[petsc-dev] Fwd: [petsc-maint] Problems building on a Mac

[Matthew Knepley]

The continual decline of the Apple Developer Experience.

   Matt

---------- Forwarded message ---------
From: Palmer, Bruce J via petsc-maint <petsc-maint at mcs.anl.gov>
Date: Fri, Jan 4, 2019 at 1:24 PM
Subject: Re: [petsc-maint] Problems building on a Mac
To: petsc-maint <petsc-maint at mcs.anl.gov>
Cc: Perkins, William A <William.Perkins at pnnl.gov>


Hi,

Your fix seems to work, although I also had to delete the lines related to
PETSC_HAVE_LIBJPEG. The warning seems to be a recent problem with Xcode. If
you google 'out of sync. Falling back to library file for linking' you get
a bunch of stuff on it, e.g.
https://forums.developer.apple.com/thread/97850#316630.  The upshot is that
Apple doesn't seem to have gotten around to fixing it.

Thanks,
Bruce

On 1/4/19, 8:40 AM, "Balay, Satish" <balay at mcs.anl.gov> wrote:

    >>>>>>>>>>>>>>>>>>>
    Executing: /opt/local/bin/mpicc  -o
/var/folders/nk/jjh_2t0x2z10kz_8z9h4jv4wp_6618/T/petsc-XHOhxO/config.setCompilers/conftest

/var/folders/nk/jjh_2t0x2z10kz_8z9h4jv4wp_6618/T/petsc-XHOhxO/config.setCompilers/conftest.o

    Possible ERROR while running linker:
    stderr:
    ld: warning: text-based stub file
/System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL.tbd and
library file /System/Library/Frameworks//OpenCL.framework/Versions/A/OpenCL
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL.tbd and
library file /System/Library/Frameworks//OpenGL.framework/Versions/A/OpenGL
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//IOKit.framework/Versions/A/IOKit.tbd and
library file /System/Library/Frameworks//IOKit.framework/Versions/A/IOKit
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics.tbd
and library file
/System/Library/Frameworks//CoreGraphics.framework/Versions/A/CoreGraphics
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//Foundation.framework/Versions/C/Foundation.tbd
and library file
/System/Library/Frameworks//Foundation.framework/Versions/C/Foundation are
out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.tbd
and library file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGFXShared.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface.tbd
and library file
/System/Library/Frameworks//IOSurface.framework/Versions/A/IOSurface are
out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices.tbd
and library file
/System/Library/Frameworks//ApplicationServices.framework/Versions/A/ApplicationServices
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//Security.framework/Versions/A/Security.tbd and
library file
/System/Library/Frameworks//Security.framework/Versions/A/Security are out
of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.tbd
and library file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.tbd
and library file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices.tbd
and library file
/System/Library/Frameworks//CoreServices.framework/Versions/A/CoreServices
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork.tbd
and library file
/System/Library/Frameworks//CFNetwork.framework/Versions/A/CFNetwork are
out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration.tbd
and library file
/System/Library/Frameworks//DiskArbitration.framework/Versions/A/DiskArbitration
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.tbd
and library file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLImage.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator.tbd
and library file
/System/Library/PrivateFrameworks/IOAccelerator.framework/Versions/A/IOAccelerator
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//CoreText.framework/Versions/A/CoreText.tbd and
library file
/System/Library/Frameworks//CoreText.framework/Versions/A/CoreText are out
of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO.tbd and
library file
/System/Library/Frameworks//ImageIO.framework/Versions/A/ImageIO are out of
sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS.tbd
and library file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices.tbd
and library file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis.tbd
and library file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/SpeechSynthesis.framework/Versions/A/SpeechSynthesis
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata.tbd
and library file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/Metadata.framework/Versions/A/Metadata
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices.tbd
and library file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices.tbd
and library file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/LaunchServices.framework/Versions/A/LaunchServices
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList.tbd
and library file
/System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/SharedFileList.framework/Versions/A/SharedFileList
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.tbd
and library file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCVMSPluginSupport.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.tbd
and library file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontParser.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio.tbd
and library file
/System/Library/Frameworks//CoreAudio.framework/Versions/A/CoreAudio are
out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox.tbd
and library file
/System/Library/Frameworks//AudioToolbox.framework/Versions/A/AudioToolbox
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.tbd
and library file
/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libCoreVMClient.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.tbd
and library file
/System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/Resources/libFontRegistry.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.tbd
and library file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJPEG.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.tbd
and library file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libTIFF.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.tbd
and library file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libPng.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.tbd
and library file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libGIF.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.tbd
and library file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libJP2.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.tbd
and library file
/System/Library/Frameworks/ImageIO.framework/Versions/A/Resources/libRadiance.dylib
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport.tbd
and library file
/System/Library/PrivateFrameworks/MultitouchSupport.framework/Versions/A/MultitouchSupport
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory.tbd
and library file
/System/Library/Frameworks/OpenDirectory.framework/Versions/A/Frameworks/CFOpenDirectory.framework/Versions/A/CFOpenDirectory
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement.tbd
and library file
/System/Library/Frameworks//ServiceManagement.framework/Versions/A/ServiceManagement
are out of sync. Falling back to library file for linking.
    ld: warning: text-based stub file
/System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS.tbd and
library file
/System/Library/PrivateFrameworks/APFS.framework/Versions/A/APFS are out of
sync. Falling back to library file for linking.
    <<<<<<<<<<<<<<

    Something is messed up on your machine that 'ld' is giving all these
warnings. This is confusing configure.

    I have no idea how one would fix the machine to get rid of these
warnings.

    One workarround you can try is - after configure step:

     - edit arch-macosx-clang-real-opt/include/petscconf.h - and remove
lines corresponding to PETSC_HAVE_LIBPNG
     - now run 'make all'

    Satish

    On Fri, 4 Jan 2019, Palmer, Bruce J via petsc-maint wrote:

    > Attached. These are for 3.8.4. I'm trying 3.10.3 at the moment.
    >
    > Bruce
    >
    > On 1/3/19, 6:29 PM, "Smith, Barry F." <bsmith at mcs.anl.gov> wrote:
    >
    >
    >     Send configure.log and make.log after you've fixed the endwith
problem but before you change anything else.
    >
    >        Barry
    >
    >
    >     > On Jan 3, 2019, at 6:19 PM, Palmer, Bruce J <
Bruce.Palmer at pnnl.gov> wrote:
    >     >
    >     > Okay, I downloaded fresh tarballs for 3.8.4, 3.7.7 and 3.9.4
and tried configuring all of them. I get the same error each time.
    >     >
    >     >
===============================================================================

    >     > TESTING: checkFortranLibraries from
config.compilers(config/BuildSystem/config/c
    >     >
*******************************************************************************
    >     >        CONFIGURATION CRASH  (Please send configure.log to
petsc-maint at mcs.anl.gov)
    >     >
*******************************************************************************
    >     >
    >     > I've attached the configure.log file for 3.8.4. This
corresponds to the endwith<->endswith error.
    >     >
    >     > Bruce
    >     >
    >     > On 1/3/19, 3:49 PM, "Smith, Barry F." <bsmith at mcs.anl.gov>
wrote:
    >     >
    >     >
    >     >       This is strange. Since you did not list the graphics
formats on your ./configure list ./configure should not be searching for
them but for some reason it is saying it found them. Perhaps something got
corrupted?
    >     >
    >     >       I would delete the entire PETSc directory and start
again. If you get a failure immediately send the failing component to us,
don't experiment with changes.
    >     >
    >     >        The flag to turn off ./configure using png is
--with-png=0 but you shouldn't need it because png is off by default
anyways.
    >     >
    >     >        Barry
    >     >
    >     >    Also we highly recommend upgrading your application to the
latest version of PETSc, it should not be difficult at all and pays off
quickly.
    >     >
    >     >> On Jan 3, 2019, at 5:21 PM, Palmer, Bruce J via petsc-maint <
petsc-maint at mcs.anl.gov> wrote:
    >     >>
    >     >> Hi,
    >     >>
    >     >> I’m trying to build PETSc on a Mac with the High Sierra OS and
I’m running into a bunch of problems. Interestingly, a colleague of mine
has been doing the same build and it seems to go fine. I’m trying to build
3.8.4. The first problem I encountered was an error in the script
config/BuildSystem/config/compilers.py. There is a typo “endwith” that
should be “endswith”. After fixing this, the configuration goes through
okay, but I can’t get it to compile (again, a colleague doesn’t seem to
have any problem). The current error is
    >     >>
    >     >>
/Users/d3g293/software/petsc-3.8.4/src/sys/classes/draw/utils/image.c:58:10:
fatal error: 'png.h' file not found
    >     >> #include <png.h>
    >     >>         ^~~~~~~
    >     >>         CXX
arch-macosx-clang-real-opt/obj/src/sys/classes/viewer/interface/viewregall.o
    >     >>
    >     >> I tried adding a line --with-libpng=0 to my configure script,
but it didn’t seem to help. I’ve attached the files recommended in the
error message
    >     >>
    >     >> Error during compile, check
arch-macosx-clang-real-opt/lib/petsc/conf/make.log
    >     >>  Send it and
arch-macosx-clang-real-opt/lib/petsc/conf/configure.log to
petsc-maint at mcs.anl.gov
    >     >>
    >     >> Bruce Palmer
    >     >> Senior Research Scientist
    >     >> Pacific Northwest National Laboratory
    >     >> Richland, WA 99352
    >     >> (509) 375-3899
    >     >>
    >     >> <make.log><configure.log>
    >     >
    >     >
    >     >
    >     > <configure.log>
    >
    >
    >
    >




-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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