[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 07:37:37 EDT 2017
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/paraview/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/paraview/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/
> paraview/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 '8f357bb5bf35419c210b3f9e0adbc9
> df08f565f2'
> 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/
> paraview-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-
> superbuild/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.
>>
>
>
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I have followed these instrunctions
git clone --recursive https://gitlab.kitware.com/paraview/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
cmmake ../paraview-superbuild
after this I am getting this error.
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.: 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)
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. 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)
Page 1 of 1
BUILD_SHARED_LIBS ON
CMAKE_INSTALL_PREFIX /cfs/klemming/nobackup/k/kriezh/PARAVIEW_SUPER_BUILD
ENABLE_boost OFF
ENABLE_bzip2 OFF
ENABLE_cxx11 OFF
ENABLE_paraview OFF
ENABLE_paraviewpluginsexternal ON
ENABLE_python ON
PARAVIEW_BUILD_WEB_DOCUMENTATI OFF
PARAVIEW_DEFAULT_SYSTEM_GL ON
PARAVIEW_FREEZE_PYTHON OFF
PARAVIEW_RENDERING_BACKEND OpenGL2
SUPERBUILD_OFFLINE_BUILD ON
paraview_PLUGINS_EXTERNAL
paraview_SOURCE_SELECTION 5.4.0
vtkm_SOURCE_SELECTION git-stable
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