A list for the developers of CellML tools

Text archives Help


Re: [[cellml-dev] ] The CellML API on Ubuntu 16.04


Chronological Thread 
  • From: Alan Garny <alan.garny AT inria.fr>
  • To: A list for the developers of CellML tools <cellml-tools-developers AT cellml.org>
  • Subject: Re: [[cellml-dev] ] The CellML API on Ubuntu 16.04
  • Date: Fri, 21 Oct 2016 10:20:01 +0200
  • Authentication-results: mx3.auckland.ac.nz; dkim=none (message not signed) header.i=none; spf=None smtp.mailfrom=alan.garny AT inria.fr
  • Ironport-phdr: 9a23:Zv8S8xBdRuqURE0hlyPrUyQJP3N1i/DPJgcQr6AfoPdwSP/6pcbcNUDSrc9gkEXOFd2CrakV0ayL4uu5AzNIyK3CmUhKSIZLWR4BhJdetC0bK+nBN3fGKuX3ZTcxBsVIWQwt1Xi6NU9IBJS2PAWK8TWM5DIfUi/yKRBybrysXNWD1YLqhqvrocKbSj4LrQL1Wal1IhSyoFeZnegtqqwmFJwMzADUqGBDYeVcyDAgD1uSmxHh+pX4p8Y7oGx48sgs/M9YUKj8Y79wDfkBVGxnYCgJ45jC/R3CVhfH6HwGGnkWn1JEDhbI6BbiU43q+iz0/sFw3C2/GYXqSrcwQnz25KpvTBrszTsAMDoitW3alMF0i7pWugmJrBF7x4vQJoaPO6wtULnaeIYzQWNHFulYTSpQSte1a4IJSeUIJ+BJh4j7vVoH6xWkU1r/TNjzwyNF0yellZYx1P4sRESfhFQt

Hi Lucian,



Indeed, Matthias should have got things to work (see
https://lists.cellml.org/sympa/arc/cellml-tools-developers/2016-10/msg00006.html).



When it comes to providing up-to-date binaries for the CellML API, I was
ready to give it a try, but then it (at least) requires installing the Java
SDK, and that’s not something I am willing to do. This being said, you may
not have seen it, but I have some basic instructions for building the CellML
API on Windows, Linux and macOS (see
https://github.com/opencor/opencor/blob/master/src/plugins/api/CellMLAPI/README.txt).
It’s all working fine for me using MSVC 2015 on Windows 7 and later, as well
as using GCC/G++ 4.9+ on Ubuntu 14.04 LTS and later (yes, including Ubuntu
16.04 LTS), and OS X 10.8 and later. On top of the CellML API services that I
personally need, Matthias needed TeLICeMS, and it should now work fine after
I fixed a couple of issues with the CellML API build system (see
https://github.com/cellmlapi/cellml-api/).



Alan



On 21/10/2016, 00:32, "Lucian Smith"
<cellml-tools-developers-request AT lists.cellml.org
on behalf of
lucianoelsmitho AT gmail.com>
wrote:



Hey, everyone! Just a note that it would be nice to have new SDKs for the
CellML API for Ubuntu 16.04--the old ones no longer work there.



It would also be nice to get SDKs for the latest versions of Visual Studio,
but that's less urgent.



Attached are the emails that Matthias and I sent earlier, but it turned out I
was only signed up under my old email address, so now I'm actually signed up
using the new one.



I believe that Matthias eventually worked through the dependencies to build
the API from source, but as noted, it was a pain.



-Lucian



On Wed, Oct 19, 2016 at 12:50 AM, Matthias König
<konigmatt AT googlemail.com>
wrote:

I already tried to build the SDK from source but never could manage to make
this work (dependency nightmare). I have no idea what are the third party
dependencies are and there are so many of them.



For instance trying to just build the barbone SDK via
cmake -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=${CELLML_BUILD} ../${API_VERSION}
make all

results in:


Scanning dependencies of target cellml
[ 1%] Building CXX object CMakeFiles/cellml.dir/sources/Utilities.cpp.o
In file included from
/home/mkoenig/tmp/cellml-api-1.13/sources/Utilities.cpp:1:0:
/home/mkoenig/tmp/cellml-api-1.13/sources/Utilities.hxx:41:26: fatal error:
Ifacexpcom.hxx: No such file or directory
compilation terminated.
CMakeFiles/cellml.dir/build.make:62: recipe for target
'CMakeFiles/cellml.dir/sources/Utilities.cpp.o' failed
make[2]: *** [CMakeFiles/cellml.dir/sources/Utilities.cpp.o] Error 1
CMakeFiles/Makefile2:1176: recipe for target 'CMakeFiles/cellml.dir/all'
failed

despite cmake-gui not showing any problems.

Looking at the SDK-build/lib directory suggests that there are around 50
library dependencies I somehow have to get installed for building.

I already fought to build the cellml SDK 2 years ago and gave up than. And
after 1h now I am at the same point.



In summary: It would be nice to have a SDK build which works on Ubuntu 16.04
or at least a way that one can build the SDK easily.





On Wed, Oct 19, 2016 at 8:35 AM, Matthias König
<konigmatt AT googlemail.com>
wrote:

Just for information:

I can reproduce this problem on all my Ubuntu 16.04 machines & in docker
images based on Ubuntu 16.04

I tried linking against 1.11, 1.12 and 1.13 from here

wget
https://sourceforge.net/projects/cellml-api/files/CellML-API-Nightly/1.12/20121031/linux-x86_64/${VERSION}.tar.bz2/download
wget
https://sourceforge.net/projects/cellml-api/files/CellML-API-Nightly/1.11/20120418/linux-x86_64/${VERSION}.tar.bz2/download
wget
https://sourceforge.net/projects/cellml-api/files/CellML-API-Nightly/1.13/20130716/linux-x86_64/${VERSION}.tar.bz2/download
but none of the SDK versions works on Ubuntu 16.04.

I have no problems in 14.04, but it is no longer supported . The current Long
term support version is 16.04 LTS and cellml SDK should work on it.

Matthias





On Tue, Oct 18, 2016 at 11:12 PM, Lucian Smith
<lucianoelsmitho AT gmail.com>
wrote:

So, it turns out that in Antimony, using the now-old CellML API, calls to the
CellML library error out with a SIGABRT if compiled on Ubuntu 16.04, but not
when compiled on Ubuntu 14.04. This is presumably an issue with the CellML
SDK.



While a new CellML library would certainly be nice, I'm unlikely to have the
time to update Antimony to use it any time soon, so if someone wouldn't mind
looking into creating a CellML SDK for these more recent versions of Ubuntu,
that'd be great.



SDKs for more recent versions of Visual Studio would also be nice, though I
haven't actually checked to see if they already exist ;-)



Thank you!



-Lucian




--

Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
Error! Filename not specified. https://www.livermetabolism.com
konigmatt AT googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480




--

Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
Error! Filename not specified. https://www.livermetabolism.com
konigmatt AT googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480






Archive powered by MHonArc 2.6.18.

Top of page