[vtkusers] Issuings running make in my VTK-build directory
Cory Quammen
cory.quammen at kitware.com
Wed Apr 12 14:11:27 EDT 2017
Andrew,
Typically, servers like the one on which I assume you are compiling
have two types of storage available:
1). A network file system that you can access on more than one server
and perhaps a personal computer. These typically hold a home directory
for you and may be backed up.
2). Local disks on the server. It is faster to access these disks
because they are local. As a result, at a number of computing centers
it is often possible to use these disks to do things like compile
source code. These disks are typically not backed up - think of them
as "scratch" paper where you do somewhat temporary work.
Is it necessary to compile VTK on the school server? If so, I suggest
asking your instructor who has hopefully done that once already and
knows how to resolve the issue you are facing.
HTH,
Cory
On Wed, Apr 12, 2017 at 1:57 PM, Andrew Lam <werdna.mal222 at gmail.com> wrote:
> Cory,
>
> I'm sorry I don't know what you mean by local scratch space.
>
> Thanks,
>
> Andrew
>
> On Wed, Apr 12, 2017 at 10:55 AM, Cory Quammen <cory.quammen at kitware.com>
> wrote:
>>
>> > I'm currently building on my school's servers.
>>
>> Is there local scratch space on which you can build software on that
>> server? My guess is you are building in a home directory that is on an
>> AFS or NFS or some other network file system, and that is causing you
>> problems.
>>
>> Thanks,
>> Cory
>>
>> > Thanks,
>> > Andrew
>> >
>> >
>> > On Wed, Apr 12, 2017 at 10:50 AM, Andrew Lam <werdna.mal222 at gmail.com>
>> > wrote:
>> >>
>> >> Cory,
>> >>
>> >> I'm currently building on my school's servers.
>> >>
>> >> Thanks,
>> >> Andrew
>> >>
>> >> On Wed, Apr 12, 2017 at 10:47 AM, Cory Quammen
>> >> <cory.quammen at kitware.com>
>> >> wrote:
>> >>>
>> >>> Andrew,
>> >>>
>> >>> Are you building on a networked file system of some sort? I've run
>> >>> into issues long ago building software before when the file system and
>> >>> computer have different ideas of what time it is.
>> >>>
>> >>> - Cory
>> >>>
>> >>> On Wed, Apr 12, 2017 at 1:29 PM, Andrew Lam <werdna.mal222 at gmail.com>
>> >>> wrote:
>> >>> > Hi Andy,
>> >>> >
>> >>> > It's still not working. I made a fresh build directory and ran
>> >>> > through
>> >>> > the
>> >>> > motions again. It still has the same issue. I've attached my
>> >>> > CMakeCache.txt
>> >>> > file from my build directory. Please let me know if you see anything
>> >>> > or
>> >>> > if
>> >>> > there is any other information that you might think would help.
>> >>> >
>> >>> > Thanks,
>> >>> > Andrew
>> >>> >
>> >>> > On Wed, Apr 12, 2017 at 8:43 AM, Andy Bauer <andy.bauer at kitware.com>
>> >>> > wrote:
>> >>> >>
>> >>> >> Hi Andrew,
>> >>> >>
>> >>> >> This should compile for you now. If it doesn't, please let us know
>> >>> >> and
>> >>> >> we
>> >>> >> can see how to get it working for you. If you do have problems I
>> >>> >> recommend
>> >>> >> attaching your CMakeCache.txt file from your build directory so
>> >>> >> it's
>> >>> >> easier
>> >>> >> for others to inspect what you did.
>> >>> >>
>> >>> >> Best,
>> >>> >> Andy
>> >>> >>
>> >>> >> On Wed, Apr 12, 2017 at 11:12 AM, Andrew Lam
>> >>> >> <werdna.mal222 at gmail.com>
>> >>> >> wrote:
>> >>> >>>
>> >>> >>> Ok Andy I can see it now thanks,
>> >>> >>>
>> >>> >>> my variables are set to
>> >>> >>>
>> >>> >>> Module_vtkParallelMPI4Py *OFF
>> >>> >>> PYTHON_EXECUTABLE */bin/python2
>> >>> >>> PYTHON_EXTRA_LIBS *
>> >>> >>> PYTHON_INCLUDE_DIR */usr/include/python2.7
>> >>> >>> PYTHON_LIBRARY *//lib64/libpython2.7.so
>> >>> >>> PYTHON_UTIL_LIBRARY */usr/lib64/libutil.so
>> >>> >>> VTK_ENABLE_VTKPYTHON *ON
>> >>> >>>
>> >>> >>> after I set VTK_WRAP_PYTHON CMake variable to ON
>> >>> >>>
>> >>> >>> it seems ok to me, but let me know if they're wrong.
>> >>> >>>
>> >>> >>> Thanks,
>> >>> >>> Andrew
>> >>> >>>
>> >>> >>> On Tue, Apr 11, 2017 at 3:30 PM, Andrew Lam
>> >>> >>> <werdna.mal222 at gmail.com>
>> >>> >>> wrote:
>> >>> >>>>
>> >>> >>>> Hi, my name is Andrew. I'm currently in a class that requires us
>> >>> >>>> to
>> >>> >>>> install VTK.
>> >>> >>>>
>> >>> >>>> I have an issue running make in my VTK-build directory. I get a
>> >>> >>>> bunch of
>> >>> >>>> clock skew issues that pop up that won't go away after calling
>> >>> >>>>
>> >>> >>>> $ touch *
>> >>> >>>>
>> >>> >>>> then it will print out
>> >>> >>>>
>> >>> >>>> make[2]: ***
>> >>> >>>> [Wrapping/Python/vtkAngularPeriodicDataArrayPython.cxx]
>> >>> >>>> Error 1
>> >>> >>>> make[1]: ***
>> >>> >>>> [Wrapping/Python/CMakeFiles/vtkCommonCorePythonD.dir/all]
>> >>> >>>> Error 2
>> >>> >>>>
>> >>> >>>> it will then run to about 32% and then end printing
>> >>> >>>>
>> >>> >>>> make: *** [all] Error 2
>> >>> >>>>
>> >>> >>>> I'm using python 2.7, VTK 7.1.1, cmake 3.7.2
>> >>> >>>> I'm also going to include the output of the make call. Please let
>> >>> >>>> me
>> >>> >>>> know if you have any suggestions or if you need any more
>> >>> >>>> information
>> >>> >>>> to
>> >>> >>>> understand the issue.
>> >>> >>>>
>> >>> >>>> [ 0%] Built target kwiml_test
>> >>> >>>> [ 0%] Built target vtksys
>> >>> >>>> [ 1%] Built target vtkWrappingTools
>> >>> >>>> [ 1%] Built target vtkalglib
>> >>> >>>> [ 1%] Built target vtkexpat
>> >>> >>>> [ 2%] Built target vtkzlib
>> >>> >>>> [ 2%] Built target vtkDICOMParser
>> >>> >>>> [ 2%] Built target vtkEncodeString
>> >>> >>>> [ 2%] Built target vtkjpeg
>> >>> >>>> [ 2%] Built target vtkHashSource
>> >>> >>>> [ 2%] Built target vtkglew
>> >>> >>>> [ 2%] Built target H5make_libsettings
>> >>> >>>> [ 2%] Built target H5detect
>> >>> >>>> [ 2%] Built target vtkWrapTcl
>> >>> >>>> [ 2%] Built target vtkParseJava
>> >>> >>>> [ 2%] Built target vtkWrapPython
>> >>> >>>> [ 2%] Built target vtkWrapPythonInit
>> >>> >>>> [ 2%] Built target vtkWrapTclInit
>> >>> >>>> [ 2%] Built target vtkWrapJava
>> >>> >>>> [ 2%] Built target vtkjsoncpp
>> >>> >>>> [ 2%] Built target verdict
>> >>> >>>> [ 2%] Built target vtksqlite
>> >>> >>>> [ 2%] Built target vtkoggtheora
>> >>> >>>> [ 2%] Built target vtkWrapHierarchy
>> >>> >>>> [ 4%] Built target vtkproj4
>> >>> >>>> [ 4%] Built target vtkfreetype
>> >>> >>>> [ 5%] Built target vtklibxml2
>> >>> >>>> [ 5%] Built target vtkpng
>> >>> >>>> [ 5%] Built target vtkmetaio
>> >>> >>>> [ 5%] Built target vtkgl2ps
>> >>> >>>> [ 5%] Built target vtktiff
>> >>> >>>> [ 20%] Built target vtkCommonCore
>> >>> >>>> [ 26%] Built target VTKData
>> >>> >>>> [ 28%] Built target vtkCommonSystem
>> >>> >>>> [ 29%] Built target vtkCommonMath
>> >>> >>>> [ 29%] Built target vtkhdf5
>> >>> >>>> [ 29%] Built target vtkWrappingPythonCore
>> >>> >>>> [ 29%] Built target vtkLocalExample
>> >>> >>>> [ 29%] Built target vtkCommonMisc
>> >>> >>>> [ 29%] Built target vtkCommonTransforms
>> >>> >>>> [ 29%] Built target vtkCommonSystemCxxTests
>> >>> >>>> [ 29%] Python Wrapping - generating vtkAbstractArrayPython.cxx
>> >>> >>>> [ 29%] Built target vtkhdf5_hl
>> >>> >>>> Usage: vtkWrapPython-7.1 [options] infile...
>> >>> >>>> --help print this help message
>> >>> >>>> --version print the VTK version
>> >>> >>>> -o <file> the output file
>> >>> >>>> -I <dir> add an include directory
>> >>> >>>> -D <macro[=def]> define a preprocessor macro
>> >>> >>>> -U <macro> undefine a preprocessor macro
>> >>> >>>> @<file> read arguments from a file
>> >>> >>>> --hints <file> the hints file to use
>> >>> >>>> --types <file> the type hierarchy file to use
>> >>> >>>> --concrete force concrete class (ignored, deprecated)
>> >>> >>>> --abstract force abstract class (ignored, deprecated)
>> >>> >>>> --vtkobject vtkObjectBase-derived class (ignored,
>> >>> >>>> deprecated)
>> >>> >>>> --special non-vtkObjectBase class (ignored, deprecated)
>> >>> >>>> make[2]: *** [Wrapping/Python/vtkAbstractArrayPython.cxx] Error 1
>> >>> >>>> make[2]: *** Waiting for unfinished jobs....
>> >>> >>>> [ 29%] Built target vtkpython
>> >>> >>>> [ 29%] Python Wrapping - generating
>> >>> >>>> vtkAngularPeriodicDataArrayPython.cxx
>> >>> >>>> Usage: vtkWrapPython-7.1 [options] infile...
>> >>> >>>> --help print this help message
>> >>> >>>> --version print the VTK version
>> >>> >>>> -o <file> the output file
>> >>> >>>> -I <dir> add an include directory
>> >>> >>>> -D <macro[=def]> define a preprocessor macro
>> >>> >>>> -U <macro> undefine a preprocessor macro
>> >>> >>>> @<file> read arguments from a file
>> >>> >>>> --hints <file> the hints file to use
>> >>> >>>> --types <file> the type hierarchy file to use
>> >>> >>>> --concrete force concrete class (ignored, deprecated)
>> >>> >>>> --abstract force abstract class (ignored, deprecated)
>> >>> >>>> --vtkobject vtkObjectBase-derived class (ignored,
>> >>> >>>> deprecated)
>> >>> >>>> --special non-vtkObjectBase class (ignored, deprecated)
>> >>> >>>> make[2]: ***
>> >>> >>>> [Wrapping/Python/vtkAngularPeriodicDataArrayPython.cxx]
>> >>> >>>> Error 1
>> >>> >>>> make[1]: ***
>> >>> >>>> [Wrapping/Python/CMakeFiles/vtkCommonCorePythonD.dir/all]
>> >>> >>>> Error 2
>> >>> >>>> make[1]: *** Waiting for unfinished jobs....
>> >>> >>>> Scanning dependencies of target vtkCommonMathCxxTests
>> >>> >>>> make[2]: Warning: File
>> >>> >>>>
>> >>> >>>>
>> >>> >>>> `Common/Math/Testing/Cxx/CMakeFiles/vtkCommonMathCxxTests.dir/depend.make'
>> >>> >>>> has modification time 0.041 s in the future
>> >>> >>>> [ 29%] Building CXX object
>> >>> >>>>
>> >>> >>>>
>> >>> >>>> Common/Math/Testing/Cxx/CMakeFiles/vtkCommonMathCxxTests.dir/vtkCommonMathCxxTests.cxx.o
>> >>> >>>> [ 29%] Building CXX object
>> >>> >>>>
>> >>> >>>>
>> >>> >>>> Common/Math/Testing/Cxx/CMakeFiles/vtkCommonMathCxxTests.dir/TestAmoebaMinimizer.cxx.o
>> >>> >>>> [ 30%] Built target vtkCommonCoreCxxTests
>> >>> >>>> [ 30%] Building CXX object
>> >>> >>>>
>> >>> >>>>
>> >>> >>>> Common/Math/Testing/Cxx/CMakeFiles/vtkCommonMathCxxTests.dir/TestMatrix3x3.cxx.o
>> >>> >>>> [ 30%] Building CXX object
>> >>> >>>>
>> >>> >>>>
>> >>> >>>> Common/Math/Testing/Cxx/CMakeFiles/vtkCommonMathCxxTests.dir/TestPolynomialSolversUnivariate.cxx.o
>> >>> >>>> [ 30%] Building CXX object
>> >>> >>>>
>> >>> >>>>
>> >>> >>>> Common/Math/Testing/Cxx/CMakeFiles/vtkCommonMathCxxTests.dir/TestQuaternion.cxx.o
>> >>> >>>> [ 30%] Linking CXX executable
>> >>> >>>> ../../../../bin/vtkCommonMathCxxTests
>> >>> >>>> [ 32%] Built target vtkCommonDataModel
>> >>> >>>> make[2]: warning: Clock skew detected. Your build may be
>> >>> >>>> incomplete.
>> >>> >>>> [ 32%] Built target vtkCommonMathCxxTests
>> >>> >>>> make: *** [all] Error 2
>> >>> >>>>
>> >>> >>>
>> >>> >>>
>> >>> >>> _______________________________________________
>> >>> >>> 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 VTK FAQ at:
>> >>> >>> http://www.vtk.org/Wiki/VTK_FAQ
>> >>> >>>
>> >>> >>> Search the list archives at:
>> >>> >>> http://markmail.org/search/?q=vtkusers
>> >>> >>>
>> >>> >>> Follow this link to subscribe/unsubscribe:
>> >>> >>> http://public.kitware.com/mailman/listinfo/vtkusers
>> >>> >>>
>> >>> >>
>> >>> >
>> >>> >
>> >>> > _______________________________________________
>> >>> > 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 VTK FAQ at:
>> >>> > http://www.vtk.org/Wiki/VTK_FAQ
>> >>> >
>> >>> > Search the list archives at: http://markmail.org/search/?q=vtkusers
>> >>> >
>> >>> > Follow this link to subscribe/unsubscribe:
>> >>> > http://public.kitware.com/mailman/listinfo/vtkusers
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> 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 VTK FAQ at:
>> > http://www.vtk.org/Wiki/VTK_FAQ
>> >
>> > Search the list archives at: http://markmail.org/search/?q=vtkusers
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/vtkusers
>> >
>>
>>
>>
>> --
>> Cory Quammen
>> Staff R&D Engineer
>> Kitware, Inc.
>
>
--
Cory Quammen
Staff R&D Engineer
Kitware, Inc.
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