installing fenics via dorsal in opensuse

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Hi!

On 07/07/2011 01:41 PM, B. Emek Abali wrote:
> New question #164054 on DOLFIN:
> https://answers.launchpad.net/dolfin/+question/164054
>
> Dear all,
>
> I need to install fenics into one of our servers running with opensuse 10

Which opensuse 10 version? There was a 10.2 and 10.3 version. Or did you
mean SUSE Linux 10 ?

>
> After some dependency problems, I am stuck with that problem:
>
> ------------------------------------------------------------------------------------------
> ...
> Processing enabled package: PyTrilinos
> -- Found PythonInterp: /usr/bin/python2.5 (Required is at least version "2.2")
> CMake Error at packages/PyTrilinos/cmake/FindNumPy.cmake:75 (MESSAGE):
> Required NumPy python module not found
> Call Stack (most recent call first):
> packages/PyTrilinos/CMakeLists.txt:148 (FIND_PACKAGE)
>
>
> CMake Error at packages/PyTrilinos/cmake/FindSWIG.cmake:68 (MESSAGE):
> SWIG was not found. Please specify Swig executable location
> Call Stack (most recent call first):
> packages/PyTrilinos/CMakeLists.txt:151 (FIND_PACKAGE)
>
>
> -- Configuring incomplete, errors occurred!
> ------------------------------------------------------------------------------------------
>
> Question: Should first the numpy installed (in standard repositories exists no package under the name numpy) ?

Since you are facing a rather old version of (open)suse and the build
service OBS does not support these ones
according to
http://software.opensuse.org/114/en ,

it will be difficult to find rpms (I guess). Have you tried to install
numpy directly, bypassing the package system? Last time I had to do that
it work flawlessly for me.

HTH
Andre

>
> You received this question notification because you are a member of
> DOLFIN Team, which is an answer contact for DOLFIN.

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sorry for the lack of info:

Linux version 2.6.25.20-0.7-default
(gcc version 4.3.1 20080507 (prerelease) [gcc-4_3-branch revision 135036] (SUSE Linux) )

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On 07/07/2011 04:06 PM, B. Emek Abali wrote:
> Question #164054 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/164054
>
> Status: Answered => Open
>
> B. Emek Abali is still having a problem:
> sorry for the lack of info:
>
> Linux version 2.6.25.20-0.7-default
> (gcc version 4.3.1 20080507 (prerelease) [gcc-4_3-branch revision 135036] (SUSE Linux) )
>

Since rpm packages are difficult to get for that old suse variant I
would try to install the needed packages manually or with dorsal. Have
you already tried to use dorsal? If not, please have a look at it:

https://launchpad.net/dorsal

and its documentation describing how to use it to install FEniCS.
You could provide your own platform file including the packages you
need, for instance with the following content (depending on the packages
you want / or can principally install onyour system,
not completely sure about the PETSC_ARCH and SCOTCH_ARCH variables):

default PETSC_ARCH=linux-gnu-cxx-opt
default SCOTCH_ARCH=pc_linux2

# Define the packages this platform needs
PACKAGES=(
swig
numpy
parmetis
trilinos
petsc
slepc
armadillo
# swiginac
mtl
cgal
scientificpython
fiat
# ferari
ufc
ufl
ffc
# syfi
viper
instant
dolfin
)

Save this into a suse10.platform file and execute
./dorsal.sh suse10.platform
from with the dorsal folder.
No promise that it will work, but with some modification you might get
it to work (don't hesitate to ask!) There were a recent post in the
dorsal ml about successful installation on a rather ancient linux
(CentOS 5.5)

God luck,
Andre

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Thanks a lot, I did a huge step, but PETSC exited somehow:

Install the project...
-- Install configuration: "RELEASE"
make: Leaving directory `/root/Work/FEniCS/src/trilinos-10.6.2-Source/dorsal_build_dir'
Fetching petsc-3.1-p7
--2011-07-07 17:53:47-- http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.1-p7.tar.gz
Resolving ftp.mcs.anl.gov... 140.221.6.23
Connecting to ftp.mcs.anl.gov|140.221.6.23|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 15458474 (15M) [application/x-gzip]
Saving to: `petsc-3.1-p7.tar.gz'

100%[======================================>] 15,458,474 5.59M/s in 2.6s

2011-07-07 17:53:50 (5.59 MB/s) - `petsc-3.1-p7.tar.gz' saved [15458474/15458474]

Unpacking petsc-3.1-p7
Building petsc-3.1-p7
===============================================================================
             Configuring PETSc to compile on your system
===============================================================================
*******************************************************************************
                ERROR in COMMAND LINE ARGUMENT to config/configure.py
-------------------------------------------------------------------------------
Nonexistent directory: /root/Work/FEniCS/include/trilinos for key with-ml-include
*******************************************************************************

after adding the directory:

Invalid library: /root/Work/FEniCS/lib/libml.so for key with-ml-lib

what is ?
with-ml

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On 07/07/2011 06:06 PM, B. Emek Abali wrote:
> Question #164054 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/164054
>
> Status: Answered => Open
>
> B. Emek Abali is still having a problem:
> Thanks a lot, I did a huge step, but PETSC exited somehow:
>
>
> Install the project...
> -- Install configuration: "RELEASE"
> make: Leaving directory `/root/Work/FEniCS/src/trilinos-10.6.2-Source/dorsal_build_dir'
> Fetching petsc-3.1-p7
> --2011-07-07 17:53:47-- http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.1-p7.tar.gz
> Resolving ftp.mcs.anl.gov... 140.221.6.23
> Connecting to ftp.mcs.anl.gov|140.221.6.23|:80... connected.
> HTTP request sent, awaiting response... 200 OK
> Length: 15458474 (15M) [application/x-gzip]
> Saving to: `petsc-3.1-p7.tar.gz'
>
> 100%[======================================>] 15,458,474 5.59M/s in
> 2.6s
>
> 2011-07-07 17:53:50 (5.59 MB/s) - `petsc-3.1-p7.tar.gz' saved
> [15458474/15458474]
>
> Unpacking petsc-3.1-p7
> Building petsc-3.1-p7
> ===============================================================================
> Configuring PETSc to compile on your system
> ===============================================================================
> *******************************************************************************
> ERROR in COMMAND LINE ARGUMENT to config/configure.py
> -------------------------------------------------------------------------------
> Nonexistent directory: /root/Work/FEniCS/include/trilinos for key with-ml-include
> *******************************************************************************
>
>
> after adding the directory:
>
> Invalid library: /root/Work/FEniCS/lib/libml.so for key with-ml-lib
>
> what is ?
> with-ml

That means that petsc is configured to use the multilevel preconditioner
from the trilinos project, IIRC.
You have probably already check the the existence of the folder in
question? If not could you check the mentioned nonexistent directory and
the invalid library?
Did you see any suspicious output while compiling and installing
trilinos via dorsal?

In any case the complete dorsal terminal output might be interesting,
you can paste it e.g. at pastebin.com or at http://susepaste.org/
(and your platform file in case you used a modified version of what I
suggested, the order of packages is important, and trilinos should come
before petsc)

Cheers,
- --
Andre

>
> You received this question notification because you are a member of
> DOLFIN Team, which is an answer contact for DOLFIN.

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I added the directory manually than in a later step it could not find the library, the lib is really not there, platform is in the order as you proposed:

PACKAGES=(
swig
numpy
parmetis
trilinos
petsc
slepc
armadillo
# swiginac
mtl
scientificpython
fiat
# ferari
ufc
ufl
ffc
# syfi
viper
instant
dolfin
)

-----------------------------------
the terminal output is http://pastebin.com/YGpTta1T

there are some NOT AVAILABLE warnings to the lapack-mtl and atlas packages, which is probably the failure of missing library, what do you think?

On 07/08/2011 12:21 PM, B. Emek Abali wrote:
> Question #164054 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/164054
>
> Status: Answered => Open
>
> B. Emek Abali is still having a problem:
> I added the directory manually than in a later step it could not find
> the library, the lib is really not there, platform is in the order as
> you proposed:
>
> PACKAGES=(
> swig
> numpy
> parmetis
> trilinos
> petsc
> slepc
> armadillo
> # swiginac
> mtl
> scientificpython
> fiat
> # ferari
> ufc
> ufl
> ffc
> # syfi
> viper
> instant
> dolfin
> )
>
> -----------------------------------
> the terminal output is http://pastebin.com/YGpTta1T
>
> there are some NOT AVAILABLE warnings to the lapack-mtl and atlas
> packages, which is probably the failure of missing library, what do you
> think?

At a first quick look that is the reasons since Trilinos configuring end
up with the message:

WARNING: There were no packages configured so no libraries or
tests/examples will be built.

But that did not issue an error message, so dorsal kept running and
assumed ML to be in place. There are also some other libs missing, for
example the atlas lib...

However, to reduce the complexity of the compiling process and to
isolated error sources I would suggest that you start of with a
simplified version of the platform file to get a basic installation up
and running.
Swig, numpy, parmetis seem to be fine, but skip the trilinos package
(comment line with #) then petsc will not rely on that. To be absolutely
sure about that, wipe out the petsc folder (just leave the downloaded
tar.gz file there), since I have no clue about what petsc config scripts
might cache during the configure process.

Just to mentally prepare :) ourselves for some of the upcoming later
build failures (there will definitely a few more, I bet) : Is a recent
vtk and python-vtk version installed on your system (which one)?

Installing such a project as FEniCS with dependencies on other large
project on a older system which does not really feed us, is quite a bit
of a hassle, but I hope we get you through :)

HTH,
Andre

thanks a lot for helping me through :)

first,l commenting trilinos helped but introduced another one: http://pastebin.com/kqX5t1vT
second, if trilinos is commented, may I use the conjugated gradient iterative solver?

I run first, as commented in opensuse platform
# sudo zypper install -C lsb bzr subversion libxml2-devel gcc gcc-c++ \
# openmpi-devel python-devel python-numpy python-numpy-devel swig \
# wget boost-devel vtk-python liblapack3 libblas3 liblapack3 \
# mpfr-devel suitesparse-common-devel gmp-devel cmake umfpack-devel \
# libumfpack5 CGAL-devel scotch-devel libatlas3-devel flex

so actually no ctk or python-vtk is installed, just get, thus:

... # rpm -qa | grep vtk
... # rpm -qa | grep python
python-doc-2.5.1-75.1
python-kde3-3.16.0-124.1
python-2.5.2-26.6
python-xml-2.5.2-26.6
gimp-plugins-python-2.4.5-41.2
python-cairo-1.4.12-19.1
libvirt-python-0.4.0-59.4
dbus-1-python-0.82.4-49.1
python-devel-2.5.2-26.6
python-numeric-24.2-162.1
python-compizconfig-0.7.4-28.1
python-qt4-4.4.2-6.1
python-opengl-2.0.1.09-224.1
python-gobject2-2.14.1-15.1
libxml2-python-2.6.32-14.1
python-qscintilla-1.73-103.1
python-tk-2.5.2-26.6
python-gtk-2.12.1-18.1
python-sip-4.7.6-5.1
python-gtksourceview-2.2.0-15.1
python-cairo-devel-1.4.12-19.1
python-idle-2.5.2-26.6
python-gobject2-devel-2.14.1-15.1
python-qt-3.17.4-49.1
python-gtk-devel-2.12.1-18.1

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Hi!

Sorry for the late reply, but I have been without internet since Saturday.

On 07/08/2011 06:31 PM, B. Emek Abali wrote:
> Question #164054 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/164054
>
> Status: Answered => Open
>
> B. Emek Abali is still having a problem:
> thanks a lot for helping me through :)
>
> first,l commenting trilinos helped but introduced another one: http://pastebin.com/kqX5t1vT

Which one introduced you? It is a little hard to see from the output.
Did you change the suse11.platform file?

> second, if trilinos is commented, may I use the conjugated gradient iterative solver?

Yes, PETSC comes with one.

>
> I run first, as commented in opensuse platform
> # sudo zypper install -C lsb bzr subversion libxml2-devel gcc gcc-c++ \
> # openmpi-devel python-devel python-numpy python-numpy-devel swig \
> # wget boost-devel vtk-python liblapack3 libblas3 liblapack3 \
> # mpfr-devel suitesparse-common-devel gmp-devel cmake umfpack-devel \
> # libumfpack5 CGAL-devel scotch-devel libatlas3-devel flex

These instruction are tailored for newer opensuse version and might not
apply in your case since
1. some of the instruction are outdated, e.g when it comes to swig and
newer dolfin version,
2. The instructions require adding some additional repos, which do
probably do not package the needed software for your suse version.
But could you specify exactly the suse version in question?
(Try a
cat /etc/issue
in a terminal)
That helps to narrow down which packages are available and which one you
have to compile yourself.

>
> so actually no ctk or python-vtk is installed, just get, thus:
>
> ... # rpm -qa | grep vtk
> ... # rpm -qa | grep python
> python-doc-2.5.1-75.1
> python-kde3-3.16.0-124.1
> python-2.5.2-26.6
> python-xml-2.5.2-26.6
> gimp-plugins-python-2.4.5-41.2
> python-cairo-1.4.12-19.1
> libvirt-python-0.4.0-59.4
> dbus-1-python-0.82.4-49.1
> python-devel-2.5.2-26.6
> python-numeric-24.2-162.1
> python-compizconfig-0.7.4-28.1
> python-qt4-4.4.2-6.1
> python-opengl-2.0.1.09-224.1
> python-gobject2-2.14.1-15.1
> libxml2-python-2.6.32-14.1
> python-qscintilla-1.73-103.1
> python-tk-2.5.2-26.6
> python-gtk-2.12.1-18.1
> python-sip-4.7.6-5.1
> python-gtksourceview-2.2.0-15.1
> python-cairo-devel-1.4.12-19.1
> python-idle-2.5.2-26.6
> python-gobject2-devel-2.14.1-15.1
> python-qt-3.17.4-49.1
> python-gtk-devel-2.12.1-18.1
>

Then we have to add vtk as well, but first we should come as far as
possible with your current platform file.

Regarding your dorsal output: Have your checked whether parmetis
correctly installed, since the message

- --with-parmetis-dir=/root/Work/FEniCS did not work

did indicate that something went wrong.
Your should have a include/parmetis.h and a lib/libparmetis.a
file in the mentioned --with-parmetis-dir directory. And please check
the configure.log mentioned in the output to get an idea why petsc
failed. Your will find the log file in your petsc directory.

HTH
- --
Andre

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hi, thanks for the reply,

 cat /etc/issue
Welcome to openSUSE 11.0 (X86-64) - Kernel \r (\l).

after commenting trilinos out in the suse11.3.platform it does not compile with errrors.

configure.log indicates that :
Possible ERROR while running linker: /root/Work/FEniCS/lib/libparmetis.a(initpart.o): In function `Mc_InitPartition_RB__':
initpart.c:(.text+0x7a7): undefined reference to `hpmp_int'
initpart.c:(.text+0x7be): undefined reference to `hpmp_sum'
initpart.c:(.text+0x8b1): undefined reference to `hpmp_max'
initpart.c:(.text+0x8da): undefined reference to `hpmp_min'
initpart.c:(.text+0x8e9): undefined reference to `hpmp_float'
initpart.c:(.text+0x987): undefined reference to `hpmp_minloc'
initpart.c:(.text+0x996): undefined reference to `hpmp_float_int'

many times and gets out with:

  File "./configure", line 257, in petsc_configure
    framework.configure(out = sys.stdout)
  File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/framework.py", line 944, in configure
    child.configure()
  File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/package.py", line 456, in configure
    self.executeTest(self.configureLibrary)
  File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/base.py", line 97, in executeTest
    ret = apply(test, args,kargs)
  File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/package.py", line 395, in configureLibrary
    for location, directory, lib, incl in self.generateGuesses():
  File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/package.py", line 220, in generateGuesses
    raise RuntimeError('--with-'+self.package+'-dir='+self.framework.argDB['with-'+self.package+'-dir']+' did not work')

by the way
/root/Work/FEniCS contains the files include/parmetis.h and lib/libparmetis.a

It is not a good idea to install as root. Install it as a regular user.

More importantly, if you have root access you probably should upgrade the system to a more recent suse.

Harish

On Jul 13, 2011, at 4:35 PM, "B. Emek Abali" <email address hidden> wrote:

> Question #164054 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/164054
>
> Status: Answered => Open
>
> B. Emek Abali is still having a problem:
> hi, thanks for the reply,
>
> cat /etc/issue
> Welcome to openSUSE 11.0 (X86-64) - Kernel \r (\l).
>
> after commenting trilinos out in the suse11.3.platform it does not
> compile with errrors.
>
>
> configure.log indicates that :
> Possible ERROR while running linker: /root/Work/FEniCS/lib/libparmetis.a(initpart.o): In function `Mc_InitPartition_RB__':
> initpart.c:(.text+0x7a7): undefined reference to `hpmp_int'
> initpart.c:(.text+0x7be): undefined reference to `hpmp_sum'
> initpart.c:(.text+0x8b1): undefined reference to `hpmp_max'
> initpart.c:(.text+0x8da): undefined reference to `hpmp_min'
> initpart.c:(.text+0x8e9): undefined reference to `hpmp_float'
> initpart.c:(.text+0x987): undefined reference to `hpmp_minloc'
> initpart.c:(.text+0x996): undefined reference to `hpmp_float_int'
>
> many times and gets out with:
>
> File "./configure", line 257, in petsc_configure
> framework.configure(out = sys.stdout)
> File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/framework.py", line 944, in configure
> child.configure()
> File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/package.py", line 456, in configure
> self.executeTest(self.configureLibrary)
> File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/base.py", line 97, in executeTest
> ret = apply(test, args,kargs)
> File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/package.py", line 395, in configureLibrary
> for location, directory, lib, incl in self.generateGuesses():
> File "/root/Work/FEniCS/src/petsc-3.1-p7/config/BuildSystem/config/package.py", line 220, in generateGuesses
> raise RuntimeError('--with-'+self.package+'-dir='+self.framework.argDB['with-'+self.package+'-dir']+' did not work')
>
>
> by the way
> /root/Work/FEniCS contains the files include/parmetis.h and lib/libparmetis.a
>
> --
> You received this question notification because you are a member of
> DOLFIN Team, which is an answer contact for DOLFIN.

hi Harish, thanks for the suggestions, recent suse does not boot from xfs file system, which we cannot change, therefore the system will not be upgraded.

Is installing w/o root permissions the more appropriate way?

On 7/14/11 10:55 AM, B. Emek Abali wrote:
> Question #164054 on DOLFIN changed:
> https://answers.launchpad.net/dolfin/+question/164054
>
> B. Emek Abali posted a new comment:
> hi Harish, thanks for the suggestions, recent suse does not boot from
> xfs file system, which we cannot change, therefore the system will not
> be upgraded.
>
> Is installing w/o root permissions the more appropriate way?
>

In general, yes. This is only so that you (or dorsal) does not
accidentally mess anything up in the rest of the system.

Harish

Thanks Andre Massing, that solved my question.