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SyneRBI / SIRF-SuperBuild

SIRF CMake SuperBuild
http://www.ccpsynerbi.ac.uk
Apache License 2.0
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OpenMP flags #95

Closed rijobro closed 2 years ago

rijobro commented 6 years ago

When building STIR, the user can enable STIR_OpenMP, reconfigure and then if necessary, set OpenMP_CXX_FLAGS, OpenMP_C_FLAGS, OpenMP_CXX_LIB_NAMES and OpenMP_C_LIB_NAMES. These aren't exposed in the superbuild, and so compilation fails on my machine.

Could we also enable a travis test with openMP enabled for STIR?

KrisThielemans commented 6 years ago

aargh. macs....

It really shouldn't be necessary to have to set these flags, but indeed we struggled with it for STIR. Have a look there. Note the end statement "CMake doesn't support OpenMP with Apple's version of clang yet." (can't remember where I found that, but I believe it was in some CMake issue).

Can you add your observations on how you did get STIR-OPENMP to work on your system (os, xcode, compiler, cmake) to the STIR issue.

In STIR, we didn't manage to get openmp on Travis yet for OSX, so no point in enabling it for SIRF.(ok, we could do it for linux).

Having said all this, it would make sense to do a find(openmp) in SuperBuild.cmake and use mark_as_superbuild on the Openmp* variables (should only need CXX). feel free to generate a PR for this.

DANAJK commented 6 years ago

Is there a work around? A super build on my Mac currently fails with the error below. In cmake-gui, the BUILD_STIR_WITH_OPENMP is not checked (so it should build?)

CMake Error at /usr/local/Cellar/cmake/3.11.0/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:137 (message): Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES) Call Stack (most recent call first): /usr/local/Cellar/cmake/3.11.0/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:378 (_FPHSA_FAILURE_MESSAGE) /usr/local/Cellar/cmake/3.11.0/share/cmake/Modules/FindOpenMP.cmake:451 (find_package_handle_standard_args) src/CMakeLists.txt:145 (find_package)

-- Configuring incomplete, errors occurred! See also "/Users/davidatkinson/devel/build/builds/STIR/build/CMakeFiles/CMakeOutput.log". make[2]: [builds/STIR/stamp/STIR-configure] Error 1 make[1]: [CMakeFiles/STIR.dir/all] Error 2 make: *** [all] Error 2

KrisThielemans commented 6 years ago

sorry. this is my update. Travis OSX was down, so I thought it'd work :-;

I don't understand what's going on though. I was specifically trying to avoid this issue by NOT enabling STIR_OPENMP on OSX. Can you attach the CMakeCache.txt of ~/devel/build/ and ~/devel/build/builds/STIR/build/?

As a work-around for now, you can edit your local SIRF-SuperBuild/SuperBuild.cmake, L116 back to

option(BUILD_STIR_WITH_OPENMP "Build STIR with OpenMP acceleration" OFF)

as that worked for you before. (you would have to delete your build directory, or create a new one such that we can debug the old one)

DANAJK commented 6 years ago

Files attached. I note their Date Modified were from yesterday so it looks like any changes I made in cmake-gui today did not affect these files.

From: Kris Thielemans notifications@github.com Reply-To: CCPPETMR/SIRF-SuperBuild reply@reply.github.com Date: Saturday, 12 May 2018 at 10:14 To: CCPPETMR/SIRF-SuperBuild SIRF-SuperBuild@noreply.github.com Cc: David Atkinson d.atkinson@ucl.ac.uk, Comment comment@noreply.github.com Subject: Re: [CCPPETMR/SIRF-SuperBuild] OpenMP flags (#95) Resent-From: David Atkinson D.Atkinson@ucl.ac.uk

sorry. this is my update. Travis OSX was down, so I thought it'd work :-;

I don't understand what's going on though. I was specifically trying to avoid this issue by NOT enabling STIR_OPENMP on OSX. Can you attach the CMakeCache.txt of ~/devel/build/ and ~/devel/build/builds/STIR/build/?

As a work-around for now, you can edit your local SIRF-SuperBuild/SuperBuild.cmake, L116 back to

option(BUILD_STIR_WITH_OPENMP "Build STIR with OpenMP acceleration" OFF)

as that worked for you before. (you would have to delete your build directory, or create a new one such that we can debug the old one)

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/CCPPETMR/SIRF-SuperBuild/issues/95#issuecomment-388541987, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AF2bnw-lgOVsGNZCeZrYy6oPDIgFzFLlks5txqf6gaJpZM4SW1_c.

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DANAJK commented 6 years ago

With the workaround applied, make now finishes, but on trying to start gadgetron:

500:~$ gadgetron

dyld: Library not loaded: @rpath/libgadgetron_gadgetbase.3.14.dylib

Referenced from: /usr/local/bin/gadgetron

Reason: image not found

Abort trap: 6

501:~$

From: Kris Thielemans notifications@github.com Reply-To: CCPPETMR/SIRF-SuperBuild reply@reply.github.com Date: Saturday, 12 May 2018 at 10:14 To: CCPPETMR/SIRF-SuperBuild SIRF-SuperBuild@noreply.github.com Cc: David Atkinson d.atkinson@ucl.ac.uk, Comment comment@noreply.github.com Subject: Re: [CCPPETMR/SIRF-SuperBuild] OpenMP flags (#95) Resent-From: David Atkinson D.Atkinson@ucl.ac.uk

sorry. this is my update. Travis OSX was down, so I thought it'd work :-;

I don't understand what's going on though. I was specifically trying to avoid this issue by NOT enabling STIR_OPENMP on OSX. Can you attach the CMakeCache.txt of ~/devel/build/ and ~/devel/build/builds/STIR/build/?

As a work-around for now, you can edit your local SIRF-SuperBuild/SuperBuild.cmake, L116 back to

option(BUILD_STIR_WITH_OPENMP "Build STIR with OpenMP acceleration" OFF)

as that worked for you before. (you would have to delete your build directory, or create a new one such that we can debug the old one)

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/CCPPETMR/SIRF-SuperBuild/issues/95#issuecomment-388541987, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AF2bnw-lgOVsGNZCeZrYy6oPDIgFzFLlks5txqf6gaJpZM4SW1_c.

KrisThielemans commented 6 years ago

unless you changed CMAKE_INSTALL_PREFIX this is another version of gadgetron. Try executing the one in .../INSTALL/bin.

we currently append our directory to the PATH in env_ccppetmr.sh. maybe that's a bad idea (i.e. we should prepend)

KrisThielemans commented 6 years ago

The SuperBuild CMake should now default to false for STIR-OPENMP for OSX. My mistake was that UNIX is also true on OSX.

By the way @DANAJK, the only way I can see that setting BUILD_STIR_WITH_OPENMP to OFF on your cmake-gui didn't end up in the CMakeCache.txt is if you forgot to press configure again.

Let us know about gadgetron (and if you think we should put our INSTALL/bin first in the path, which would prevent people using other stuff by mistake).

KrisThielemans commented 6 years ago

@rijobro, regarding your original observation, could you maybe check at some point what Gadgetron does for OPENMP on OSX, as we don't have that problem there.

DANAJK commented 6 years ago

Gadgetron in ../INSTALL/bin started OK. However, there were subsequent problems that stopped after I put the SIRF stuff first on my path. This would suggest the order should be reversed, but I have many other problems so I can't be sure about cause and effect.

rijobro commented 5 years ago

Sorry, just revisiting this and I can't remember what I need to test. On OSX, BUILD_STIR_WITH_OPENMP defaults to OFF and that works just fine.

Does that mean this issue is resolved?

KrisThielemans commented 5 years ago

At some point, we have to get OpenMP support on working on Macs. We might then have to pass the flags through that you mentioned in your first comment. Let's leave this for later though, so I'll reassign to 2.1.

KrisThielemans commented 4 years ago

@rijobro says this should now all work with Python and C++, but not with MATLAB.

KrisThielemans commented 3 years ago

see also #502

KrisThielemans commented 2 years ago

we won't support MATLAB anymore in the future, so we close this.