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Bugfix : add missing link to libscopmath #307

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pramodk merged 1 commit into from
May 19, 2020
Merged

Bugfix : add missing link to libscopmath #307

pramodk merged 1 commit into from
May 19, 2020

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@pramodk pramodk commented May 19, 2020 •
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  • libscopmath.a was linked to libcorenrnmech with shared library
    but was missing in case of static library
  • ar doesnt provide way to link two static libraries together.
    Hence extrat objects and then combined those together.

fixes #303 #306

@pramodk
Bugfix : add missing link to libscopmath
37337b1 
  - libscopmath.a was linked to libcorenrnmech with shared library
    but was missing in case of static library
  - ar doesnt provide way to link two static libraries together.
    Hence extrat objects and then combined those together.

fixes #303
@pramodk pramodk requested review from iomaganaris and nrnhines May 19, 2020 00:26
@pramodk pramodk mentioned this pull request May 19, 2020
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@alkino alkino mentioned this pull request May 19, 2020
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@pramodk pramodk requested a review from alkino May 19, 2020 01:12
iomaganaris
iomaganaris approved these changes May 19, 2020
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LGTM

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pramodk commented May 19, 2020

Interesting that travis CI is showing:

 Simulation Statistics
1861 Number of cells: 20
1862 Number of compartments: 804
1863 Number of presyns: 21
1864 Number of input presyns: 20
1865 Number of synapses: 21
1866 Number of point processes: 41
1867 Number of transfer (gap) targets: 0
1868 Number of spikes: 37
1869 Number of spikes with non negative gid-s: 37
1870
1871
1872[Traviss-Mac:63157] *** Process received signal ***
1873[Traviss-Mac:63157] Signal: Segmentation fault: 11 (11)
1874[Traviss-Mac:63157] Signal code: Address not mapped (1)
1875[Traviss-Mac:63157] Failing at address: 0x0
1876[Traviss-Mac:63157] [ 0] 0   libsystem_platform.dylib            0x00007fff7afb5b5d _sigtramp + 29
1877[Traviss-Mac:63157] [ 1] 0   ???                                 0x000070000043a6f0 0x0 + 123145306744560
1878[Traviss-Mac:63157] [ 2] 0   mca_rml_oob.so                      0x000000010ca55db0 orte_rml_oob_send_buffer_nb + 942
1879[Traviss-Mac:63157] [ 3] 0   libopen-rte.40.dylib                0x000000010be419c7 pmix_server_log_fn + 308
1880[Traviss-Mac:63157] [ 4] 0   mca_pmix_pmix3x.so                  0x000000010c8dd563 server_log + 850
1881[Traviss-Mac:63157] [ 5] 0   mca_plog_default.so                 0x000000010ca13846 mylog + 503
1882[Traviss-Mac:63157] [ 6] 0   mca_pmix_pmix3x.so                  0x000000010c95a08f pmix_plog_base_log + 1015
1883[Traviss-Mac:63157] [ 7] 0   mca_pmix_pmix3x.so                  0x000000010c924ff2 pmix_server_log + 2059
1884[Traviss-Mac:63157] [ 8] 0   mca_pmix_pmix3x.so                  0x000000010c90bcbb pmix_server_message_handler + 5279
1885[Traviss-Mac:63157] [ 9] 0   mca_pmix_pmix3x.so                  0x000000010c9626e3 OPAL_MCA_PMIX3X_pmix_ptl_base_process_msg + 735
1886[Traviss-Mac:63157] [10] 0   libevent-2.1.7.dylib                0x000000010bf8b2e6 event_process_active_single_queue + 633
1887[Traviss-Mac:63157] [11] 0   libevent-2.1.7.dylib                0x000000010bf886ba event_base_loop + 1062
1888[Traviss-Mac:63157] [12] 0   mca_pmix_pmix3x.so                  0x000000010c930338 progress_engine + 26
1889[Traviss-Mac:63157] [13] 0   libsystem_pthread.dylib             0x00007fff7afbe2eb _pthread_body + 126
1890[Traviss-Mac:63157] [14] 0   libsystem_pthread.dylib             0x00007fff7afc1249 _pthread_start + 66
1891[Traviss-Mac:63157] [15] 0   libsystem_pthread.dylib             0x00007fff7afbd40d thread_start + 13
1892[Traviss-Mac:63157] *** End of error message ***
1893/Users/travis/build/BlueBrain/CoreNeuron/build/tests/integration/ring_permute2/integration_test.sh: line 13: 63157 Segmentation fault: 11  /usr/local/bin/mpiexec -n 2 $SRUN_EXTRA /Users/travis/build/BlueBrain/CoreNeuron/build/bin/x86_64/special-core --datpath /Users/travis/build/BlueBrain/CoreNeuron/tests/integration/ring --tstop 100. --celsius 6.3 --mpi --outpath /Users/travis/build/BlueBrain/CoreNeuron/build/tests/integration/ring_permute2 --cell-permute 2
1894Error status value: 139

I will take a look!

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pramodk commented May 19, 2020

Couldn't reproduce the issue again on travis or locally with valgrind. As we are not changing any MPI logic in this PR, I will go ahead with the merge.

@pramodk pramodk merged commit 02b5550 into master May 19, 2020
@pramodk pramodk deleted the pramodk/scopmath_link_issue branch May 19, 2020 12:37
@mkuron mkuron mentioned this pull request Aug 19, 2020
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pramodk added a commit to neuronsimulator/nrn that referenced this pull request Nov 2, 2022
@pramodk
Bugfix : add missing link to libscopmath (BlueBrain/CoreNeuron#307)
660fec2 
- libscopmath.a was linked to libcorenrnmech with shared library
    but was missing in case of static library
- ar doesnt provide way to link two static libraries together.
    Hence extrat objects and then combined those together.

fixes BlueBrain/CoreNeuron#303

CoreNEURON Repo SHA: BlueBrain/CoreNeuron@02b5550
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Link errors when generating special-core with kinetic scheme NMOD files

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