Compilation from source probably miss some documentation

[Bruno Chareyre]

It seems the instructions for installing prerequisites [1] will fail on ubuntu 12.04 if yade-users ppa is not enabled first.
Trying to compile anyway leads to a few cmake warnings but it will let one build. Then boot failure because of missing lib (didn't do the build myself, I've seen the result on a colleagues computer).

The bug is that the ppa is not mentionned anywhere on the installation page.
If anyone confirm I can update the doc, though I'm not sure if this situation is for 12.04 only, or if the ppa should be considered mandatory for all platforms.

[1] https://yade-dem.org/doc/installation.html#prerequisites

[Klaus Thoeni (klaus.thoeni)]

Hi Bruno

it probably depends on which options you are using when compiling. I am not
using the ppa and everything is working for me on 12.04.

Nevertheless, you are right the ppa should probably be mentioned in the
installation section. But I don't think it is mandatory.

Cheers
Klaus

On Wednesday 13 November 2013 16:23:49 Bruno Chareyre wrote:
> Public bug reported:
>
>
> It seems the instructions for installing prerequisites [1] will fail on
> ubuntu 12.04 if yade-users ppa is not enabled first. Trying to compile
> anyway leads to a few cmake warnings but it will let one build. Then boot
> failure because of missing lib (didn't do the build myself, I've seen the
> result on a colleagues computer).
>
> The bug is that the ppa is not mentionned anywhere on the installation page.
> If anyone confirm I can update the doc, though I'm not sure if this
> situation is for 12.04 only, or if the ppa should be considered mandatory
> for all platforms.
>
> [1] https://yade-dem.org/doc/installation.html#prerequisites
>
> ** Affects: yade
> Importance: Undecided
> Status: New
>
> --
> You received this bug notification because you are a member of Yade
> developers, which is subscribed to Yade.
> https://bugs.launchpad.net/bugs/1250928
>
> Title:
> Compilation from source probably miss some documentation
>
> Status in Yet Another Dynamic Engine:
> New
>
> Bug description:
>
> It seems the instructions for installing prerequisites [1] will fail on
> ubuntu 12.04 if yade-users ppa is not enabled first. Trying to compile
> anyway leads to a few cmake warnings but it will let one build. Then boot
> failure because of missing lib (didn't do the build myself, I've seen the
> result on a colleagues computer).
>
> The bug is that the ppa is not mentionned anywhere on the installation
> page. If anyone confirm I can update the doc, though I'm not sure if this
> situation is for 12.04 only, or if the ppa should be considered mandatory
> for all platforms.
>
> [1] https://yade-dem.org/doc/installation.html#prerequisites
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/yade/+bug/1250928/+subscriptions
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-dev
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-dev
> More help : https://help.launchpad.net/ListHelp
--
Dr. Klaus Thoeni - Centre for Geotechnical and Materials Modelling
Civil, Surveying and Environmental Engineering - Engineering Building EA
The University of Newcastle, Callaghan, NSW 2308, Australia
web: http://www.newcastle.edu.au/research-centre/cgmm
phone: [phone]

[Alexander Eulitz [Eugen] (kubeu)]

Hi,
I encountered this problem some weeks ago [1] and proposed a new version of the installation manual.
This was done with the github online tool.
My proposed revision was not accepted because I was not able to create a patch from it.

Alex

[1] https://answers.launchpad.net/yade/+question/235466

-----Ursprüngliche Nachricht-----
Von: Yade-dev [mailto:<email address hidden>] Im Auftrag von Klaus Thoeni
Gesendet: Donnerstag, 14. November 2013 01:29
An: <email address hidden>; Bug 1250928
Betreff: Re: [Yade-dev] [Bug 1250928] [NEW] Compilation from source probablymiss some documentation

Hi Bruno

it probably depends on which options you are using when compiling. I am not using the ppa and everything is working for me on 12.04.

Nevertheless, you are right the ppa should probably be mentioned in the installation section. But I don't think it is mandatory.

Cheers
Klaus

On Wednesday 13 November 2013 16:23:49 Bruno Chareyre wrote:
> Public bug reported:
>
>
> It seems the instructions for installing prerequisites [1] will fail
> on ubuntu 12.04 if yade-users ppa is not enabled first. Trying to
> compile anyway leads to a few cmake warnings but it will let one
> build. Then boot failure because of missing lib (didn't do the build
> myself, I've seen the result on a colleagues computer).
>
> The bug is that the ppa is not mentionned anywhere on the installation page.
> If anyone confirm I can update the doc, though I'm not sure if this
> situation is for 12.04 only, or if the ppa should be considered
> mandatory for all platforms.
>
> [1] https://yade-dem.org/doc/installation.html#prerequisites
>
> ** Affects: yade
> Importance: Undecided
> Status: New
>
> --
> You received this bug notification because you are a member of Yade
> developers, which is subscribed to Yade.
> https://bugs.launchpad.net/bugs/1250928
>
> Title:
> Compilation from source probably miss some documentation
>
> Status in Yet Another Dynamic Engine:
> New
>
> Bug description:
>
> It seems the instructions for installing prerequisites [1] will fail
> on ubuntu 12.04 if yade-users ppa is not enabled first. Trying to
> compile anyway leads to a few cmake warnings but it will let one
> build. Then boot failure because of missing lib (didn't do the build
> myself, I've seen the result on a colleagues computer).
>
> The bug is that the ppa is not mentionned anywhere on the
> installation page. If anyone confirm I can update the doc, though I'm
> not sure if this situation is for 12.04 only, or if the ppa should be
> considered mandatory for all platforms.
>
> [1] https://yade-dem.org/doc/installation.html#prerequisites
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/yade/+bug/1250928/+subscriptions
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-dev
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-dev
> More help : https://help.launchpad.net/ListHelp
--
Dr. Klaus Thoeni - Centre for Geotechnical and Materials Modelling Civil, Surveying and Environmental Eng...

[Bruno Chareyre (bruno-chareyre)]

@Klaus
It works for you because you have enough packages installed. This is why this type error is not very easy to spot. If you install a fresh 12.04 however, it will not work, whatever the compilation options.

@Alexender
Thanks for mentionning that. You are right it is the same problem.
I replied in your thread: never use online tools for modifying the sources.
Let me know if you want to try again, else I will make the change.

[Anton Gladky (gladky-anton)]

For ubuntu 12.10 and older, please, install libqglviewer-qt4-dev instead of
libqglviewer-dev

Anton

[Klaus Thoeni (klaus.thoeni)]

There seams to be another problem with libopenblas-dev on 12.04. I was not using it but I installed it today and during cmake I got something like:

ImportError: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv

It looks like a incompatibility between numpy and lapack.

After "sudo apt-get remove libopenblas-base" everything is working again.

Anyone can confirm this?

Klaus

[Bruno Chareyre (bruno-chareyre)]

@Klaus
Is it with yade-users ppa available?
In that case it should work like a charm in my experience.

Bruno

[Klaus Thoeni (klaus.thoeni)]

Yes, yade-users ppa is available. However, I have not installed metis. But
this shouldn't have an influence on this specific problem with lapack, or I am
wrong? I can't see any other package on the ppa which might be relevant.

Anyway, I will see if I can reproduce the problem on my desktop.

Klaus

On Tuesday 19 November 2013 11:00:13 Bruno Chareyre wrote:
> @Klaus
> Is it with yade-users ppa available?
> In that case it should work like a charm in my experience.
>
> Bruno
>
> --
> You received this bug notification because you are a member of Yade
> developers, which is subscribed to Yade.
> https://bugs.launchpad.net/bugs/1250928
>
> Title:
> Compilation from source probably miss some documentation
>
> Status in Yet Another Dynamic Engine:
> New
>
> Bug description:
>
> It seems the instructions for installing prerequisites [1] will fail on
> ubuntu 12.04 if yade-users ppa is not enabled first. Trying to compile
> anyway leads to a few cmake warnings but it will let one build. Then boot
> failure because of missing lib (didn't do the build myself, I've seen the
> result on a colleagues computer).
>
> The bug is that the ppa is not mentionned anywhere on the installation
> page. If anyone confirm I can update the doc, though I'm not sure if this
> situation is for 12.04 only, or if the ppa should be considered mandatory
> for all platforms.
>
> [1] https://yade-dem.org/doc/installation.html#prerequisites
>
> To manage notifications about this bug go to:
> https://bugs.launchpad.net/yade/+bug/1250928/+subscriptions
>
> _______________________________________________
> Mailing list: https://launchpad.net/~yade-dev
> Post to : <email address hidden>
> Unsubscribe : https://launchpad.net/~yade-dev
> More help : https://help.launchpad.net/ListHelp
--
Dr. Klaus Thoeni - Centre for Geotechnical and Materials Modelling
Civil, Surveying and Environmental Engineering - Engineering Building EA
The University of Newcastle, Callaghan, NSW 2308, Australia
web: http://www.newcastle.edu.au/research-centre/cgmm
phone: [phone]

[Klaus Thoeni (klaus.thoeni)]

Ok, same problem on my Desktop with 12.04. Here the exact cmake output:

-- Found Qt4: /usr/bin/qmake (found version "4.8.1")
-- Version is set to 2013-11-18.git-7f86f06
-- GTS using gts-config /usr/bin/gts-config
-- Using GTS from /usr
-- Boost_VERSION: 104601
-- Boost_LIB_VERSION: 1_46_1
-- Boost_INCLUDE_DIRS: /usr/include
-- Boost_LIBRARIES: /usr/lib/libboost_python.so/usr/lib/libboost_thread-mt.so/usr/lib/libboost_date_time-mt.so/usr/lib/libboost_filesystem-mt.so/usr/lib/libboost_iostreams-mt.so/usr/lib/libboost_regex-mt.so/usr/lib/libboost_serialization-mt.so/usr/lib/libboost_system-mt.so
CMake Error at cMake/FindNumPy.cmake:64 (message):
  NumPy import failure:

  Traceback (most recent call last):

    File "<string>", line 1, in <module>
    File "/usr/lib/python2.7/dist-packages/numpy/__init__.py", line 137, in <module>
      import add_newdocs
    File "/usr/lib/python2.7/dist-packages/numpy/add_newdocs.py", line 9, in <module>
      from numpy.lib import add_newdoc
    File "/usr/lib/python2.7/dist-packages/numpy/lib/__init__.py", line 13, in <module>
      from polynomial import *
    File "/usr/lib/python2.7/dist-packages/numpy/lib/polynomial.py", line 17, in <module>
      from numpy.linalg import eigvals, lstsq
    File "/usr/lib/python2.7/dist-packages/numpy/linalg/__init__.py", line 48, in <module>
      from linalg import *
    File "/usr/lib/python2.7/dist-packages/numpy/linalg/linalg.py", line 23, in <module>
      from numpy.linalg import lapack_lite

  ImportError: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv

Call Stack (most recent call first):
  CMakeLists.txt:90 (FIND_PACKAGE)

-- Configuring incomplete, errors occurred!

[Anton Gladky (gladky-anton)]

There is definitely a conflict between numpy and lapack. We can nothing to
do
with that, especially on Ubuntu released 1.5 years ago.

Do the newer Ubuntu versions have the same problem, or it is only
12.04-specific?

Anton

2013/11/20 Klaus Thoeni <email address hidden> from numpy.linalg
import lapack_lite

>
> ImportError: /usr/lib/liblapack.so.3gf: undefined symbol: ATL_chemv
>

[Bruno Chareyre (bruno-chareyre)]

I'm curious to know what versions you have for the following
things: openblas, suitesparse, metis, lapack. Could you make keyword
searches on them [1]?
This set of libraries was difficult to use with combined packaged
versions in the recent years but it should be ok >=12.04. There seem to
be a few things to fix in doc and/or cmake, but I'm not sure what.

There is no conflict with lapack itslef but possibly with some replacements of it (especially openblas). Still, some of us can compile and run without problem on ubuntu 12.04.

Bruno

[1] aptitude search '~i' | grep metis; aptitude search '~i' | grep openblas; aptitude search '~i' | grep suitesparse

[Bruno Chareyre (bruno-chareyre)]

And, by the way, launchpad can build for 12.04 without trouble. So, reproducing the same steps should succeed for everyone, shouldn't it?

[Bruno Chareyre (bruno-chareyre)]

So. I tried a fresh 12.04 in chroot. Followed the documentation strictly to install prerequisites, then compiled. Without the ppa and without metis.
I am a bit disappointed: nothing happens. Compiled normally, and runs the fluid-coupling example script without problems (just extremely slow, as expected without metis).
So what people do to get in troubles is still not clear. Could it be that some of the libs in the ppa are the source of problems? It would be surprising.

I actually got problems when I forgot to replace qgl by qgl-qt4. This is the only critical point, and it is explained in the doc.
I'm closing the bug. Re-open with detailed explanations if you still have problems.

[Klaus Thoeni (klaus.thoeni)]

Hi Bruno,

the only library of you list I have installed at the moment is:
libsuitesparse-dev 1:3.4.0-2ubuntu3

Not sure why openblas is giving trouples on my machines. Just to verify, my Kubuntu version is 12.04.3 LTS. Are you using the same? Here the python verison installed on my machines:
python 2.7.3-0ubuntu2.2
python-numpy 1:1.6.1-6ubuntu1

Well, if I am the nly one having this problem we can close the bug. I don't need this feature at the moment and I am alread looking forward to the 14.04 LTS

Cheers
Klaus

[Bruno Chareyre (bruno-chareyre)]

@Klaus
If you don't have them installed at all it means you did not read the install manual.
How is it supposed to work? :)

[Klaus Thoeni (klaus.thoeni)]

@Bruno
Well I copy pasted the sudo apt-get install from the instructions. But this did't work in my case. I got the cmake error I showed above. Nervertheless, un-installing libopenblas-base solved the problem for me. That's whay it's not installed ;-)

[Bruno Chareyre (bruno-chareyre)]

I checked version numbers Klaus, they are the same.
It seems we will never know what exactly the problem was.

Bruno