Dear all, I have run into some problems when trying to run the compressible flow solver. First, some background:- code build was complete without any issues, with all dependencies pre-installed system-wide, and without any problems in linking to these libraries - ran all regression tests, all successful- ran the Incompressible NS Solver, both serial and parallel without issues- ran the ADR Solver without issues The code was compiled and ran on a personal workstation, with Ubuntu 16.04 as the Linux distribution. I am not an advanced Linux user, having started to work in it only recently, and thus identifying the exact issue is not possible for me at this stage. The compressible flow solver always fails, even for the isentropic vortex case provided as example with the distribution. When running in serial, the error is:--------------------------------------------------------------------------------------------------------------------------------------------------------------- [salv08976-ub:03370] *** Process received signal ***[salv08976-ub:03370] Signal: Segmentation fault (11) [salv08976-ub:03370] Signal code: Address not mapped (1) [salv08976-ub:03370] Failing at address: 0x1573bc50 [salv08976-ub:03370] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x354b0)[0x7fb38f0b04b0] [salv08976-ub:03370] [ 1] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8StorePrm8run_onceEv+0xb)[0x7fb39087b39b] [salv08976-ub:03370] [ 2] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8EvaluateEi+0x6e)[0x7fb39087514e] [salv08976-ub:03370] [ 3] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libSolverUtils.so.4.4.1(_ZNK6Nektar12LibUtilities8Equation8EvaluateEv+0x38)[0x7fb391cc8508] [salv08976-ub:03370] [ 4] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader14ReadParametersEP12TiXmlElement+0x26d)[0x7fb3907bacbd] [salv08976-ub:03370] [ 5] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader13ParseDocumentEv+0x92)[0x7fb3907c2612] [salv08976-ub:03370] [ 6] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader11InitSessionEv+0x4f)[0x7fb3907c6aff] [salv08976-ub:03370] [ 7] ./CompressibleFlowSolver(_ZN6Nektar12LibUtilities13SessionReader14CreateInstanceEiPPc+0x16d)[0x48ef6d] [salv08976-ub:03370] [ 8] ./CompressibleFlowSolver(main+0x62)[0x454b52] [salv08976-ub:03370] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fb38f09b830] [salv08976-ub:03370] [10] ./CompressibleFlowSolver(_start+0x29)[0x463219] [salv08976-ub:03370] *** End of error message *** Segmentation fault (core dumped)--------------------------------------------------------------------------------------------------------------------------------------------------------------- When running in parallel the error is:The error message is pretty mush the same, only repeated a number of times equal to the number of processing cores, plus the following message at the end:--------------------------------------------------------------------------------------------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 13368 on node salv08976-ub exited on signal 11 (Segmentation fault).--------------------------------------------------------------------------------------------------------------------------------------------------------------- Any guidance with this issue would be much appreciated. Thank you.Oliviu
Hi Oliviu, Looks like there is something wrong in the session configuration for the cases you are running. There should be a check which tells you exactly what but it is clearly not working! Test_IsentropicVortex1.xml Has not been touched in 4+ years and isn’t part of the test suite so chances are something in the file has become out of date. I will see if I can replicate your error and back-trace it when I get a chance. In the mean time it might be better for you to build your session from one of the working tests, for example solvers/CompressibleFlowSolver/Tests/Euler1D.xml Is a simple case which passes the test suite so should give you a good place to start. There are loads more xml sessions in that directory which (in theory) all currently work. Thanks Mike From: Oliviu Sugar<mailto:oliviu_sugar@yahoo.com> Sent: 25 October 2017 12:20 To: nektar-users<mailto:nektar-users@imperial.ac.uk> Subject: [Nektar-users] Issue with CompressibleFlowSolver Dear all, I have run into some problems when trying to run the compressible flow solver. First, some background: - code build was complete without any issues, with all dependencies pre-installed system-wide, and without any problems in linking to these libraries - ran all regression tests, all successful - ran the Incompressible NS Solver, both serial and parallel without issues - ran the ADR Solver without issues The code was compiled and ran on a personal workstation, with Ubuntu 16.04 as the Linux distribution. I am not an advanced Linux user, having started to work in it only recently, and thus identifying the exact issue is not possible for me at this stage. The compressible flow solver always fails, even for the isentropic vortex case provided as example with the distribution. When running in serial, the error is: --------------------------------------------------------------------------------------------------------------------------------------------------------------- [salv08976-ub:03370] *** Process received signal *** [salv08976-ub:03370] Signal: Segmentation fault (11) [salv08976-ub:03370] Signal code: Address not mapped (1) [salv08976-ub:03370] Failing at address: 0x1573bc50 [salv08976-ub:03370] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x354b0)[0x7fb38f0b04b0] [salv08976-ub:03370] [ 1] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8StorePrm8run_onceEv+0xb)[0x7fb39087b39b] [salv08976-ub:03370] [ 2] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8EvaluateEi+0x6e)[0x7fb39087514e] [salv08976-ub:03370] [ 3] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libSolverUtils.so.4.4.1(_ZNK6Nektar12LibUtilities8Equation8EvaluateEv+0x38)[0x7fb391cc8508] [salv08976-ub:03370] [ 4] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader14ReadParametersEP12TiXmlElement+0x26d)[0x7fb3907bacbd] [salv08976-ub:03370] [ 5] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader13ParseDocumentEv+0x92)[0x7fb3907c2612] [salv08976-ub:03370] [ 6] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader11InitSessionEv+0x4f)[0x7fb3907c6aff] [salv08976-ub:03370] [ 7] ./CompressibleFlowSolver(_ZN6Nektar12LibUtilities13SessionReader14CreateInstanceEiPPc+0x16d)[0x48ef6d] [salv08976-ub:03370] [ 8] ./CompressibleFlowSolver(main+0x62)[0x454b52] [salv08976-ub:03370] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fb38f09b830] [salv08976-ub:03370] [10] ./CompressibleFlowSolver(_start+0x29)[0x463219] [salv08976-ub:03370] *** End of error message *** Segmentation fault (core dumped) --------------------------------------------------------------------------------------------------------------------------------------------------------------- When running in parallel the error is: The error message is pretty mush the same, only repeated a number of times equal to the number of processing cores, plus the following message at the end: --------------------------------------------------------------------------------------------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 13368 on node salv08976-ub exited on signal 11 (Segmentation fault). --------------------------------------------------------------------------------------------------------------------------------------------------------------- Any guidance with this issue would be much appreciated. Thank you. Oliviu
Hi Mike, Managed to solve the problem. Looking over the newer test examples, I saw that the basis expansion type I chose was at fault for crashing the solver run. Changing this solved the problem, so now I have a configuration that works. Will have to look in more depth over the available options implemented in the solver, and how to achieve consistent over-integration by increasing the number of quadrature points without crashing the solver. Guess the choice I made initially (thinking it would be OK) turned out to be a problem. Thanks,Oliviu On Wednesday, October 25, 2017, 12:33:46 PM GMT+1, Turner, Michael <m.turner14@imperial.ac.uk> wrote: #yiv0004338173 #yiv0004338173 -- _filtered #yiv0004338173 {panose-1:2 4 5 3 5 4 6 3 2 4;} _filtered #yiv0004338173 {font-family:Calibri;panose-1:2 15 5 2 2 2 4 3 2 4;} _filtered #yiv0004338173 {panose-1:2 11 5 2 4 2 4 2 2 3;}#yiv0004338173 #yiv0004338173 p.yiv0004338173MsoNormal, #yiv0004338173 li.yiv0004338173MsoNormal, #yiv0004338173 div.yiv0004338173MsoNormal {margin:0cm;margin-bottom:.0001pt;font-size:11.0pt;}#yiv0004338173 a:link, #yiv0004338173 span.yiv0004338173MsoHyperlink {color:blue;text-decoration:underline;}#yiv0004338173 a:visited, #yiv0004338173 span.yiv0004338173MsoHyperlinkFollowed {color:#954F72;text-decoration:underline;}#yiv0004338173 .yiv0004338173MsoChpDefault {} _filtered #yiv0004338173 {margin:72.0pt 72.0pt 72.0pt 72.0pt;}#yiv0004338173 div.yiv0004338173WordSection1 {}#yiv0004338173 Hi Oliviu, Looks like there is something wrong in the session configuration for the cases you are running. There should be a check which tells you exactly what but it is clearly not working! Test_IsentropicVortex1.xml Has not been touched in 4+ years and isn’t part of the test suite so chances are something in the file has become out of date. I will see if I can replicate your error and back-trace it when I get a chance. In the mean time it might be better for you to build your session from one of the working tests, for example solvers/CompressibleFlowSolver/Tests/Euler1D.xml Is a simple case which passes the test suite so should give you a good place to start. There are loads more xml sessions in that directory which (in theory) all currently work. Thanks Mike From: Oliviu Sugar Sent: 25 October 2017 12:20 To: nektar-users Subject: [Nektar-users] Issue with CompressibleFlowSolver Dear all, I have run into some problems when trying to run the compressible flow solver. First, some background:- code build was complete without any issues, with all dependencies pre-installed system-wide, and without any problems in linking to these libraries - ran all regression tests, all successful- ran the Incompressible NS Solver, both serial and parallel without issues- ran the ADR Solver without issues The code was compiled and ran on a personal workstation, with Ubuntu 16.04 as the Linux distribution. I am not an advanced Linux user, having started to work in it only recently, and thus identifying the exact issue is not possible for me at this stage. The compressible flow solver always fails, even for the isentropic vortex case provided as example with the distribution. When running in serial, the error is:--------------------------------------------------------------------------------------------------------------------------------------------------------------- [salv08976-ub:03370] *** Process received signal ***[salv08976-ub:03370] Signal: Segmentation fault (11) [salv08976-ub:03370] Signal code: Address not mapped (1) [salv08976-ub:03370] Failing at address: 0x1573bc50 [salv08976-ub:03370] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x354b0)[0x7fb38f0b04b0] [salv08976-ub:03370] [ 1] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8StorePrm8run_onceEv+0xb)[0x7fb39087b39b] [salv08976-ub:03370] [ 2] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities27AnalyticExpressionEvaluator8EvaluateEi+0x6e)[0x7fb39087514e] [salv08976-ub:03370] [ 3] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libSolverUtils.so.4.4.1(_ZNK6Nektar12LibUtilities8Equation8EvaluateEv+0x38)[0x7fb391cc8508] [salv08976-ub:03370] [ 4] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader14ReadParametersEP12TiXmlElement+0x26d)[0x7fb3907bacbd] [salv08976-ub:03370] [ 5] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader13ParseDocumentEv+0x92)[0x7fb3907c2612] [salv08976-ub:03370] [ 6] /home/local/ISDADS/sgs475/Nektar++/nektar++-4.4.1/build/dist/lib64/nektar++-4.4.1/libLibUtilities.so.4.4.1(_ZN6Nektar12LibUtilities13SessionReader11InitSessionEv+0x4f)[0x7fb3907c6aff] [salv08976-ub:03370] [ 7] ./CompressibleFlowSolver(_ZN6Nektar12LibUtilities13SessionReader14CreateInstanceEiPPc+0x16d)[0x48ef6d] [salv08976-ub:03370] [ 8] ./CompressibleFlowSolver(main+0x62)[0x454b52] [salv08976-ub:03370] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7fb38f09b830] [salv08976-ub:03370] [10] ./CompressibleFlowSolver(_start+0x29)[0x463219] [salv08976-ub:03370] *** End of error message *** Segmentation fault (core dumped)--------------------------------------------------------------------------------------------------------------------------------------------------------------- When running in parallel the error is:The error message is pretty mush the same, only repeated a number of times equal to the number of processing cores, plus the following message at the end:--------------------------------------------------------------------------------------------------------------------------------------------------------------- mpirun noticed that process rank 3 with PID 13368 on node salv08976-ub exited on signal 11 (Segmentation fault).--------------------------------------------------------------------------------------------------------------------------------------------------------------- Any guidance with this issue would be much appreciated. Thank you.Oliviu
participants (2)
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Oliviu Sugar
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Turner, Michael