OpenMP flags #95
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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 |
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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?)
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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 As a work-around for now, you can edit your local 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) |
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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)
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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 GitHub<#95 (comment)>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AF2bnw-lgOVsGNZCeZrYy6oPDIgFzFLlks5txqf6gaJpZM4SW1_c>.
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unless you changed we currently append our directory to the |
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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 Let us know about gadgetron (and if you think we should put our |
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@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. |
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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.
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Sorry, just revisiting this and I can't remember what I need to test. On OSX, Does that mean this issue is resolved? |
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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. |
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@rijobro says this should now all work with Python and C++, but not with MATLAB. |
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see also #502 |
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we won't support MATLAB anymore in the future, so we close this. |
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When building STIR, the user can enable
STIR_OpenMP, reconfigure and then if necessary, setOpenMP_CXX_FLAGS,OpenMP_C_FLAGS,OpenMP_CXX_LIB_NAMESandOpenMP_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?
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