{"id":899,"date":"2023-03-31T13:32:23","date_gmt":"2023-03-31T04:32:23","guid":{"rendered":"http:\/\/blog.marubaram.wo.tc\/?p=899"},"modified":"2023-03-31T13:32:23","modified_gmt":"2023-03-31T04:32:23","slug":"%eb%b3%91%eb%a0%ac%ed%99%94-%ea%b4%80%eb%a0%a8-%eb%a9%94%eb%aa%a8%eb%a6%ac-%eb%ac%b8%ec%a0%9c","status":"publish","type":"post","link":"https:\/\/blog.marubaram.wo.tc\/?p=899","title":{"rendered":"\ubcd1\ub82c\ud654 \uad00\ub828 \uba54\ubaa8\ub9ac \ubb38\uc81c"},"content":{"rendered":"

NEURON + NetPyNE \ub85c \ubcd1\ub82c\ud654\uac00 \ub9e4\uc6b0 \uc27d\uac8c \ucc98\ub9ac\uac00 \ub418\uc5b4\uc11c, Large-Scale\ub85c \uc27d\uac8c \ud655\uc7a5\ud588\ub2e4.
\uadf8\ub7f0\ub370, \uc2dc\ubbac\ub808\uc774\uc158\uc774 \ub3cc\uc544\uac00\ub294\uac74 \uad1c\ucc2e\uc740\ub370 \uc2dc\ubbac\ub808\uc774\uc158 \uc774\ud6c4 Gather \uacfc\uc815\uc5d0\uc11c \ubb38\uc81c\uac00 \ubc1c\uc0dd\ud55c\ub2e4.<\/p>\n\n\n

<\/p> [comet-20-53:27930] *** Process received signal *** [comet-20-53:27930] Signal: Aborted (6) [comet-20-53:27930] Signal code: (-6) [comet-20-53:27930] [ 0] \/lib64\/libpthread.so.0[0x3aa140f7e0] [comet-20-53:27930] [ 1] \/lib64\/libc.so.6(gsignal+0x35)[0x3aa0832495] [comet-20-53:27930] [ 2] \/lib64\/libc.so.6(abort+0x175)[0x3aa0833c75] [comet-20-53:27930] [ 3] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x15d)[0x2b1e0b64c07d] [comet-20-53:27930] [ 4] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(+0x5e0e6)[0x2b1e0b64a0e6] [comet-20-53:27930] [ 5] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(+0x5e131)[0x2b1e0b64a131] [comet-20-53:27930] [ 6] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(+0x5e348)[0x2b1e0b64a348] [comet-20-53:27930] [ 7] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(+0x5e859)[0x2b1e0b64a859] [comet-20-53:27930] [ 8] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(_Znam+0x9)[0x2b1e0b64a8b9] [comet-20-53:27930] [ 9] \/projects\/ps-nsg\/home\/nsguser\/applications\/osbneuron74_py\/nrn-7.4\/installdir\/x86_64\/lib\/libnrnpython.so.0(+0x130d6)[0x2b1e0a84e0d6] [comet-20-53:27930] [10] \/projects\/ps-nsg\/home\/nsguser\/applications\/osbneuron74_py\/nrn-7.4\/installdir\/x86_64\/lib\/libnrniv.so.0(+0x802c7)[0x2b1e0903e2c7] [comet-20-53:27930] [11] \/projects\/ps-nsg\/home\/nsguser\/applications\/osbneuron74_py\/nrn-7.4\/installdir\/x86_64\/lib\/libnrnoc.so.0(hoc_call_ob_proc+0x2ab)[0x2b1e08d977cb] [comet-20-53:27930] [12] \/projects\/ps-nsg\/home\/nsguser\/applications\/osbneuron74_py\/nrn-7.4\/installdir\/x86_64\/lib\/libnrnoc.so.0(hoc_object_component+0x76e)[0x2b1e08d9868e] [comet-20-53:27930] [13] \/projects\/ps-nsg\/home\/nsguser\/applications\/osbneuron74_py\/nrn-7.4\/installdir\/x86_64\/lib\/libnrnpython.so.0(+0xb0fe)[0x2b1e0a8460fe] [comet-20-53:27930] [14] \/projects\/ps-nsg\/home\/nsguser\/applications\/osbneuron74_py\/nrn-7.4\/installdir\/x86_64\/lib\/libnrniv.so.0(_ZN10OcJumpImpl7fpycallEPFPvS0_S0_ES0_S0_+0x61)[0x2b1e090174e1] [comet-20-53:27930] [15] \/projects\/ps-nsg\/home\/nsguser\/applications\/osbneuron74_py\/nrn-7.4\/installdir\/x86_64\/lib\/libnrnpython.so.0(+0xb392)[0x2b1e0a846392] [comet-20-53:27930] [16] \/opt\/python\/lib\/libpython2.7.so.1.0(PyObject_Call+0x43)[0x2b1e0aaa7b73] [comet-20-53:27930] [17] \/opt\/python\/lib\/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x3b2e)[0x2b1e0ab5c00e] [comet-20-53:27930] [18] \/opt\/python\/lib\/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5a5d)[0x2b1e0ab5df3d] [comet-20-53:27930] [19] \/opt\/python\/lib\/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5a5d)[0x2b1e0ab5df3d] [comet-20-53:27930] [20] \/opt\/python\/lib\/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x5a5d)[0x2b1e0ab5df3d] [comet-20-53:27930] [21] \/opt\/python\/lib\/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x830)[0x2b1e0ab5f320] [comet-20-53:27930] [22] \/opt\/python\/lib\/libpython2.7.so.1.0(PyEval_EvalCode+0x19)[0x2b1e0ab5f449] [comet-20-53:27930] [23] \/opt\/python\/lib\/libpython2.7.so.1.0(PyImport_ExecCodeModuleEx+0x99)[0x2b1e0ab72c79] [comet-20-53:27930] [24] \/opt\/python\/lib\/libpython2.7.so.1.0(+0x11dfce)[0x2b1e0ab72fce] [comet-20-53:27930] [25] \/opt\/python\/lib\/libpython2.7.so.1.0(+0x11edb9)[0x2b1e0ab73db9] [comet-20-53:27930] [26] \/opt\/python\/lib\/libpython2.7.so.1.0(PyImport_ImportModuleLevel+0x1dd)[0x2b1e0ab74a2d] [comet-20-53:27930] [27] \/opt\/python\/lib\/libpython2.7.so.1.0(+0x1013e8)[0x2b1e0ab563e8] [comet-20-53:27930] [28] \/opt\/python\/lib\/libpython2.7.so.1.0(PyObject_Call+0x43)[0x2b1e0aaa7b73] [comet-20-53:27930] [29] \/opt\/python\/lib\/libpython2.7.so.1.0(PyEval_CallObjectWithKeywords+0x47)[0x2b1e0ab57ee7] [comet-20-53:27930] *** End of error message *** <\/code><\/cite><\/blockquote>\n\n\n\n

\ubaa8\ub2c8\ud130\ub9c1\uc744 \ud574\ubd24\uc744 \ub54c\ub294 \ub531\ud788 \uba54\ubaa8\ub9ac\uac00 \ubd80\uc871\ud55c \uac83\uc73c\ub85c \ubcf4\uc774\uc9c0\ub294 \uc54a\ub294\ub370, \ubb54\uac00 \ub370\uc774\ud130\ub97c \uc8fc\uace0\ubc1b\uae30 \uc704\ud55c OpenMPI \ub0b4\uc5d0\uc11c\uc758 \uba54\ubaa8\ub9ac \ud55c\uacc4\uac00 \ubd80\uc871\ud55c \uac83\uc73c\ub85c \ubcf4\uc778\ub2e4.<\/p>\n\n\n\n

NEURON \ud3ec\ub7fc\uc5d0\uc11c\ub294 \ub370\uc774\ud130\ub97c \uc904\uc5ec\uc11c \ud558\ub294 \ubc29\ubc95\uc744 \uc598\uae30\ud558\uae30\ub294 \ud558\ub294\ub370, \ub2e4 \ud544\uc694\ud558\ub2c8 \uadf8\uac74 \ubd88\uac00\ub2a5\ud55c \uc635\uc158<\/p>\n\n\n\n

\ucd5c\uc120\uc758 \ubc29\ubc95\uc740 \ub530\ub85c \ucf54\ub4dc \uc218\uc815 \uc5c6\uc774, \uc804\uccb4\uc801\uc778 \uc2dc\uc2a4\ud15c \uc124\uc815\uc744 \uc218\uc815\ud574\uc11c \ucc98\ub9ac\ud558\ub294 \ubc29\ubc95\uc778\ub370, \uba54\uc2dc\uc9c0 \uc804\ub2ec \uc778\ud130\ud398\uc774\uc2a4\uc758 \ud06c\uae30\uac00 MEMLock \uc124\uc815\uacfc \uc5f0\uad00\ub418\uc5b4 \uc788\ub2e4\ub294 \ub0b4\uc6a9\uc744 \ubcf4\uac8c \ub418\uc5c8\ub2e4.<\/p>\n\n\n\n

ulimit -a \ud574\uc11c \ubcf4\uc774\ub294 Memory Locking \uacfc \uad00\ub828<\/p>\n\n\n\n

  1. \/etc\/security\/limits.conf \uc218\uc815 –> \uc774\uac83\ub9cc\uc73c\ub85c\ub294 \uc548\ub428<\/li>
  2. \/etc\/systemd\/system.conf, \/etc\/systemd\/user.conf \uc758 defaultLimitMEMLOCK \uc744 \uc218\uc815<\/li>
  3. \/etc\/sysctl.conf<\/strong>\u00a0\ud30c\uc77c\uc5d0\uc11c vm.max_map_count\u00a0 \ubcc0\uacbd<\/li><\/ol>\n\n\n\n

    \uadfc\ub370 \uc548 \ub428..
    \ub2e4\ub978 \ubc29\ubc95\uc740 \ud2b9\uc815 Interval \ub9c8\ub2e4 \ucabc\uac1c\uc11c \ub123\ub294 \uac74\ub370, \uc6b0\uc120\uc740 Synaptic weight \ubcc0\ud654\uc5d0 \ub300\ud55c \uba54\ubaa8\ub9ac\uac00 \ud070 \uac83\uc774\uace0 \ud574\ub2f9 \ub0b4\uc6a9\uc740 \uacb0\uad6d \uac1c\ubcc4 node\uc5d0 \uc800\uc7a5\ub418\uc5b4 \uc788\uae30 \ub54c\ubb38\uc5d0 \uc6b0\uc120 \uadf8\ub0e5 Node \uc5d0\uc11c \uac1c\ubcc4\uc801\uc73c\ub85c \uc800\uc7a5\ud558\ub3c4\ub85d \ud558\ub294 \ucf54\ub4dc\ub97c \uc791\uc131.<\/p>\n\n\n\n

    NetPyNE\uc5d0\ub3c4 \ud574\ub2f9 method\uac00 \uc788\uae34 \ud55c\ub370.. \ub77c\uc774\ube0c\ub7ec\ub9ac\ubcf4\ub2e4\ub294 \uc9c1\uc811 \uc9dc\ub294\uac8c \ub354 \uc775\uc219<\/p>\n\n\n\n

    # save SynWeight without gather and remove \nif sim.nhosts > 1:\n    sim.pc.barrier()\n\n# # fix matlab save all sim data\nprint(f'Saving SynWeight Data on node {sim.rank}')\nfrom scipy.io import savemat\nfor cell_key, cell in sim.simData['SynWeight'].items():\n    weightData = {}\n    for conn_key, conn in cell.items():\n        weightData[conn_key] = list(conn)\n    if cell_key != '__dict__':\n        savemat(f'{sim.cfg.filename}_SynWeight_{cell_key}.mat', weightData)\nprint('  Done; ')\ndel sim.simData['SynWeight']<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"
    NEURON + NetPyNE \ub85c \ubcd1\ub82c\ud654\uac00 \ub9e4\uc6b0 \uc27d\uac8c \ucc98\ub9ac\uac00 \ub418\uc5b4\uc11c, Large-Scale\ub85c \uc27d\uac8c \ud655\uc7a5\ud588\ub2e4.\uadf8\ub7f0\ub370, \uc2dc\ubbac\ub808\uc774\uc158\uc774 \ub3cc\uc544\uac00\ub294\uac74 \uad1c\ucc2e\uc740\ub370 \uc2dc\ubbac\ub808\uc774\uc158 \uc774\ud6c4 Gather \uacfc\uc815\uc5d0\uc11c \ubb38\uc81c\uac00 \ubc1c\uc0dd\ud55c\ub2e4. [comet-20-53:27930] *** Process received signal *** [comet-20-53:27930] Signal: Aborted (6) [comet-20-53:27930] Signal code: (-6) [comet-20-53:27930] [ 0] \/lib64\/libpthread.so.0[0x3aa140f7e0] [comet-20-53:27930] [ 1] \/lib64\/libc.so.6(gsignal+0x35)[0x3aa0832495] [comet-20-53:27930] [ 2] \/lib64\/libc.so.6(abort+0x175)[0x3aa0833c75] [comet-20-53:27930] [ 3] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x15d)[0x2b1e0b64c07d] [comet-20-53:27930] [ 4] \/opt\/gnu\/gcc\/lib64\/libstdc++.so.6(+0x5e0e6)[0x2b1e0b64a0e6] […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[1],"tags":[],"_links":{"self":[{"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=\/wp\/v2\/posts\/899"}],"collection":[{"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=899"}],"version-history":[{"count":3,"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=\/wp\/v2\/posts\/899\/revisions"}],"predecessor-version":[{"id":903,"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=\/wp\/v2\/posts\/899\/revisions\/903"}],"wp:attachment":[{"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=899"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=899"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blog.marubaram.wo.tc\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=899"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}