[Paraview] how to build the paraview superbuild with mesa on a cluster (where user is not a root user)

Ezhilmathi Krishnasamy ezhkr601 at student.liu.se
Sun Jul 2 11:56:34 EDT 2017 

Hi,

I am still having some problem with enabling the
build shared libs. I am trying to install it on a Cray machine.
I have already locally installed cmake and anaconda on their latest version.

I am attaching here the image.
Could any one tell me how to fix this issue

Kind regards,
Mathi

On 2 July 2017 at 14:54, Ezhilmathi Krishnasamy <ezhkr601 at student.liu.se>
wrote:

> Hi,
>
> I have almost build it, but getting this error:
>
>  CMake Warning (dev) at /pdc/vol/anaconda/4.3/py36/lib/cmake/Qt5Core/Qt5CoreConfig.cmake:115
> (add_library):
>    ADD_LIBRARY called with SHARED option but the target platform does not
>    support dynamic linking.  Building a STATIC library instead.  This may
> lead
>    to problems.
>  Call Stack (most recent call first):
>    /pdc/vol/anaconda/4.3/py36/lib/cmake/Qt5/Qt5Config.cmake:26
> (find_package)
>    superbuild/projects/qt5.system.cmake:1 (find_package)
>    superbuild/cmake/SuperbuildMacros.cmake:640 (include)
>    superbuild/CMakeLists.txt:115 (superbuild_process_dependencies)
>  This warning is for project developers.  Use -Wno-dev to suppress it.
>
>
>
> On 2 July 2017 at 14:17, Ezhilmathi Krishnasamy <ezhkr601 at student.liu.se>
> wrote:
>
>> Thanks!
>>
>> Now it shows this kind of error
>>
>> /cfs/klemming/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD/paraview-superbuild>
>> git fetch origin
>> /cfs/klemming/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD/paraview-superbuild>
>> git checkout v5.4.0
>> HEAD is now at 7c510fe... Update to 5.4.0
>> /cfs/klemming/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD/paraview-superbuild>
>> git submodule update
>> /cfs/klemming/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD/paraview-superbuild>
>> cd ..
>> /cfs/klemming/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD> cd ..
>> /cfs/klemming/nobackup/k/kriezh> cd build/
>> /cfs/klemming/nobackup/k/kriezh/build> ccmake
>> ../PARAVIEW_SUPER_BUILD/paraview-superbuild/
>>
>>
>>  CMake Error at superbuild/cmake/SuperbuildMacros.cmake:289 (message):
>>    The build tree appears to be inside of the git repository located at
>>    /cfs/klemming/nobackup/k/kriezh.  This interferes with the way the
>>    superbuild applies patches to projects and is not supported.  Please
>>    relocate the build tree to a directory which is not under a git
>> repository.
>>  Call Stack (most recent call first):
>>    superbuild/projects/bzip2.cmake:7 (superbuild_apply_patch)
>>    superbuild/cmake/SuperbuildMacros.cmake:477 (include)
>>    superbuild/CMakeLists.txt:113 (_superbuild_discover_projects)
>>
>>
>>
>>
>> On 2 July 2017 at 14:03, Patrick Bégou <Patrick.Begou at legi.grenoble-i
>> np.fr> wrote:
>>
>>> Like you, I got this error some months ago when trying to build paraview
>>> superbuild:
>>>
>>> *error: unknown option `is-ancestor'*
>>>
>>> It was my git version wich was too old. May be try to compile a more up
>>> to date version of git in your home and set the path to access it.
>>>
>>> I have installed git from https://www.kernel.org/pub/sof
>>> tware/scm/git/git-2.12.2.tar.xz
>>>
>>> Patrick
>>>
>>> Ezhilmathi Krishnasamy a écrit :
>>>
>>> Hi,
>>>
>>> I have followed these instructions. I am trying to install it where I am
>>> not a root user.
>>> Can someone help to fix this issue.
>>>
>>>  git clone --recursive https://gitlab.kitware.com/par
>>> aview/paraview-superbuild.git
>>>  cd paraview-superbuild
>>>  git fetch origin # ensure you have the latest state from the main repo
>>>  git checkout v5.2.0 # replace `v5.2.0` with tag name of your choice
>>>  git submodule update
>>>
>>>  cd ..
>>>  mkdir build
>>>  cd build
>>>  ccmake ../paraview-superbuild
>>>
>>> Kind regards,
>>> Mathi
>>>
>>>
>>> On 30 June 2017 at 18:54, Ezhilmathi Krishnasamy <
>>> ezhkr601 at student.liu.se> wrote:
>>>
>>>> Hi Thanks!
>>>>
>>>> When I try to install Paraview,  I am getting the following error.
>>>> Could some one please tell me how to fix this issue.
>>>> I am trying to install the Paraview on a super computer to use it
>>>> for remote rendering without using the GUI,  like with mesa support.
>>>>
>>>> kriezh at beskow-login2:/cfs/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD> git
>>>> clone --recursive https://gitlab.kitware.com/par
>>>> aview/paraview-superbuild.git
>>>> Cloning into 'paraview-superbuild'...
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> remote: Counting objects: 6723, done.
>>>> remote: Compressing objects: 100% (2459/2459), done.
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> remote: Total 6723 (delta 4451), reused 6342 (delta 4201)
>>>> Receiving objects: 100% (6723/6723), 2.05 MiB | 741 KiB/s, done.
>>>> Resolving deltas: 100% (4451/4451), done.
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> Checking out files: 100% (196/196), done.
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> Submodule 'superbuild' (https://gitlab.kitware.com/pa
>>>> raview/common-superbuild.git) registered for path 'superbuild'
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> Cloning into 'superbuild'...
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> remote: Counting objects: 6752, done.
>>>> remote: Compressing objects: 100% (2235/2235), done.
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> remote: Total 6752 (delta 4505), reused 6574 (delta 4395)
>>>> Receiving objects: 100% (6752/6752), 1.59 MiB | 592 KiB/s, done.
>>>> Resolving deltas: 100% (4505/4505), done.
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> Submodule path 'superbuild': checked out '8f357bb5bf35419c210b3f9e0adbc
>>>> 9df08f565f2'
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>> warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission denied
>>>>
>>>>
>>>> kriezh at beskow-login2:/cfs/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD/paraview-superbuild>
>>>> cmake .
>>>> -- The C compiler identification is Intel 14.0.4.20140805
>>>> -- The CXX compiler identification is Intel 14.0.4.20140805
>>>> -- Cray Programming Environment 2.2.1 C
>>>> -- Check for working C compiler: /opt/cray/craype/2.2.1/bin/cc
>>>> -- Check for working C compiler: /opt/cray/craype/2.2.1/bin/cc -- works
>>>> -- Detecting C compiler ABI info
>>>> -- Detecting C compiler ABI info - done
>>>> -- Detecting C compile features
>>>> -- Detecting C compile features - done
>>>> -- Cray Programming Environment 2.2.1 CXX
>>>> -- Check for working CXX compiler: /opt/cray/craype/2.2.1/bin/CC
>>>> -- Check for working CXX compiler: /opt/cray/craype/2.2.1/bin/CC --
>>>> works
>>>> -- Detecting CXX compiler ABI info
>>>> -- Detecting CXX compiler ABI info - done
>>>> -- Detecting CXX compile features
>>>> -- Detecting CXX compile features - done
>>>> CMake Warning at superbuild/cmake/SuperbuildUtils.cmake:242 (message):
>>>>   Failed to determine if the common superbuild is an old checkout.  The
>>>>   common superbuild may be out of date, but cannot be verified.:
>>>> warning:
>>>>   unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>> Permission
>>>>   denied
>>>>
>>>>   warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>>   Permission denied
>>>>
>>>>   warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>>   Permission denied
>>>>
>>>>   warning: unable to access '/afs/pdc.kth.se/home/k/kriezh/.gitconfig':
>>>>   Permission denied
>>>>
>>>>   error: unknown option `is-ancestor'
>>>>
>>>>   usage: git merge-base [-a|--all] <commit> <commit>...
>>>>
>>>>      or: git merge-base [-a|--all] --octopus <commit>...
>>>>      or: git merge-base --independent <commit>...
>>>>
>>>>
>>>>
>>>>       -a, --all             output all common ancestors
>>>>       --octopus             find ancestors for a single n-way merge
>>>>       --independent         list revs not reachable from others
>>>> Call Stack (most recent call first):
>>>>   superbuild/CMakeLists.txt:28 (_superbuild_check_up_to_date)
>>>>
>>>>
>>>> -- Check size of void*
>>>> -- Check size of void* - done
>>>> -- Found Git: /usr/bin/git (found version "1.7.12.4")
>>>> -- Determined source version for paraview: 5.4.0
>>>> CMake Error at superbuild/cmake/SuperbuildMacros.cmake:289 (message):
>>>>   The build tree appears to be inside of the git repository located at
>>>>   /cfs/klemming/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD/paravie
>>>> w-superbuild.
>>>>   This interferes with the way the superbuild applies patches to
>>>> projects and
>>>>   is not supported.  Please relocate the build tree to a directory
>>>> which is
>>>>   not under a git repository.
>>>> Call Stack (most recent call first):
>>>>   superbuild/projects/bzip2.cmake:7 (superbuild_apply_patch)
>>>>   superbuild/cmake/SuperbuildMacros.cmake:477 (include)
>>>>   superbuild/CMakeLists.txt:113 (_superbuild_discover_projects)
>>>>
>>>>
>>>> -- Configuring incomplete, errors occurred!
>>>> See also "/cfs/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD/paraview-superb
>>>> uild/CMakeFiles/CMakeOutput.log".
>>>>
>>>>
>>>> Kind regards,
>>>> Mathi
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On 30 June 2017 at 04:13, Cory Quammen <cory.quammen at kitware.com>
>>>> wrote:
>>>>
>>>>> On Wed, Jun 28, 2017 at 1:14 PM, Ezhilmathi Krishnasamy
>>>>> <ezhkr601 at student.liu.se> wrote:
>>>>> > Hi,
>>>>> >
>>>>> > Can anyone please give me some instructions how to Paraview Superbuid
>>>>> > to install and use them with out using the GUI (using the python
>>>>> script to
>>>>> > render the images on the cluster or super computer).
>>>>> >
>>>>> > I see there are some instructions in here:
>>>>> > https://gitlab.kitware.com/paraview/paraview-superbuild/
>>>>> >
>>>>> > But I could not find any build instructions.
>>>>>
>>>>> Take a look again, that page includes the README.md file contents
>>>>> which includes build instructions.
>>>>>
>>>>> To build without the GUI, you should just need to set the options
>>>>> ENABLE_qt4 and ENABLE_qt5 to OFF. To build with Python, set
>>>>> ENABLE_python to ON.
>>>>>
>>>>> Best regards,
>>>>> Cory
>>>>>
>>>>> >
>>>>> > Kind regards,
>>>>> > Mathi
>>>>> >
>>>>> > _______________________________________________
>>>>> > Powered by www.kitware.com
>>>>> >
>>>>> > Visit other Kitware open-source projects at
>>>>> > http://www.kitware.com/opensource/opensource.html
>>>>> >
>>>>> > Please keep messages on-topic and check the ParaView Wiki at:
>>>>> > http://paraview.org/Wiki/ParaView
>>>>> >
>>>>> > Search the list archives at: http://markmail.org/search/?q=ParaView
>>>>> >
>>>>> > Follow this link to subscribe/unsubscribe:
>>>>> > http://public.kitware.com/mailman/listinfo/paraview
>>>>> >
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Cory Quammen
>>>>> Staff R&D Engineer
>>>>> Kitware, Inc.
>>>>>
>>>>
>>>>
>>>
>>>
>>> _______________________________________________
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
>>>
>>> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
>>>
>>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>>
>>> Follow this link to subscribe/unsubscribe:http://public.kitware.com/mailman/listinfo/paraview
>>>
>>>
>>>
>>
>
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