[Paraview] how to build the paraview superbuild with mesa on a cluster (where user is not a root user)
Patrick Bégou
Patrick.Begou at legi.grenoble-inp.fr
Sun Jul 2 08:03:20 EDT 2017
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/software/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/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 <mailto: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
> <https://gitlab.kitware.com/paraview/paraview-superbuild.git>
> Cloning into 'paraview-superbuild'...
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://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
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://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
> <http://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
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> Submodule 'superbuild'
> (https://gitlab.kitware.com/paraview/common-superbuild.git
> <https://gitlab.kitware.com/paraview/common-superbuild.git>)
> registered for path 'superbuild'
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> Cloning into 'superbuild'...
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://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
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://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
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> Submodule path 'superbuild': checked out
> '8f357bb5bf35419c210b3f9e0adbc9df08f565f2'
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission denied
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://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
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>': Permission
> denied
>
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>':
> Permission denied
>
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://pdc.kth.se/home/k/kriezh/.gitconfig>':
> Permission denied
>
> warning: unable to access
> '/afs/pdc.kth.se/home/k/kriezh/.gitconfig
> <http://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
> <mailto:cory.quammen at kitware.com>> wrote:
>
> On Wed, Jun 28, 2017 at 1:14 PM, Ezhilmathi Krishnasamy
> <ezhkr601 at student.liu.se <mailto: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/
> <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 <http://www.kitware.com>
> >
> > Visit other Kitware open-source projects at
> > http://www.kitware.com/opensource/opensource.html
> <http://www.kitware.com/opensource/opensource.html>
> >
> > Please keep messages on-topic and check the ParaView Wiki at:
> > http://paraview.org/Wiki/ParaView
> <http://paraview.org/Wiki/ParaView>
> >
> > Search the list archives at:
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> >
> > Follow this link to subscribe/unsubscribe:
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> <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:
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