sbmlsolver-discuss — support and discussion for the SBML ODE Solver Library

[SOSlib-discuss] problem installing on linux

[Ivan M. <iva...@it...>]

Dear all,

we have a nasty problem with the installation on linux (Fedora Core 5)
of the SBML Ode Solver. I have installed libsbml version 2.3.4 and
sundials 2.2.0 (but I tried even with the version 2.4). 

The problem is that there is no way to pass the ./configure step of the
installation because of this error:

checking correct functioning of SUNDIALS CVODE... no:
                   CFLAGS=-g -O2 -I/usr/local/include
                   LDFLAGS= -L/usr/local/lib
                   LIBS= -lsundials_kinsol -lsundials_cvodes
-lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm
configure: error: Can not link to SUNDIALS CVODE Library

I tried to specify in different ways the path of the library, that are
correctly installed in /usr/lib. There is anyone who has been able to
install SBML ode Solver on linux?

Ivan

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[SOSlib-discuss] test

[Rainer M. <ra...@tb...>]

sorry. as we don't use the sbmlsolver-discuss list, i removed all 
subscribers there and added the sbmlsolver-devel address as the only 
subscriber. so emails to this public list (by soslib users with questions) 
are forwarded to this list. Ok?

[SOSlib-discuss] Problem with odeSolver

[Vladislav V V. <vv...@dc...>]

Dear developers of odeSolver,
=20
I have found a problem in the library sources from the last release.
It is impossible to compile the library with the sources using C++.
=20
The problem is in sbmlsolver/odeSolver.h file.
Line number 95 should be changed from=20
extern "C" {
to
}
=20
Seems to be just a typo.
=20
Kind regards,
Vladislav Vyshemirsky.
--
Vladislav Vyshemirsky
Bioinformatics Research Centre
Department of Computing Science
University of Glasgow
tel: 0141-330 8751
fax: 0141-330 8627
http://www.brc.dcs.gla.ac.uk/~vlad
=20

[SOSlib-discuss] (Re:) SOSlib error and mxstep settings

[Rainer M. <ra...@tb...>]

Dear Tatsunori,


I have also sent this email to the official email list with a more 
specific subject, so people can find it there if they have similar 
problems.

> 1. default conditions
>
> I entered the following command.
>
> SBML_odeSolverAPP sample.xml --time 1500 --printstep 150 > sample.txt
>
> The odes were not solved and the error message as sample.txt was output. 
> But with the same condition, when I entered
>
> SMBL_odeSolverApp sample.xml --time 1500 --printstep 150 --error 1e-9
> --rerror 1e-3 --mxstep 1e4 > sample.txt


Type SMBL_odeSolverApp --help to find out the actual default values!

For my copy of version 1.6.0 I have 1e-4 as a default for rerror. This 
might the reason for the different behaviour. Sorry, if I gave you a wrong 
number in one of my previous emails.


> 2. If I changed the error tolerance, is there a possibility that the
> resolutions will change ? For example, with the same .xml file, at the time
> error tolerance is 1e-6 and at the time error tolerance is 1e-12 ?

The error tolerances and max. number of steps set via above options are 
constant throughout one integration.

Note, that the tolerances are used for each timestep (the number given via 
the --printstep option) separately, i.e. errors can accumulate. If you use 
--printstep 1 and integration succeeds, then you get the results which are 
actually within this error tolerance.

This is also the reason, why SOSlib/CVODES sometimes fails with high error 
tolerances but succeeds with more restrictive tolerances. The high error 
tolerances causes errors to accumulate and can lead to numerical 
instabilities!

This should only happen with printsteps > 1 because of above reasons of 
error accumulation.

In a future version, we might provide a simple option to use the error 
tolerances for the whole time series. This however requires to 
re-initialize CVODES for every printstep and will significantly slow down 
the performance!

>
> 3. How wide are the ranges of conditions, error tolerance, rerror tolerance
> and mxstep ?

The absolute error should fit to the values of your system. If the 
time-courses are in the range of, e.g. 1e-10 you should use a similar 
tolerance. In principle there are no restriction, I think.

The relative error tolerances should be below 0 but not go too far below 
0. They are relative to the values of the solution time curves. The actual 
error tolerance is calculated from both values.

You will get a message like

Integrating        CVode-- At t = 0, too much accuracy requested.

if you set the error tolerance too low for CVODES.

I have to refer to the sundials documentation for the details on error 
tolerances used in the sundials algorithms.

--mxstep must be positive and has no restriction. CVODES will try mxstep 
times with different internally chosen values (e.g. with 
increasingly small internal time step h) to reach the next requested 
output time. We had problems for which --mxstep 1e6 or higher was required 
to be solved successfully.


> 4. Does the smaller error tolerance brings more accurate resolution ? For
> example, when I set the error tolerance 1e-16, the resolution will be better
> than I set the error tolerance at 1e-12 ?

The solutions x(t) will be more accurate with smaller error tolerances:
Yes, 1e-16 will give more accurate results than 1e-12, but might take 
longer to calculate. It might however also be faster, because of error 
accumulation and numerical instabilities as described above.


Taken together, the decision for good settings depends on the system you 
want to solve.
Compare timecourses and performance for different settings and choose 
accordingly.

* If the timecourses looks the same for higher error tolerance, 
you can use those.

* If you don't much about the system you send through SOSlib, e.g. a set 
of automatically generated models with different 
structures/parameters/initial conditions you might want to be careful and 
use higher tolerances.

I hope that helped. Keep asking, if you experience further problems!

Rainer





On Thu, 11 May 2006, Tatsunori Nishimura wrote:

>
>  Dear Dr. Rainer Machne
>
>
>
>
> My name is Tastunori Nishimura, a student of University of Tsukuba in Japan 
> (I'm sorry but I'm not a doctor, a mater course student).
>
>
>
> I really appreciate your kind advices and help every time. Thank you very 
> much indeed.
>
>
>
> Last time, Im so sorry that I asked you questions when you were very busy. 
> Im not in hurry, so please reply me when you could make several times.
>
>
>
> In my last mail, I asked several questions. Please forgive me asking you 
> again. I wish to confirm the following points.
>
>
>
> 1. default conditions
>
> I entered the following command.
>
>
>
> SBML_odeSolverAPP sample.xml --time 1500 --printstep 150 > sample.txt
>
>
>
> The odes were not solved and the error message as sample.txt was output. But 
> with the same condition, when I entered
>
>
>
> SMBL_odeSolverApp sample.xml --time 1500 --printstep 150 --error 1e-9 
> --rerror 1e-3 --mxstep 1e4 > sample.txt
>
>
>
> the odes were solved. What could be the reason ? I think the conditions are 
> same. Am I misunderstanding the default values ?
>
>
>
> 2. If I changed the error tolerance, is there a possibility that the 
> resolutions will change ? For example, with the same .xml file, at the time 
> error tolerance is 1e-6 and at the time error tolerance is 1e-12 ?
>
>
>
> 3. How wide are the ranges of conditions, error tolerance, rerror tolerance 
> and mxstep ?
>
>
>
> 4. Does the smaller error tolerance brings more accurate resolution ? For 
> example, when I set the error tolerance 1e-16, the resolution will be better 
> than I set the error tolerance at 1e-12 ?
>
>
>
> I'm so sorry for the fundamental questions, and asking you several times.
>
>
>
> Thank you very much indeed again, and thank you very much in advance for 
> giving me advices.
>
> Yours faithfully,
> Tatsunori Nishimura
>
> Tatsunori Nishimura
> e-mail: tni...@co...
> Tateno Labo.
> Computational Life Sciences Group,
> Institute of Physics, Graduate School of Pure and Applied Sciences,
> University of Tsukuba
>

[SOSlib-discuss] Request on solving installation problem with SBMLodesolver

[Arunkumar S. <ar...@nc...>]

Dear Sir,

I am facing a problem in the installation of SBMLodesolver. I have Fedora
Core 4 installed. Also, I have made a request in here:

http://sourceforge.net/tracker/index.php?func=3Ddetail&aid=3D1444623&grou=
p_id=3D139893&atid=3D744811

I get "undefined reference to `ParseMessage_getId'" error during the
"make" command of installation. Could you please help me solving this
problem.

Thanking You,

Yours Sincerely,

Arun (Short-Term Trainee) Email:ar...@nc...
Dr.Upinder S Bhalla       Email:bh...@nc...
Computational Neurosciences Lab
NCBS, TIFR
Bangalore.560065 INDIA.
ph:+91-(80)23636420-28 Extn:(3221)
Web: http://www.ncbs.res.in

Re: [SOSlib-discuss] Installing problems: expat/xerces

[Rainer M. <ra...@tb...>]

Hi Adri,

this is quite an embarassing bug. We once thought of it, and wanted to=20
include libSBML/expat in the configure process, but then seem to have=20
forgotten about it. Sorry!

Maybe you can try to replace each occurence of

`-lxerces-c'

in the files

configure
examples/Makefile.am
examples/Makefile.in
odeSolver/Makefile.am
odeSolver/Makefile.in

with `-lexpat'

e.g. by usind sed:

 	sed 's/xerces-c/expat/g' configure > configure.new
 	mv configure.new configure

Do this for all above files.

This might work, as our configure never directly searches for or requires=
=20
expat/xerces-c.


Please let me know, if that worked for you. Sorry for the trouble and=20
thanks for reporting! We will fix this for the next release (in 2-3=20
months).

Rainer


On Fri, 27 Jan 2006, LOPEZ GARCIA DE LOMANA, ADRIAN wrote:

> Hi all,
>
> I'm trying to install odeSolver on my Red Hat 9.0 machine and I have so=
me problems at the configuration step. I have installed libSBML (with exp=
at, not xerces!!!) and Sundials with no apparent errors. While I execute =
./configure I get this:
>
>
> [root@nerium SBML_odeSolver-1.6.0]# ./configure
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking build system type... i686-pc-linux-gnu
> checking host system type... i686-pc-linux-gnu
> checking for g++... g++
> checking for C++ compiler default output file name... a.out
> checking whether the C++ compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++ accepts -g... yes
> checking for style of include used by make... GNU
> checking dependency style of g++... gcc3
> checking for gcc... gcc
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ANSI C... none needed
> checking dependency style of gcc... gcc3
> checking how to run the C preprocessor... gcc -E
> checking for ranlib... ranlib
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether make sets $(MAKE)... (cached) yes
> checking for autoconf... /usr/bin/autoconf
> checking for aclocal... /usr/local/bin/aclocal
> checking for make... /usr/bin/make
> checking for ar... /usr/bin/ar
> checking for swig... /usr/bin/swig
> checking for perl... /usr/bin/perl
> checking for SBML Library headers... yes
> checking for SBML Library... yes
> configure: found SBML Library Version 2.3.4
> checking correct functioning of SBML... no:
>                   CFLAGS=3D-g -O2 -I/usr/local/include -I/usr/local/inc=
lude/sbml
>                   LDFLAGS=3D -Wl,-rpath,/usr/local/lib -L/usr/local/lib
>                   LIBS=3D -lxerces-c -lsbml
> configure: error: Can not link to SBML Library:
>                  Please, make sure to use libSBML version >=3D 2.3.2
>
> Seems to be trying to call libSBML with LIBS=3D-lxerces-c which I do no=
t have. I've tried
>
> ./configure LIBS=3D-lexpat
>
> instead, but the error was very similar:
> checking correct functioning of SBML... no:
>                   CFLAGS=3D-g -O2 -I/usr/local/include -I/usr/local/inc=
lude/sbml
>                   LDFLAGS=3D -Wl,-rpath,/usr/local/lib -L/usr/local/lib
>                   LIBS=3D-lexpat -lxerces-c -lsbml
> configure: error: Can not link to SBML Library:
>                  Please, make sure to use libSBML version >=3D 2.3.2
>
> Is it mandatory to have libSBML installed with xerces or there is a way=
 to keep on using expat?
>
> Thanks for your time,
>
>
>
>
> Adri=E1n.
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log =
files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://sel.as-us.falkag.net/sel?cmd____________________________________=
___________
> sbmlsolver-discuss mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss
>

[SOSlib-discuss] Installing problems: expat/xerces

[LOPEZ G. DE L. A. <al...@im...>]

Hi all,=20

I'm trying to install odeSolver on my Red Hat 9.0 machine and I have =
some problems at the configuration step. I have installed libSBML (with =
expat, not xerces!!!) and Sundials with no apparent errors. While I =
execute ./configure I get this:


[root@nerium SBML_odeSolver-1.6.0]# ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking build system type... i686-pc-linux-gnu
checking host system type... i686-pc-linux-gnu
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for autoconf... /usr/bin/autoconf
checking for aclocal... /usr/local/bin/aclocal
checking for make... /usr/bin/make
checking for ar... /usr/bin/ar
checking for swig... /usr/bin/swig
checking for perl... /usr/bin/perl
checking for SBML Library headers... yes
checking for SBML Library... yes
configure: found SBML Library Version 2.3.4
checking correct functioning of SBML... no:
                   CFLAGS=3D-g -O2 -I/usr/local/include =
-I/usr/local/include/sbml
                   LDFLAGS=3D -Wl,-rpath,/usr/local/lib -L/usr/local/lib
                   LIBS=3D -lxerces-c -lsbml
configure: error: Can not link to SBML Library:
                  Please, make sure to use libSBML version >=3D 2.3.2

Seems to be trying to call libSBML with LIBS=3D-lxerces-c which I do not =
have. I've tried=20

 ./configure LIBS=3D-lexpat

instead, but the error was very similar:
checking correct functioning of SBML... no:
                   CFLAGS=3D-g -O2 -I/usr/local/include =
-I/usr/local/include/sbml
                   LDFLAGS=3D -Wl,-rpath,/usr/local/lib -L/usr/local/lib
                   LIBS=3D-lexpat -lxerces-c -lsbml
configure: error: Can not link to SBML Library:
                  Please, make sure to use libSBML version >=3D 2.3.2

Is it mandatory to have libSBML installed with xerces or there is a way =
to keep on using expat?

Thanks for your time,=20




Adri=E1n.

[SOSlib-discuss] Re: Installation summary for Solaris 9

[Tommi A. <tom...@tu...>]

Happy if it helps :-)

I can open an account to sourceforge. Feel free to forward the instructions.

Do you mean a link to my homepage? I really should prepare one. I'll 
email you when there is something.

Thanks,
Tommi


Rainer Machne wrote:

> Hi Tommi,
>
> On Thu, 22 Dec 2005, Tommi Aho wrote:
>
>> ...
>>
>> SBML_RPATH="-Wl,-rpath,$with_libsbml/lib"
>> Modified line:
>> SBML_RPATH="-Wl,-R,$with_libsbml/lib"
>>
>
> Thanks. I have already moved this message from your old bug report to 
> a new one. We will fix this for the next release.
>
>
>> ...
>> getopt has problems with portability.
>
>
> We already needed a separate version for Windows! I will add another 
> bug report, unless you want to do so yourself (as you have found it) 
> from your own sourceforge account.
>
>
>> ... and the system is running. :-)
>>
>> Best regards,
>> Tommi
>
>
> Great work! Thank you so much. This is to our knowledge the first 
> installation on Solaris.
>
> We will fix this for the next release. In the meantime, I hope you 
> don't mind if I put this instructions online to the installGnu.html 
> file, linked as `Installation on Unix', of course with full credits 
> for you.
> If you send me an URL, I could add a link to your website for credits.
>
> Thanks again.
>
> best regards,
> Rainer

[SOSlib-discuss] Re: Installation summary for Solaris 9

[Rainer M. <ra...@tb...>]

Hi Tommi,

On Thu, 22 Dec 2005, Tommi Aho wrote:
> ...
>
> SBML_RPATH="-Wl,-rpath,$with_libsbml/lib"
> Modified line:
> SBML_RPATH="-Wl,-R,$with_libsbml/lib"
>

Thanks. I have already moved this message from your old bug report to a 
new one. We will fix this for the next release.


> ...
> getopt has problems with portability.

We already needed a separate version for Windows! I will add another 
bug report, unless you want to do so yourself (as you have found it) from 
your own sourceforge account.


> ... and the system is running. :-)
>
> Best regards,
> Tommi

Great work! Thank you so much. This is to our knowledge the first 
installation on Solaris.

We will fix this for the next release. In the meantime, I hope you don't 
mind if I put this instructions online to the installGnu.html file, linked 
as `Installation on Unix', of course with full credits for you.
If you send me an URL, I could add a link to your website for credits.

Thanks again.

best regards,
Rainer

[SOSlib-discuss] Installation summary for Solaris 9

[Tommi A. <tom...@tu...>]

Hi!

There were some difficulties with Solaris 9 and odeSolver 1.6.0. Here is 
a summary how I got it done. Maybe this helps you.


sbmlsolver> gunzip  SBML_odeSolver-1.6.0.tar.gz
sbmlsolver> tar -xvvf SBML_odeSolver-1.6.0.tar

Change into configure, line 4192 (only this line because the following 
configuration doesn't use the other lines including the -rpath switch):
Original line 4192:
SBML_RPATH="-Wl,-rpath,$with_libsbml/lib"
Modified line:
SBML_RPATH="-Wl,-R,$with_libsbml/lib"

sbmlsolver/SBML_odeSolver-1.6.0> ./configure 
--prefix=/home/u2/univ2/ttkk/tomaho/sbmlsolver/local_installation \
--with-libsbml=/home/u2/univ2/ttkk/tomaho/libsbml/local_installation \
--with-sundials=/home/u2/univ2/ttkk/tomaho/sundials/sundials

...
Build Settings for SBML_odeSolver v1.6.0:
----------------------------------
  host type            = solaris
  shared lib extension = so
  install dir          = 
/home/u2/univ2/ttkk/tomaho/sbmlsolver/local_installation
  CC                   = gcc
  CFLAGS               =
  LDFLAGS              =
  LIBS                 = -lm
  SBML Library         = yes
       CFLAGS          = 
-I/home/u2/univ2/ttkk/tomaho/libsbml/local_installation/include
-I/home/u2/univ2/ttkk/tomaho/libsbml/local_installation/include/sbml
       LDFLAGS         = 
-L/home/u2/univ2/ttkk/tomaho/libsbml/local_installation/lib
       LIBS            = -lsbml
SUNDIALS Library         = yes
       CFLAGS          = 
-I/home/u2/univ2/ttkk/tomaho/sundials/sundials/include
       LDFLAGS         = -L/home/u2/univ2/ttkk/tomaho/sundials/sundials/lib
       LIBS            = -lsundials_kinsol -lsundials_cvodes 
-lsundials_cvode -lsundials_nvecserial -lsundials_shared
  GRACE                = no
XMGRACE functionality will NOT be installed!
  GRAPHVIZ             = no
GRAPHVIZ functionality will NOT be installed!


sbmlsolver/SBML_odeSolver-1.6.0> make
...
options.c:7:20: getopt.h: No such file or directory
...

getopt has problems with portability. See e.g. 
http://www.thedotin.net/maillists/coldsync-hackers/msg01314.html

Download the needed getopt files, e.g. from 
http://www.molpopgen.org/krthornt/gccSolaris/
Compile them
sbmlsolver/SBML_odeSolver-1.6.0/odeSolver> gcc --pedantic -c getopt.c
sbmlsolver/SBML_odeSolver-1.6.0/odeSolver> gcc --pedantic -c getopt1.c

Add the object files to the linking by modifying
odeSolver/Makefile and odeSolver/Makefile.in:
The following 2 lines exist in both of these files. The third line is 
added (and the slash in the 2nd line).
am_odeSolver_OBJECTS = main.$(OBJEXT) commandLine.$(OBJEXT) \
        options.$(OBJEXT) printModel.$(OBJEXT) interactive.$(OBJEXT) \
        getopt1.$(OBJEXT) getopt.$(OBJEXT)

sbmlsolver/SBML_odeSolver-1.6.0> make

sbmlsolver/SBML_odeSolver-1.6.0> make install

... and the system is running. :-)

Best regards,
Tommi

Re: [SOSlib-discuss] crash in configuration script

[Rainer M. <ra...@tb...>]

Tommi,

On Wed, 21 Dec 2005, Tommi Aho wrote:

>
> Hello,
>
> Yes, it was about using '--with-sundials' instead of '--with-sundialscvode'.

Good. Sorry for that change and the not corresponding change in the 
configure script messages. I thought, it might be misleading to keep the 
old switch, while we also use other sundials stuff now.

>
> Are the other errors in the output (in the sourceforge link below) also due 
> to the libSBML / harmful?
>
> ...
> checking for SBML Library Version... expr: syntax
> error
> expr: syntax error
> expr: syntax error
> ...
>

This comes from libSBML version checking. We haven't looked into the 
details of this error, but it shouldn't cause a problem, if you have a 
recent libSBML version installed (greater then 2.3.2 should be Ok).
If the make process is Ok, then there is no problem.

Rainer


> -Tommi
>
>
> Rainer Machne wrote:
>
>> Hi Tommi
>> 
>> 
>> The line ./configure: line 4278: test: -eq: unary operator expected
>> comes from the libSBML test and shouldn't be the problem.
>> 
>> I have seen this error before.
>> The only difference to the SUNDIALS test is, that SOSlib now requires not 
>> only CVODE, but CVODES and KINSOL, and thus now links to
>> -lsundials_kinsol -lsundials_cvodes -lsundials_cvode -lsundials_nvecserial 
>> -lsundials_shared
>> 
>> Do you have the full Sundials package, or just the cvode or cvodes part?
>> 
>> Rainer
>> 
>> 
>> On Tue, 20 Dec 2005, Tommi Aho wrote:
>> 
>>> 
>>> Hello,
>>> 
>>> There was a crash when running the configuration    script of the library 
>>> version 1.6.
>>> 
>>> See details in 
>>> http://sourceforge.net/tracker/index.php?func=detail&aid=1386145&group_id=139893&atid=744811 
>>> 
>>> Thanks,
>>> Tommi Aho
>>> 
>>> tommi.aho at tut.fi
>>> 
>>> 
>>> 
>>> -------------------------------------------------------
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>>> _______________________________________________
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>>> sbm...@li...
>>> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss
>>> 
>
>
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Re: [SOSlib-discuss] crash in configuration script

[Tommi A. <tom...@tu...>]

Hello,

Yes, it was about using '--with-sundials' instead of '--with-sundialscvode'.

Are the other errors in the output (in the sourceforge link below) also 
due to the libSBML / harmful?

...
checking for SBML Library Version... expr: syntax
 error
 expr: syntax error
 expr: syntax error
...

-Tommi


Rainer Machne wrote:

> Hi Tommi
>
>
> The line ./configure: line 4278: test: -eq: unary operator expected
> comes from the libSBML test and shouldn't be the problem.
>
> I have seen this error before.
> The only difference to the SUNDIALS test is, that SOSlib now requires 
> not only CVODE, but CVODES and KINSOL, and thus now links to
> -lsundials_kinsol -lsundials_cvodes -lsundials_cvode 
> -lsundials_nvecserial -lsundials_shared
>
> Do you have the full Sundials package, or just the cvode or cvodes part?
>
> Rainer
>
>
> On Tue, 20 Dec 2005, Tommi Aho wrote:
>
>>
>> Hello,
>>
>> There was a crash when running the configuration    script of the 
>> library version 1.6.
>>
>> See details in 
>> http://sourceforge.net/tracker/index.php?func=detail&aid=1386145&group_id=139893&atid=744811 
>>
>>
>> Thanks,
>> Tommi Aho
>>
>> tommi.aho at tut.fi
>>
>>
>>
>> -------------------------------------------------------
>> This SF.net email is sponsored by: Splunk Inc. Do you grep through 
>> log files
>> for problems?  Stop!  Download the new AJAX search engine that makes
>> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
>> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
>> _______________________________________________
>> sbmlsolver-discuss mailing list
>> sbm...@li...
>> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss
>>

Re: [SOSlib-discuss] crash in configuration script

[Rainer M. <ra...@tb...>]

Hi Tommi,

I think I found the error,
as we now use more of Sundials then just cvode the corresponding argument 
to configure has changed (unfortunately, the message haven't yet).

Instead of

--with-sundialscvode=/home/tommi/tutkimus/simulointi/cvode/sundials

it should be

--with-sundials=/home/tommi/tutkimus/simulointi/cvode/sundials

I hope that helps.

Rainer


On Tue, 20 Dec 2005, Tommi Aho wrote:

>
> Hello,
>
> There was a crash when running the configuration    script of the library 
> version 1.6.
>
> See details in 
> http://sourceforge.net/tracker/index.php?func=detail&aid=1386145&group_id=139893&atid=744811
>
> Thanks,
> Tommi Aho
>
> tommi.aho at tut.fi
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> _______________________________________________
> sbmlsolver-discuss mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss
>

Re: [SOSlib-discuss] crash in configuration script

[Rainer M. <ra...@tb...>]

Hi Tommi

Thanks for reporting. This is the first email to our new list, btw :)

You wrote that the same call worked with SOSlib 1.6.0pre.

The line ./configure: line 4278: test: -eq: unary operator expected
comes from the libSBML test and shouldn't be the problem.

I have seen this error before.
The only difference to the SUNDIALS test is, that SOSlib now requires not 
only CVODE, but CVODES and KINSOL, and thus now links to
-lsundials_kinsol -lsundials_cvodes -lsundials_cvode -lsundials_nvecserial 
-lsundials_shared

Do you have the full Sundials package, or just the cvode or cvodes part?

Rainer


On Tue, 20 Dec 2005, Tommi Aho wrote:

>
> Hello,
>
> There was a crash when running the configuration    script of the library 
> version 1.6.
>
> See details in 
> http://sourceforge.net/tracker/index.php?func=detail&aid=1386145&group_id=139893&atid=744811
>
> Thanks,
> Tommi Aho
>
> tommi.aho at tut.fi
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> _______________________________________________
> sbmlsolver-discuss mailing list
> sbm...@li...
> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss
>

[SOSlib-discuss] crash in configuration script

[Tommi A. <tom...@tu...>]

Hello,

There was a crash when running the configuration    
script of the library version 1.6.

See details in 
http://sourceforge.net/tracker/index.php?func=detail&aid=1386145&group_id=139893&atid=744811

Thanks,
Tommi Aho

tommi.aho at tut.fi

[SOSlib-discuss] Test 2

[Rainer M. <ra...@tb...>]

Hi Andrew and Xtof

this is another test email to our public email list SOSlib-discuss.

We also have a private list SOSlib-devel, which should replace the emails 
to all developers, that we sometimes have.

Rainer