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

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
>
>
>
> -------------------------------------------------------
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> 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!
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>> _______________________________________________
>> 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...>]

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
>>> 
>>> 
>>> 
>>> -------------------------------------------------------
>>> 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
>>> 
>
>
> -------------------------------------------------------
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[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

[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] 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

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
>