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amusecode / amuse

Astrophysical Multipurpose Software Environment. This is the main repository for AMUSE
http://www.amusecode.org
Apache License 2.0
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Segmentation Fault with ph4 #716

Closed cheekyparticle closed 3 years ago

cheekyparticle commented 3 years ago

Hi,

I was using Amuse-ph4 last November and everything was working fine.

In the intervening time I updated my OS to ubuntu 20.04

Now, trying to picking up Amuse again, I get some kind of segmentation fault when trying to use ph4. I have made a quick script to reproduce the following error

$ python run_evol.py [andrew-XPS-13-9360:72878] *** Process received signal *** [andrew-XPS-13-9360:72878] Signal: Segmentation fault (11) [andrew-XPS-13-9360:72878] Signal code: Address not mapped (1) [andrew-XPS-13-9360:72878] Failing at address: (nil) [andrew-XPS-13-9360:72878] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x46210)[0x7fa148935210] [andrew-XPS-13-9360:72878] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_ess_singleton.so(+0x319b)[0x7fa11fbc119b] [andrew-XPS-13-9360:72878] [ 2] /usr/lib/x86_64-linux-gnu/libopen-rte.so.20(orte_init+0x22e)[0x7fa12133d1de] [andrew-XPS-13-9360:72878] [ 3] /usr/lib/x86_64-linux-gnu/libmpi.so.20(ompi_mpi_init+0x30e)[0x7fa1215f827e] [andrew-XPS-13-9360:72878] [ 4] /usr/lib/x86_64-linux-gnu/libmpi.so.20(PMPI_Init_thread+0x79)[0x7fa121619439] [andrew-XPS-13-9360:72878] [ 5] /home/andrew/Documents/Physics/Tools/Amuse-env4/lib/python3.8/site-packages/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so(+0x3046d)[0x7fa1218d346d] [andrew-XPS-13-9360:72878] [ 6] python(PyModule_ExecDef+0x4c)[0x6a592c] [andrew-XPS-13-9360:72878] [ 7] python[0x684437] [andrew-XPS-13-9360:72878] [ 8] python[0x5c4b10] [andrew-XPS-13-9360:72878] [ 9] python(PyVectorcall_Call+0x58)[0x5f3798] [andrew-XPS-13-9360:72878] [10] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [11] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [12] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [13] python(_PyEval_EvalFrameDefault+0x5736)[0x570286] [andrew-XPS-13-9360:72878] [14] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [15] python(_PyEval_EvalFrameDefault+0x849)[0x56b399] [andrew-XPS-13-9360:72878] [16] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [17] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [18] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [19] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [20] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [21] python[0x5f4ca1] [andrew-XPS-13-9360:72878] [22] python(_PyObject_CallMethodIdObjArgs+0x198)[0x5f5108] [andrew-XPS-13-9360:72878] [23] python(PyImport_ImportModuleLevelObject+0x823)[0x552f53] [andrew-XPS-13-9360:72878] [24] python[0x4f5bd8] [andrew-XPS-13-9360:72878] [25] python(PyCFunction_Call+0x59)[0x5f4249] [andrew-XPS-13-9360:72878] [26] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [27] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [28] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [29] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] *** End of error message *** Segmentation fault (core dumped)

I've attached the script and an additional document.

I have performed a clean environment install and still I get the same error.

If anyone has any suggestions, I would appreciate it a lot.

Cheers

ph4issue.zip

spzwart commented 3 years ago

Dear Andrew,

runs fine with me (see below): Mayn you can try to make clean and make again, and then retry?

(base) spz@Flater:~/AMUSE/tmp/ph4$ python run_evol.py

You have used the following codes, which contain literature references: "AMUSE" Portegies Zwart, S. & McMillan, S.L.W., 2018, "Astrophysical Recipes: the art of AMUSE", AAS IOP Astronomy publishing (411 pages) [2018araa.book.....P] Portegies Zwart, S. et al., 2013, Multi-physics Simulations Using a Hierarchical Interchangeable Software Interface, Computer Physics Communications 183, 456-468 [2013CoPhC.183..456P] Pelupessy, F. I. et al., 2013, The Astrophysical Multipurpose Software Environment, Astronomy and Astrophysics 557, 84 [2013A&A...557A..84P] Portegies Zwart, S. et al., 2009, A multiphysics and multiscale software environment for modeling astrophysical systems, New Astronomy, Volume 14, Issue 4, 369-378 [2009NewA...14..369P]

Simon On Jan 5 2021, at 4:01 pm, Andrew Cheek notifications@github.com wrote:

Hi, I was using Amuse-ph4 last November and everything was working fine. In the intervening time I updated my OS to ubuntu 20.04 Now, trying to picking up Amuse again, I get some kind of segmentation fault when trying to use ph4. I have made a quick script to reproduce the following error $ python run_evol.py [andrew-XPS-13-9360:72878] Process received signal [andrew-XPS-13-9360:72878] Signal: Segmentation fault (11) [andrew-XPS-13-9360:72878] Signal code: Address not mapped (1) [andrew-XPS-13-9360:72878] Failing at address: (nil) [andrew-XPS-13-9360:72878] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x46210)[0x7fa148935210] [andrew-XPS-13-9360:72878] [ 1] /usr/lib/x86_64-linux-gnu/openmpi/lib/openmpi/mca_ess_singleton.so(+0x319b)[0x7fa11fbc119b] [andrew-XPS-13-9360:72878] [ 2] /usr/lib/x86_64-linux-gnu/libopen-rte.so.20(orte_init+0x22e)[0x7fa12133d1de] [andrew-XPS-13-9360:72878] [ 3] /usr/lib/x86_64-linux-gnu/libmpi.so.20(ompi_mpi_init+0x30e)[0x7fa1215f827e] [andrew-XPS-13-9360:72878] [ 4] /usr/lib/x86_64-linux-gnu/libmpi.so.20(PMPI_Init_thread+0x79)[0x7fa121619439] [andrew-XPS-13-9360:72878] [ 5] /home/andrew/Documents/Physics/Tools/Amuse-env4/lib/python3.8/site-packages/mpi4py/MPI.cpython-38-x86_64-linux-gnu.so(+0x3046d)[0x7fa1218d346d] [andrew-XPS-13-9360:72878] [ 6] python(PyModule_ExecDef+0x4c)[0x6a592c] [andrew-XPS-13-9360:72878] [ 7] python[0x684437] [andrew-XPS-13-9360:72878] [ 8] python[0x5c4b10] [andrew-XPS-13-9360:72878] [ 9] python(PyVectorcall_Call+0x58)[0x5f3798] [andrew-XPS-13-9360:72878] [10] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [11] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [12] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [13] python(_PyEval_EvalFrameDefault+0x5736)[0x570286] [andrew-XPS-13-9360:72878] [14] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [15] python(_PyEval_EvalFrameDefault+0x849)[0x56b399] [andrew-XPS-13-9360:72878] [16] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [17] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [18] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [19] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] [20] python(_PyFunction_Vectorcall+0x1b6)[0x5f7146] [andrew-XPS-13-9360:72878] [21] python[0x5f4ca1] [andrew-XPS-13-9360:72878] [22] python(_PyObject_CallMethodIdObjArgs+0x198)[0x5f5108] [andrew-XPS-13-9360:72878] [23] python(PyImport_ImportModuleLevelObject+0x823)[0x552f53] [andrew-XPS-13-9360:72878] [24] python[0x4f5bd8] [andrew-XPS-13-9360:72878] [25] python(PyCFunction_Call+0x59)[0x5f4249] [andrew-XPS-13-9360:72878] [26] python(_PyEval_EvalFrameDefault+0x6435)[0x570f85] [andrew-XPS-13-9360:72878] [27] python(_PyEval_EvalCodeWithName+0x26a)[0x56955a] [andrew-XPS-13-9360:72878] [28] python(_PyFunction_Vectorcall+0x393)[0x5f7323] [andrew-XPS-13-9360:72878] [29] python(_PyEval_EvalFrameDefault+0x71e)[0x56b26e] [andrew-XPS-13-9360:72878] End of error message Segmentation fault (core dumped) I've attached the script and an additional document. I have performed a clean environment install and still I get the same error. If anyone has any suggestions, I would appreciate it a lot. Cheers ph4issue.zip (https://github.com/amusecode/amuse/files/5770883/ph4issue.zip) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub (https://github.com/amusecode/amuse/issues/716), or unsubscribe (https://github.com/notifications/unsubscribe-auth/ABCPFTC7EPBWTMSE534MGL3SYMSTRANCNFSM4VVKLRQA).

cheekyparticle commented 3 years ago

Indeed I performed a clean installation and it worked this time.

I'm not sure exactly what happened here.

Thanks,