >
> > > > > Anyway, I tried this issue on my laptop (usually I use it) and got
> same
> > > > > behavior. My environment is follow,
> > > > > * Celeron 600MHz, 500MB physical memory, 40GB HDD
> > > > > * MS-Windows XP Home edition [Japanese]
> > > > > * Many software's is installed.
> > > > >
> > > > > And I got one solution which enables the drawing and changing the
> time
> > > > > indicator. It is that the "EntryListWindow" must not be invoked on
> the
> > > same
> > > > > time of run the simulation with drawing graph. I don't know why that
> > > > > interferes this behavior, but I wonder this is caused from the low
> spec
> > > > > machine. do you catch the point?
> > > > >
> > > > >
> > > > > The behavior is follow,
> > > > > 1. Invoke E-Cell3 from Start menu.
> > > > > 2. load sample("simple") model on the osogo.
> > > > > 3. Push Entry List panel
> > > > > 4. Select 'S', 'P', and 'E'. and push 'Create with Tracer'
> > > > > 5. Run the simulator (push run)
> > > > >
> > > > > then,  I got these messages
> > > > >
> > > > > > Loading Model file C:\E-Cell3\work\simple\simple.eml
> > > > > >
> > > > > > There is no osogo.ini file in this directory.
> > > > > >  Falling back to system defauls.
> > > > > >
> > > > > > Logger created for Variable:/:E:Value
> > > > > > Logger created for Variable:/:P:Value
> > > > > > Logger created for Variable:/:S:Value
> > > > > >             0.0:Start
> > > > > >
> > > > >
> > > > > so, The drawing graph was stopped at about 20 seconds and the time
> box
> > > was
> > > > > still indicate zero "0". But once I pushed "stop" button and The
> time
> > > was
> > > > > changed and following message was put on the MessageWindow
> > > > >
> > > > > >         22.919:Stop
> > > > >
> > > > > and I put "start"
> > > > >
> > > > > >         22.919:Start
> > > > >
> > > > > time was changed to 45.059 and also graph was drawn at about same
> time,
> > > but
> > > > > didn't work anymore. and the I pushed "stop" button , I got similar
> > > > > behavior.
> > > > >
> > > > > But once I closed EntryWindow before or after run the simulation,
> the
> > > time
> > > > > indicator and drawing graph did work.
> > > > >
> > > > > -Zak
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > -------------------------------------------------------
> > > > > This sf.net email is sponsored by:ThinkGeek
> > > > > Welcome to geek heaven.
> > > > > http://thinkgeek.com/sf
> > > > > _______________________________________________
> > > > > Ecell-devel mailing list
> > > > > Ece...@li...
> > > > > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> > > > >
> > > >
> > > >
> > >
> > >
> > >
> >
> >
> >
> > -------------------------------------------------------
> > This sf.net email is sponsored by:ThinkGeek
> > Welcome to geek heaven.
> > http://thinkgeek.com/sf
> > _______________________________________________
> > Ecell-devel mailing list
> > Ece...@li...
> > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> >
> 
> 
> 
> 
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Ecell-devel mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-devel
> 

Gabor,

> did you have the problem with the time counter too? this would be
> important to know.

yes, I got time counter(indicator) problem(doesn't work) at the same time.

I added the line before "return return_list" as following.

---------------------
  if value_from<value_to:
      a=self.theSession.theSimulator.getLoggerData(aFullPNString,
     value_from,
     value_to,interval)
      dimension = shape(a)[1]
      for t in range(size(a,0)):
   if dimension==2:
    return_list.append([ a[t,0], a[t,1], a[t,1], a[t,1], a[t,1] ])

   else:
    return_list.append([ a[t,0], a[t,1], a[t,2], a[t,3], a[t,4] ])


   print "data from logger", len(return_list), " from ", return_list[0][0],
"to", return_list[len(return_list)-1][0]
  return return_list

---------------------

and then, loaded Drosophila-cpp model and run.

[first run]
....
data from logger 455  from  0.0 to 165.963333469
data from logger 456  from  0.0 to 166.329546141
data from logger 457  from  0.0 to 166.695758813
data from logger 458  from  0.0 to 167.061971485
data from logger 459  from  0.0 to 167.428184156
data from logger 460  from  0.0 to 167.794396828
data from logger 461  from  0.0 to 168.115943817
data from logger 462  from  0.0 to 168.437490806
data from logger 463  from  0.0 to 168.711786363
data from logger 464  from  0.0 to 169.260377478
data from logger 465  from  0.0 to 169.492579162
data from logger 466  from  0.0 to 169.956982531
data from logger 467  from  0.0 to 170.189184215
data from logger 468  from  0.0 to 170.595171793
data from logger 469  from  0.0 to 171.00115937
data from logger 470  from  0.0 to 171.407146948
data from logger 471  from  0.0 to 171.610140736
gtk update
gtk update
gtk update
...

Once 'gtk update' strings appeared, the graph was drawn and time indicator
was changed at same time. but after the once drawing and time changing,
tracer and time indicator didn't work and the 'gtk update' strings still was
putting on the console.

then, I pushed 'stop' and restarted the simulation, I got following
messages.
...
data from logger 267  from  387.494631285 to 607.012101224
data from logger 268  from  387.494631285 to 607.852425257
data from logger 269  from  387.494631285 to 608.69274929
data from logger 270  from  387.494631285 to 609.533073323
data from logger 271  from  387.494631285 to 610.373397356
data from logger 272  from  387.494631285 to 610.933613378
data from logger 273  from  387.494631285 to 611.777677214
data from logger 274  from  387.494631285 to 612.656568537
data from logger 275  from  387.494631285 to 613.579061856
data from logger 276  from  387.494631285 to 614.542745114
data from logger 277  from  387.494631285 to 615.200759063
data from logger 278  from  387.494631285 to 616.207180944
data from logger 279  from  387.494631285 to 616.883601093
data from logger 280  from  387.494631285 to 617.567267887
data from logger 281  from  387.494631285 to 618.599860585
data from logger 282  from  387.494631285 to 619.303467052
data from logger 283  from  387.494631285 to 620.030078248
data from logger 284  from  387.494631285 to 621.130772295
gtk update
gtk update
gtk update
gtk update
gtk update
gtk update
gtk update
gtk update
gtk update

after the 'logger 284', the 'gtk update' strings added on the console, at
the same time I got same behavior (graph and time changed)


btw;
I found that similar behavior in the EntryListWindow. If some variables were
selected and checked the value in the window, I got similar behavior ( time
counter doesn't work ). and in the console window, only the 'gtk update'
strings still were putting.
And once all variables was hidden, there are no problem (including time
counter) but the 'gtk update' strings were still putting.


-zak

----- Original Message ----- 
From: "Gabor Bereczki" <ga...@e-...>
To: "Takeshi Sakurada" <sak...@sf...>
Cc: "Satya Arjunan" <sa...@tt...>;
<ece...@li...>
Sent: Monday, October 06, 2003 5:13 PM
Subject: Re: [Ecell-devel] Re: [Koyurugi] Re: ecell3 bugs


> Hi,
> did you have the problem with the time counter too? this would be
> important to know.
> have you tried the other suggestion (just creating loggers not
> tracerwindows)
>
> also I think we have to go one step forward.
> please insert the following code into TracerWindow:
> from line 180 in function recache, right before line "return
> return_list"
>
> print "data from logger", len(return_list), " from ",
> return_list[0][0], "to", return_list[len(return_list)-1][0]
> return return_list
>
> Gabor
>
> On Mon, 2003-10-06 at 16:54, Takeshi Sakurada wrote:
> > Hi gabor, sorry the delay.
> > I tried your suggestion.
> >
> > I put 'print gtk update' into beginning __updateByTimeOut function.
> >  #
> >
==========================================================================
> >  def __updateByTimeOut( self, arg ):
> >   """when time out, calls updates method()
> >   Returns None
> >   """
> >   print "gtk update"
> >   self.updateWindows()
> >   self.theTimer = gtk.timeout_add( self.theUpdateInterval,
> > self.__updateByTimeOut, 0 )
> >
> >
> > then try the Drosophila-cpp model, and got same problem. The string 'gtk
> > update' were still written on E-Cell3 console windows(over 10 times),
but
> > the graph drawing didn't work. and I restart run, I got same behavior.
> > -zak
> >
> > ----- Original Message ----- 
> > From: "Gabor Bereczki" <ga...@e-...>
> > To: "Takeshi Sakurada" <sak...@sf...>
> > Cc: "Satya Arjunan" <sa...@tt...>;
> > <ece...@li...>
> > Sent: Monday, October 06, 2003 9:52 AM
> > Subject: Re: [Ecell-devel] Re: [Koyurugi] Re: ecell3 bugs
> >
> >
> > > Hi,
> > >
> > > Unforunatelly we still couldnt reproduce the BUG, I would like to
> > > suggest two possible investigations so that we could find out at least
> > > which software part misbehaves (gtk, osogo, logger).
> > > Please try to do the following:
> > > do everything as you described below, but dont create TracerWindow
from
> > > the 3 traces. instead of that please create just loggers for them on
the
> > > EntityWindow.
> > > then try to push start and watch if the time counter gets blocked
again.
> > > Second investigation
> > > please insert a new line into GtkSessionMonitor.py line 327 at the
> > > beginnning of function __updateByTimeOut. insert some tracer line like
> > > 'print "gtk update"'
> > > run simulation normally. watch how many "gtk update" was written on
the
> > > screen.
> > > then restart osogo and try to reproduce the BUG and count how many
times
> > > the "gtk update" appears on the screen.
> > > this would take us closer to some solution.
> > > Gabor
> > >
> > > On Sun, 2003-10-05 at 19:41, Takeshi Sakurada wrote:
> > > > hi Satya,
> > > >
> > > > > As Gabor mentioned, he could not reproduce the last bug. Could you
> > > > > explain in more detail in what situation the bug appears? Eg. with
> > what
> > > > > E-Cell model, OS, does it happen in all tested computers? If I am
not
> > > > > mistaken you had the same problem the last time.
> > > >
> > > > hmm, yes. Although that issue was same as the last version which was
> > caught
> > > > by me, but this issue was reported from other tester with other
machine.
> > I'm
> > > > going to check the environment which is used for last week's testing
at
> > the
> > > > next morning.
> > > >
> > > > Anyway, I tried this issue on my laptop (usually I use it) and got
same
> > > > behavior. My environment is follow,
> > > > * Celeron 600MHz, 500MB physical memory, 40GB HDD
> > > > * MS-Windows XP Home edition [Japanese]
> > > > * Many software's is installed.
> > > >
> > > > And I got one solution which enables the drawing and changing the
time
> > > > indicator. It is that the "EntryListWindow" must not be invoked on
the
> > same
> > > > time of run the simulation with drawing graph. I don't know why that
> > > > interferes this behavior, but I wonder this is caused from the low
spec
> > > > machine. do you catch the point?
> > > >
> > > >
> > > > The behavior is follow,
> > > > 1. Invoke E-Cell3 from Start menu.
> > > > 2. load sample("simple") model on the osogo.
> > > > 3. Push Entry List panel
> > > > 4. Select 'S', 'P', and 'E'. and push 'Create with Tracer'
> > > > 5. Run the simulator (push run)
> > > >
> > > > then,  I got these messages
> > > >
> > > > > Loading Model file C:\E-Cell3\work\simple\simple.eml
> > > > >
> > > > > There is no osogo.ini file in this directory.
> > > > >  Falling back to system defauls.
> > > > >
> > > > > Logger created for Variable:/:E:Value
> > > > > Logger created for Variable:/:P:Value
> > > > > Logger created for Variable:/:S:Value
> > > > >             0.0:Start
> > > > >
> > > >
> > > > so, The drawing graph was stopped at about 20 seconds and the time
box
> > was
> > > > still indicate zero "0". But once I pushed "stop" button and The
time
> > was
> > > > changed and following message was put on the MessageWindow
> > > >
> > > > >         22.919:Stop
> > > >
> > > > and I put "start"
> > > >
> > > > >         22.919:Start
> > > >
> > > > time was changed to 45.059 and also graph was drawn at about same
time,
> > but
> > > > didn't work anymore. and the I pushed "stop" button , I got similar
> > > > behavior.
> > > >
> > > > But once I closed EntryWindow before or after run the simulation,
the
> > time
> > > > indicator and drawing graph did work.
> > > >
> > > > -Zak
> > > >
> > > >
> > > >
> > > >
> > > > -------------------------------------------------------
> > > > This sf.net email is sponsored by:ThinkGeek
> > > > Welcome to geek heaven.
> > > > http://thinkgeek.com/sf
> > > > _______________________________________________
> > > > Ecell-devel mailing list
> > > > Ece...@li...
> > > > https://lists.sourceforge.net/lists/listinfo/ecell-devel
> > > >
> > >
> > >
> >
> >
> >
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Ecell-devel mailing list
> Ece...@li...
> https://lists.sourceforge.net/lists/listinfo/ecell-devel
>

hi satya,

----- Original Message ----- 
From: "Satya Arjunan" <sa...@tt...>
Sent: Monday, October 06, 2003 8:52 AM
Subject: Re: [Ecell-devel] Re: [Koyurugi] Re: ecell3 bugs


> Zak (and Shafi),
>
> I have made the changes that you have requested.
> Changelog:
> - Added all sample models except 'sessionmanager' and 'ga' under Start
> menu, such that it would be possible to start each model with a single
> click.
> - Included the shortcuts to API Reference Manual and User's Manual in
> both pdf and html in the Start menu
> - The location of the models are in share/doc as the case with the
> conventional linux E-Cell

Okay, thanks.

> - I have omitted 'sessionmanager' because it gives me the following error:

I think that bug was fixed by sugimoto-san. did you try new one?

> - I am also not including the 'ga' sample because it uses sh scripts
> which needs to be converted to python first.

this issue was also solved by sugimoto-san.


> Zak, as usual the files are in /home/satya/zak. Please update the new
> Inno script files as well because it implements the new shortcuts in the
> Start menu.

Sure.

> For the last bug that you have mentioned, I followed exactly as you have
> described but I could not reproduce it, probably because it is my
> development machine. To verify this, in the computer that is causing the
> bug:
>
> 1. can you first install the GTK-Runtime-Environment-2.2.1.2.exe
> available in my home directory and check if the bug persists.
> 2. if the bug persists, can you check again after installing
> pygtk-1.99.14.win32-py2.2.exe (also from my home directory) if it still
> exists.

Okay, I tried to install and run the simulation on both of cases. First I
installed GTK-Runtime-Environment as a default option, but I got same
problem at run. Additionally, I also set up pygtk and tried the simulation,
but the problem issue was still on going..

Do you have any other idea to dig this issue?

BTW: could you make some cool screenshot(.png) of E-Cell3 on Windows?
because, we would like to use it with the software description on the CD-ROM
package. And it is prefer to a English environment (such as locale..) but I
don't have it.


-zak