Run a single networkSimulation.hoc without MPI

Kenkentake commented 3 years ago

Summary

Goal

Run a single networkSimulation.hoc without MPI

Todo

[ ] 引数の受け渡しの調査
[ ] hocファイルの実行

Deadline

06/27

Parent issue

None

References

None

Notes

None

Kenkentake commented 3 years ago

cluster:/mnt/nas2/data/kbaklastでMPI_Comm_spawnでgrepした結果

./sb_estimation/src_k/make_neuro_spawn.c
./sb_estimation/src_k/estimate_main.c
./sb_estimation/src_k/make_neuro_spawn
./sb_estimation/src_k/estimate_main.o
./sb_estimation/src_k/estimate_main
./sb_estimation/src_local/estimate_main
./sb_estimation/src_local/estimate_main.c
./sb_estimation/src_local/estimate_main.o
./sb_estimation/src_local/make_neuro_spawn
./sb_estimation/src_local/make_neuro_spawn.c
./sb_estimation/src_local/make_neuro_spawn.c.past
./home/hp160269/k03180/para/estimator/estimation/bin/estimation_main
./home/hp160269/k03180/para/estimator/estimation/bin/estimation_main_restart
./home/hp160269/k03180/para/estimator/estimation/bin/landscape2d
./home/hp160269/k03180/para/estimator/estimation/src/estimation_main.c
./home/hp160269/k03180/para/estimator/estimation/src/estimation_main_restart.c
./home/hp160269/k03180/para/estimator/estimation/src/landscape2d.c
./home/hp160269/k03180/para/estimator/estimation/src/estimation_main.o
./home/hp160269/k03180/para/estimator/estimation/src/estimation_main_restart.o
./home/hp160269/k03180/para/estimator/estimation/src/landscape2d.o
./home/hp160269/k03180/estimator/estimator/estimation/bin/estimation_main
./home/hp160269/k03180/estimator/estimator/estimation/bin/estimation_main_restart
./home/hp160269/k03180/estimator/estimator/estimation/bin/landscape2d
./home/hp160269/k03180/estimator/estimator/estimation/src/estimation_main.c
./home/hp160269/k03180/estimator/estimator/estimation/src/estimation_main_restart.c
./home/hp160269/k03180/estimator/estimator/estimation/src/landscape2d.c
./home/hp160269/k03180/estimator/estimator/estimation/src/estimation_main.o
./home/hp160269/k03180/estimator/estimator/estimation/src/estimation_main_restart.o
./home/hp160269/k03180/estimator/estimator/estimation/src/landscape2d.o
./home/hp160269/k03180/estimator/sb_estimation/src_k/estimate_main.c
./home/hp160269/k03180/estimator/sb_estimation/src_k/new-test31.sh.o7325099
./home/hp160269/k03180/estimator/sb_estimation/src_k/new-test31.sh.o7480002
./home/hp160269/k03180/estimator/sb_estimation/src_k/new-test31.sh.o7319481
./home/hp160269/k03180/estimator/sb_estimation/src_k/make_neuro_spawn.c
./home/hp160269/k03180/estimator/sb_estimation/src_k/estimate_main
./home/hp160269/k03180/estimator/sb_estimation/src_k/test21.sh.o7313345
./home/hp160269/k03180/estimator/sb_estimation/src_k/new-test31.sh.o7319477
./home/hp160269/k03180/estimator/sb_estimation/src_k/new-test31.sh.o7313359
./home/hp160269/k03180/estimator/sb_estimation/src_k/test21.sh.o7313354
./home/hp160269/k03180/estimator/sb_estimation/src_k/estimate_main.o
./home/hp160269/k03180/estimator/sb_estimation/src_k/new-test41.sh.o7480003
./home/hp160269/k03180/estimator/sb_estimation/src_k/new-test31.sh.o7314684
./home/hp160269/k03180/estimator/sb_estimation/src_k/make_neuro_spawn
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test1.sh.o7218718
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test2.sh.o7219704
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test2.sh.o7304733
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test2.sh.o7306847
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test2.sh.o7308295
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test3.sh.e7221810
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test3.sh.o7221810
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test3.sh.o7304723
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test3.sh.o7304736
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test3.sh.o7308294
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test3.sh.o7310290
./home/hp160269/k03180/estimator/sb_estimation/src_k/results/new-test3.sh.o7313358
./home/hp160269/k03180/estimator/sb_estimation/src_local/estimate_main
./home/hp160269/k03180/estimator/sb_estimation/src_local/estimate_main.c
./home/hp160269/k03180/estimator/sb_estimation/src_local/estimate_main.o
./home/hp160269/k03180/estimator/sb_estimation/src_local/make_neuro_spawn
./home/hp160269/k03180/estimator/sb_estimation/src_local/make_neuro_spawn.c
./home/hp160269/k03180/estimator/sb_estimation/src_local/make_neuro_spawn.c.past
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_k/make_neuro_spawn.c
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_k/estimate_main.c
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_k/make_neuro_spawn
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_k/estimate_main.o
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_k/estimate_main
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_local/estimate_main
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_local/estimate_main.c
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_local/estimate_main.o
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_local/make_neuro_spawn
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_local/make_neuro_spawn.c
./home/hp160269/k03180/estimator/fsb/sb_estimation/src_local/make_neuro_spawn.c.past
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/memo.txt
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/comm_test/comm_test.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/comm_test/mpi_opt
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/comm_test/mpi_opt.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/comm_test/test
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/command_spawn
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/command_spawn.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/mpi.h
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/mpi_opt.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/simple_spawn.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/simple_spawn2
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/spawn_neuron
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/spawn_print_k
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/spawn_test/spawn_print_k.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/split_gather_test/mpi_opt.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/simples/split_gather_test/mpi_opt
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/estimate1.sh.e5182204
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/estimate_main
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/estimate_main.c
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/estimate_main.o
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/test.sh.e5187114
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/estimate1.sh.e5182209
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/estimate1.sh.e5182215
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/estimate1.sh.e5182221
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/exec_results/estimate1.sh.e5182196
./home/hp160269/k03180/fukuda/optimizePara.withJOBFILES/src/past/estimate_main
./home/hp160269/k03180/send-log
./fukuda-files/optimizePara.withJOBFILES/simples/comm_test/comm_test.c
./fukuda-files/optimizePara.withJOBFILES/simples/comm_test/mpi_opt
./fukuda-files/optimizePara.withJOBFILES/simples/comm_test/mpi_opt.c
./fukuda-files/optimizePara.withJOBFILES/simples/comm_test/test
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/command_spawn
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/command_spawn.c
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/mpi.h
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/mpi_opt.c
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/simple_spawn.c
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/simple_spawn2
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/spawn_neuron
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/spawn_print_k
./fukuda-files/optimizePara.withJOBFILES/simples/spawn_test/spawn_print_k.c
./fukuda-files/optimizePara.withJOBFILES/simples/split_gather_test/mpi_opt.c
./fukuda-files/optimizePara.withJOBFILES/simples/split_gather_test/mpi_opt
./fukuda-files/optimizePara.withJOBFILES/src/exec_results/estimate1.sh.e5182196
./fukuda-files/optimizePara.withJOBFILES/src/past/estimate_main
./fukuda-files/optimizePara.withJOBFILES/src/estimate1.sh.e5182204
./fukuda-files/optimizePara.withJOBFILES/src/estimate_main
./fukuda-files/optimizePara.withJOBFILES/src/estimate_main.c
./fukuda-files/optimizePara.withJOBFILES/src/estimate_main.o
./fukuda-files/optimizePara.withJOBFILES/src/test.sh.e5187114
./fukuda-files/optimizePara.withJOBFILES/src/estimate1.sh.e5182209
./fukuda-files/optimizePara.withJOBFILES/src/estimate1.sh.e5182215
./fukuda-files/optimizePara.withJOBFILES/src/estimate1.sh.e5182221
./fukuda-files/optimizePara.withJOBFILES/memo.txt

Kenkentake commented 3 years ago

とりあえずは、/mnt/nas2/data/kbaklast/home/hp160269/k03180/estimator/sb_estimation を参考にしたら良さそう。

Kenkentake commented 3 years ago

下記2つのnetworkSimulation.hocの中身を比較して見ると、パラメータ・ファイルパス・細かな変更が異なるだけでメインのプログラムは同じだった。ただどっちが新しいのか不明。

/mnt/nas2/data/kbaklast/home/hp160269/k03180/estimator/sb_estimation/hocfile_forSB/networkSimulation.hoc
~/optimizePara/hocfile_forSB/networkSimulation.hoc

Kenkentake commented 3 years ago

networkSimulation.hocを単体で渡して実行した結果

[takemoto@Cluster ~/optimizePara/hocfile_forSB]$./x86_64/special networkSimulation.hoc
NEURON -- Release 7.2 (562:42a47463b504) 2011-12-21
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

loading membrane mechanisms from /home/takemoto/neuron_kplus/specials/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
 ../mod/exp2syn_k.mod ../mod/hh2CW.mod ../mod/hh2CW_many.mod ../mod/hh2F.mod ../mod/hh_cnexp.mod ../mod/hh_cnexp_notable.mod ../mod/hh_euler.mod ../mod/hh_impl.mod ../mod/hh_k.mod ../mod/hh_merge.mod ../mod/hh_runge.mod ../mod/hh_runge_notable.mod ../mod/pGPeA_k.mod ../mod/pGPeA_mine.mod ../mod/par_ggap.mod ../mod/preNoisyI.mod ../mod/region.mod
############ newtworkSimulation.hoc #############       49
load : standardbrain_swcs/1020_regist.swc ok
load : standardbrain_swcs/1020_regist.swc ok
load : standardbrain_swcs/0663_regist.swc ok
/home/takemoto/neuron_kplus/exec/x86_64/bin/nrniv: division by zero
 in networkSimulation.hoc near line 30
 p_mkcells("../hocfile_forSB/list/neuronlist.txt", 0)
                                                     ^
        CellSwc[2].lambda_f(100)
      CellSwc[2].geom_nseg()
    CellSwc[2].init("standardbrain_swcs/0663_regist.swc")
  p_mkcells("../hocfile_forSB/list/neuronlist.txt", 0)

p_mkcells()で転けている。ここを調査する

Kenkentake commented 3 years ago

networkSimulation.hocがMPI並列での実行を想定しているので、MPI並列なしのミニマル実行では無く初めからMPI並列での実行を目指す。

Kenkentake / optimizePara