Dear all, I am having troubles compiling nektar 4.4.1 on Centos 7. I linked it with MKL, and was able to compile it, but it failed from test 5 till the last test (test 1 to 4 were successful though). My cmake command was ``` cmake\ -DCMAKE_CXX_FLAGS_RELEASE=" -I${MKLROOT}/include " \ -DNEKTAR_USE_MKL=ON \ -DMKL_LAPACK=${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a \ -DNEKTAR_USE_MPI=ON .. ``` I have tried linked with ThirdParty Boost following the FAQ page, but it does not help. I suspect the error was from linking with MKL? The deatailed error message was attached below. Start 4: Collections 4: Test command: /home/public/nektar/nektar++-4.4.1/build/library/UnitTests/Collections/CollectionsUnitTests "--detect_memory_leaks=0" 4: Test timeout computed to be: 9.99988e+06 4: Running 160 test cases... 4: 4: *** No errors detected 4/436 Test #4: Collections ....................................................................... Passed 0.37 sec test 5 Start 5: LibUtilities_NodalDemo_Tri_Deriv_P8 5: Test command: /home/public/nektar/nektar++-4.4.1/build/tests/Tester "/home/public/nektar/nektar++-4.4.1/library/Demos/LibUtilities/Tests/NodalDemo_Tri_Deriv_P8.tst" 5: Test timeout computed to be: 9.99988e+06 5: Error occurred running test: 5: Command: NodalDemo-g --order 8 --type 22 --deriv 1>output.out 2>output.err 5: === Output === 5: 5: === Errors === 5: sh: NodalDemo-g: command not found 5: 5/436 Test #5: LibUtilities_NodalDemo_Tri_Deriv_P8 ...............................................***Failed 0.02 sec Error occurred running test: Command: NodalDemo-g --order 8 --type 22 --deriv 1>output.out 2>output.err === Output === === Errors === sh: NodalDemo-g: command not found test 6 Start 6: LibUtilities_NodalDemo_Tri_Integral_P6 6: Test command: /home/public/nektar/nektar++-4.4.1/build/tests/Tester "/home/public/nektar/nektar++-4.4.1/library/Demos/LibUtilities/Tests/NodalDemo_Tri_Integral_P6.tst" 6: Test timeout computed to be: 9.99988e+06 6: Error occurred running test: 6: Command: NodalDemo-g --order 6 --type 23 --integral 1>output.out 2>output.err 6: === Output === 6: 6: === Errors === 6: sh: NodalDemo-g: command not found 6: 6/436 Test #6: LibUtilities_NodalDemo_Tri_Integral_P6 ............................................***Failed 0.02 sec Error occurred running test: Command: NodalDemo-g --order 6 --type 23 --integral 1>output.out 2>output.err === Output === === Errors === sh: NodalDemo-g: command not found Any help to resolve this issue or suggestions will be greatly appreciated. Thank you! Best Regards, Ziji
Hi, I think this will likely be a system library related issue. However I am not familiar with the Centos operating system. Possibly Chris will be able to help you with this Cheers, Spencer. On 18 Apr 2018, at 10:10, #SHI ZIJI# <ZSHI005@e.ntu.edu.sg<mailto:ZSHI005@e.ntu.edu.sg>> wrote: Dear all, I am having troubles compiling nektar 4.4.1 on Centos 7. I linked it with MKL, and was able to compile it, but it failed from test 5 till the last test (test 1 to 4 were successful though). My cmake command was ``` cmake\ -DCMAKE_CXX_FLAGS_RELEASE=" -I${MKLROOT}/include " \ -DNEKTAR_USE_MKL=ON \ -DMKL_LAPACK=${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a \ -DNEKTAR_USE_MPI=ON .. ``` I have tried linked with ThirdParty Boost following the FAQ page, but it does not help. I suspect the error was from linking with MKL? The deatailed error message was attached below. Start 4: Collections 4: Test command: /home/public/nektar/nektar++-4.4.1/build/library/UnitTests/Collections/CollectionsUnitTests "--detect_memory_leaks=0" 4: Test timeout computed to be: 9.99988e+06 4: Running 160 test cases... 4: 4: *** No errors detected 4/436 Test #4: Collections ....................................................................... Passed 0.37 sec test 5 Start 5: LibUtilities_NodalDemo_Tri_Deriv_P8 5: Test command: /home/public/nektar/nektar++-4.4.1/build/tests/Tester "/home/public/nektar/nektar++-4.4.1/library/Demos/LibUtilities/Tests/NodalDemo_Tri_Deriv_P8.tst" 5: Test timeout computed to be: 9.99988e+06 5: Error occurred running test: 5: Command: NodalDemo-g --order 8 --type 22 --deriv 1>output.out 2>output.err 5: === Output === 5: 5: === Errors === 5: sh: NodalDemo-g: command not found 5: 5/436 Test #5: LibUtilities_NodalDemo_Tri_Deriv_P8 ...............................................***Failed 0.02 sec Error occurred running test: Command: NodalDemo-g --order 8 --type 22 --deriv 1>output.out 2>output.err === Output === === Errors === sh: NodalDemo-g: command not found test 6 Start 6: LibUtilities_NodalDemo_Tri_Integral_P6 6: Test command: /home/public/nektar/nektar++-4.4.1/build/tests/Tester "/home/public/nektar/nektar++-4.4.1/library/Demos/LibUtilities/Tests/NodalDemo_Tri_Integral_P6.tst" 6: Test timeout computed to be: 9.99988e+06 6: Error occurred running test: 6: Command: NodalDemo-g --order 6 --type 23 --integral 1>output.out 2>output.err 6: === Output === 6: 6: === Errors === 6: sh: NodalDemo-g: command not found 6: 6/436 Test #6: LibUtilities_NodalDemo_Tri_Integral_P6 ............................................***Failed 0.02 sec Error occurred running test: Command: NodalDemo-g --order 6 --type 23 --integral 1>output.out 2>output.err === Output === === Errors === sh: NodalDemo-g: command not found Any help to resolve this issue or suggestions will be greatly appreciated. Thank you! Best Regards, Ziji _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus, London, SW7 2AZ, UK s.sherwin@imperial.ac.uk<mailto:s.sherwin@imperial.ac.uk> +44 (0)20 7594 5052 http://www.imperial.ac.uk/people/s.sherwin/
Hi, This could be for a number of reasons and we could do with seeing your CMakeCache.txt file to help identify the cause. If you are not seeing compiler errors this does not appear to be MKL related at first glance. Some things to check: - Check you have NEKTAR_BUILD_DEMOS enabled in the cmake configuration. - The Ctest command suggests it is looking for a debug build, but your cmake configuration does not specifically change the configuration from the default release build. Possibly you have rerun cmake over previous configurations and confused ctest? Therefore, - Build from a completely empty build directory. Hope that helps. Cheers, Chris On 22/04/18 22:35, Sherwin, Spencer J wrote:
Hi,
I think this will likely be a system library related issue. However I am not familiar with the Centos operating system. Possibly Chris will be able to help you with this
Cheers, Spencer.
On 18 Apr 2018, at 10:10, #SHI ZIJI# <ZSHI005@e.ntu.edu.sg <mailto:ZSHI005@e.ntu.edu.sg>> wrote:
Dear all,
I am having troubles compiling nektar 4.4.1 on Centos 7. I linked it with MKL, and was able to compile it, but it failed from test 5 till the last test (test 1 to 4 were successful though).
My cmake command was
``` cmake\ -DCMAKE_CXX_FLAGS_RELEASE=" -I${MKLROOT}/include " \ -DNEKTAR_USE_MKL=ON \ -DMKL_LAPACK=${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a \ -DNEKTAR_USE_MPI=ON .. ```
I have tried linked with ThirdParty Boost following the FAQ page, but it does not help. I suspect the error was from linking with MKL? The deatailed error message was attached below.
Start 4: Collections
4: Test command: /home/public/nektar/nektar++-4.4.1/build/library/UnitTests/Collections/CollectionsUnitTests "--detect_memory_leaks=0" 4: Test timeout computed to be: 9.99988e+06 4: Running 160 test cases... 4: 4: *** No errors detected 4/436 Test #4: Collections ....................................................................... Passed 0.37 sec test 5 Start 5: LibUtilities_NodalDemo_Tri_Deriv_P8
5: Test command: /home/public/nektar/nektar++-4.4.1/build/tests/Tester "/home/public/nektar/nektar++-4.4.1/library/Demos/LibUtilities/Tests/NodalDemo_Tri_Deriv_P8.tst" 5: Test timeout computed to be: 9.99988e+06 5: Error occurred running test: 5: Command: NodalDemo-g --order 8 --type 22 --deriv 1>output.out 2>output.err 5: === Output === 5: 5: === Errors === 5: sh: NodalDemo-g: command not found 5: 5/436 Test #5: LibUtilities_NodalDemo_Tri_Deriv_P8 ...............................................***Failed 0.02 sec Error occurred running test: Command: NodalDemo-g --order 8 --type 22 --deriv 1>output.out 2>output.err === Output ===
=== Errors === sh: NodalDemo-g: command not found
test 6 Start 6: LibUtilities_NodalDemo_Tri_Integral_P6
6: Test command: /home/public/nektar/nektar++-4.4.1/build/tests/Tester "/home/public/nektar/nektar++-4.4.1/library/Demos/LibUtilities/Tests/NodalDemo_Tri_Integral_P6.tst" 6: Test timeout computed to be: 9.99988e+06 6: Error occurred running test: 6: Command: NodalDemo-g --order 6 --type 23 --integral 1>output.out 2>output.err 6: === Output === 6: 6: === Errors === 6: sh: NodalDemo-g: command not found 6: 6/436 Test #6: LibUtilities_NodalDemo_Tri_Integral_P6 ............................................***Failed 0.02 sec Error occurred running test: Command: NodalDemo-g --order 6 --type 23 --integral 1>output.out 2>output.err === Output ===
=== Errors === sh: NodalDemo-g: command not found
Any help to resolve this issue or suggestions will be greatly appreciated. Thank you!
Best Regards, Ziji
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk <mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Spencer Sherwin FREng, FRAeS Head, Aerodynamics, Professor of Computational Fluid Mechanics, Department of Aeronautics, Imperial College London South Kensington Campus, London, SW7 2AZ, UK s.sherwin@imperial.ac.uk <mailto:s.sherwin@imperial.ac.uk> +44 (0)20 7594 5052 http://www.imperial.ac.uk/people/s.sherwin/
-- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell@imperial.ac.uk www.imperial.ac.uk/people/c.cantwell
participants (3)
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#SHI ZIJI#
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Chris Cantwell
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Sherwin, Spencer J