{"id":1931,"date":"2020-02-06T14:49:32","date_gmt":"2020-02-06T05:49:32","guid":{"rendered":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=1931"},"modified":"2021-08-19T10:03:13","modified_gmt":"2021-08-19T01:03:13","slug":"%e3%83%af%e3%83%bc%e3%82%af%e3%82%b9%e3%83%86%e3%83%bc%e3%82%b7%e3%83%a7%e3%83%b3%e5%b0%8e%e5%85%a5%e3%81%ae%e8%a8%98%e9%8c%b2%e3%80%81feb-6-2020-%e3%80%82","status":"publish","type":"post","link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/2020\/02\/06\/%e3%83%af%e3%83%bc%e3%82%af%e3%82%b9%e3%83%86%e3%83%bc%e3%82%b7%e3%83%a7%e3%83%b3%e5%b0%8e%e5%85%a5%e3%81%ae%e8%a8%98%e9%8c%b2%e3%80%81feb-6-2020-%e3%80%82\/","title":{"rendered":"\u30ef\u30fc\u30af\u30b9\u30c6\u30fc\u30b7\u30e7\u30f3\u5c0e\u5165\u306e\u8a18\u9332\u3001Feb. 6\u201317, 2020\u3002"},"content":{"rendered":"

“Great Red Oystrich Makes All Chemists Sane”<\/p>\n

\u74b0\u5883: CentOS Linux release 7.7.1908 (Core) + GNOME, GCC 4.8.5<\/p>\n

\u4fbf\u5229\u30b3\u30de\u30f3\u30c9<\/h3>\n

\u30fbnvidia-smi – GPU\u306e\u4f7f\u7528\u7387\u3001\u72b6\u614b\u3092\u78ba\u8a8d
\n\u30fbsensors – CPU\u6e29\u5ea6\u306e\u8868\u793a<\/p>\n

yum\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305flm_sensors 3.4.0\u30d1\u30c3\u30b1\u30fc\u30b8\u3067\u306fCPU\u6e29\u5ea6\u306f\u8868\u793a\u3055\u308c\u305f\u3082\u306e\u306e\u3001\u30d5\u30a1\u30f3\u3084\u96fb\u5727\u3092\u30e2\u30cb\u30bf\u30fc\u3059\u308b “Nuvoton NCT6796D Super IO Sensors” \u304csensors-detect\u3067\u691c\u51fa\u3055\u308c\u306a\u304b\u3063\u305f\u3002\u624b\u52d5\u3067lm_sensors (3.6.0) \u3092\u30d3\u30eb\u30c9\u3057\u3066\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\u3068\u3053\u308d\u691c\u51fa\u3055\u308c\u308b\u3088\u3046\u306b\u306a\u3063\u305f\u3002\u3057\u304b\u3057<\/span><\/p>\n

sudo modprobe nct6775 force_id=0x290 \u3057\u3066\u3082 “<\/span>modprobe: ERROR: could not insert ‘nct6775’: No such device” \u3068\u306e\u30a8\u30e9\u30fc\u304c\u51fa\u308b\u3002<\/span><\/p>\n

NCT6796D\u306b\u5bfe\u5fdc\u3057\u305fdriver\u306b\u30a2\u30c3\u30d7\u30c7\u30fc\u30c8\u3059\u308b\u305f\u3081\u3001ELRepo\u30ec\u30dd\u30b8\u30c8\u30ea\u3092\u6709\u52b9\u306b\u3057\u3066kernel module\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308b\u3002<\/span><\/p>\n

$ sudo rpm --import https:\/\/www.elrepo.org\/RPM-GPG-KEY-elrepo.org\n$ sudo yum install https:\/\/www.elrepo.org\/elrepo-release-7.0-4.el7.elrepo.noarch.rpm\n$ sudo yum install kmod-nct6775\n$ sudo \/usr\/local\/sbin\/sensors-detect --auto<\/code><\/pre>\n
\u3042\u308b\u3044\u306fKernel\u3092\u6700\u65b0\u5b89\u5b9a\u677f\uff08kernel-ml\uff09\u306b\u30a2\u30c3\u30d7\u30c7\u30fc\u30c8\u3059\u308b\u3002<\/p>\n
\u30fbcat \/proc\/driver\/nvidia\/version – nvidia\u30c9\u30e9\u30a4\u30d0\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u78ba\u8a8d
\n\u30fbmake -jN \u30fc N\u306bCPU\u306e\u30b3\u30a2\uff08\u30b9\u30ec\u30c3\u30c9\uff09\u6570\u3092\u5165\u308c\u308b\u3068\u4e26\u5217\u30b3\u30f3\u30d1\u30a4\u30eb\u3002
\n\u30fbnohup – \u7aef\u672b\u3092\u9589\u3058\u3066\u3082\u8a08\u7b97\u3092\u7d9a\u3051\u305f\u3044\u6642\u306b\u30b3\u30de\u30f3\u30c9\u306e\u982d\u306b\u5165\u308c\u308b\u3002<\/p>\n
\u65e5\u672c\u8a9e\u5165\u529b<\/h3>\n
\u53c2\u8003\u30b5\u30a4\u30c8: CentOS7\u3067\u65e5\u672c\u8a9e\u3092\u5165\u529b\u3059\u308b\u65b9\u6cd5 – Mikitechnica<\/a><\/p>\n
\u5de6\u4e0a\u306e\u300c\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3\u300d\u2192\u300c\u30b7\u30b9\u30c6\u30e0\u30c4\u30fc\u30eb\u300d\u2192\u300c\u8a2d\u5b9a\u300d\u3002\u300c\u5730\u57df\u3068\u8a00\u8a9e\u300d\u2192\u5165\u529b\u30bd\u30fc\u30b9\u306e\u5de6\u4e0b\u306e\u300c+\u300d\u30dc\u30bf\u30f3\u2192\u300c\u65e5\u672c\u8a9e\u300d\u2192\u300c\u65e5\u672c\u8a9e\uff08\u304b\u306a\u6f22\u5b57\uff09\u300d\u3092\u9078\u629e\u3057\u3001\u300c\u8ffd\u52a0\u300d\u3002Windows + Space\u3067\u5165\u529b\u30bd\u30fc\u30b9\u3092\u5207\u308a\u63db\u3048\u3002<\/p>\n
\u30db\u30b9\u30c8\u540d\u306e\u5909\u66f4<\/h3>\n
$ sudo hostnamectl set-hostname *****\n<\/code><\/pre>\n
\u30d5\u30a1\u30a4\u30eb\u306e\u8ee2\u9001<\/h3>\n
Samba\u306f\u4f7f\u308f\u306a\u3044\u3053\u3068\u306b\u3057\u305f\u3002macOS\u304b\u3089ssh\u3068Cyberduck\u3067sftp\u3067\u30ed\u30b0\u30a4\u30f3\u3067\u304d\u308b\u3053\u3068\u3092\u78ba\u8a8d\u3057\u305f\u3002<\/p>\n
GUI\u3001CUI\u306e\u5207\u308a\u63db\u3048<\/h3>\n
\u53c2\u8003\u30b5\u30a4\u30c8: CentOS 7\u3092CUI\u3067\u8d77\u52d5\u3059\u308b\u65b9\u6cd5 – \u30af\u30ed\u306e\u601d\u8003\u30ce\u30fc\u30c8<\/a><\/p>\n
GUI \u2192 CUI<\/p>\n
$ sudo systemctl disable gdm.service<\/code><\/pre>\n
CUI \u2192 GUI<\/p>\n
$ sudo systemctl enable gdm.service<\/code><\/pre>\n
\u8981\u518d\u8d77\u52d5\u3002<\/p>\n
\u30ed\u30b0\u30a4\u30f3\u753b\u9762\u3067 Ctrl + Alt + F2\u3067\u30b3\u30f3\u30bd\u30fc\u30eb\u30e2\u30fc\u30c9\u306b\u3001Ctrl + Alt + F1\u3067GUI\u30e2\u30fc\u30c9\u306b\u5207\u308a\u66ff\u3048\u3089\u308c\u308b\u3002<\/p>\n
Kernel<\/h3>\n
\u53c2\u8003\u30b5\u30a4\u30c8: CentOS 7\uff5e8 \u6700\u65b0\u5b89\u5b9a\u7248\u30ab\u30fc\u30cd\u30eb\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3001\u53ca\u3073\u5207\u308a\u66ff\u3048 – etuts+<\/a><\/p>\n
ELRepo\u30ec\u30dd\u30b8\u30c8\u30ea\u304b\u3089\u6700\u65b0\u5b89\u5b9a\u677f\uff082020\u5e743\u6708\u73fe\u5728\uff09kernel-ml 5.5.13-1\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u3066\u3001\u5143\u3005\u306e3.10\u304b\u3089\u5207\u308a\u63db\u3048\u305f\u3002\u518d\u8d77\u52d5\u3067\u304d\u305f\u304c\u3001\u30ed\u30b0\u30a4\u30f3\u753b\u9762\u306b\u306a\u3089\u306a\u3044\u3002\u95a2\u9023\u30d1\u30c3\u30b1\u30fc\u30b8kernel-ml-* \u3082\u5165\u308c\u66ff\u3048\u5f8c\u306b\u3001NVIDIA\u30c9\u30e9\u30a4\u30d0\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u304d\u3066\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u306a\u304a\u3057\u305f\u3002\u6b63\u5e38\u306b\u8d77\u52d5\u3002\u3053\u308c\u3067\u3001USB 3.1\u304c\u4f7f\u3048\u308b\u3088\u3046\u306b\u306a\u308b\u306f\u305a\u3002<\/p>\n
GPU\u30c9\u30e9\u30a4\u30d0\u3001CUDA<\/h3>\n
GPU\u30c9\u30e9\u30a4\u30d0: 440.44 \u2192 440.59 \uff082020\/2\/7\uff09 \u2192 440.64\uff082020\/3\/26\uff09
\nCUDA:<\/p>\n
$ sudo mv \/usr\/local\/cuda \/usr\/local\/cuda-10.0\n$ wget http:\/\/developer.download.nvidia.com\/compute\/cuda\/10.2\/Prod\/local_installers\/cuda_10.2.89_440.33.01_linux.run\n$ sudo sh cuda_10.2.89_440.33.01_linux.run<\/code><\/pre>\n
Developer Toolset 6\uff08including GCC 6.3.1\uff09 \u3092\u4f7f\u7528<\/h3>\n
\u53c2\u7167\u30b5\u30a4\u30c8: Developer Toolset 6 by Software Collections<\/a><\/p>\n
$ scl enable devtoolset-6 bash<\/code><\/pre>\n
$ exit \u3067\u5143\u306b\u623b\u308b\u3002
\n\u203b “$sudo make” \u3059\u308b\u3068\u5143\u306eGCC4.8.5\u304c\u4f7f\u308f\u308c\u3066\u3057\u307e\u3046\u306e\u3067\u6ce8\u610f\u3002root\u306b\u5207\u308a\u66ff\u3048\u3066\u304b\u3089 “# scl enable devtoolset-6 bash” \u3059\u308b\u3068\u5b89\u5fc3\u3002
\n\u5e38\u306bdevtools\u3092\u4f7f\u3046\u306b\u306f ~\/.bashrc \u306b “source \/opt\/rh\/devtoolset-6\/enable” \u3092\u66f8\u3044\u3066\u304a\u304f\u3002\u305f\u3060\u3057\u5143\u306b\u306f\u623b\u305b\u306a\u3044\u3002
\n<\/p>\n
\u30b8\u30e7\u30d6\u7ba1\u7406\u30b7\u30b9\u30c6\u30e0\u306e\u5c0e\u5165<\/h3>\n
\u53c2\u8003: CentOS 7\u3067Torque\u306e\u30bb\u30c3\u30c8\u30a2\u30c3\u30d7 – Qiita<\/a><\/p>\n
$ sudo yum install -enablerepo=epel torque-client torque-mom torque-server torque-scheduler torque-devel\n$ sudo su\n# create-munge-key\n\n# pbs_server -t create -f -D &\n# pbs_server_pid=$!\n\n# kill $pbs_server_pid\n\n# echo "$HOSTNAME np=$(nproc) num_node_boards=1 numa_board_str=$(nproc) gpus=2" > \/var\/lib\/torque\/server_priv\/nodes\n\n# systemctl start munge\n# systemctl start trqauthd\n# systemctl start pbs_server\n# systemctl start pbs_sched\n# systemctl start pbs_mom\n# systemctl enable munge trqauthd pbs_server pbs_sched pbs_mom\n\n# qmgr -c "create queue batch queue_type=execution"\n# qmgr -c "set queue batch started=true"\n# qmgr -c "set queue batch enabled=true"\n# qmgr -c "set queue batch resources_default.nodes=1"\n# qmgr -c "set queue batch resources_default.walltime=3600"\n# qmgr -c "set server default_queue=batch"\n# qmgr -c "set server scheduling=true"\n\n$ qmgr -c 'p s'\n$ pbsnodes -a \n#\u8a2d\u5b9a\u306e\u78ba\u8a8d\u3068\u30ce\u30fc\u30c9\u72b6\u614b\u306e\u78ba\u8a8d\u3002status = free\u3001\u3060\u3068\u30b8\u30e7\u30d6\u3092\u53d7\u3051\u3089\u308c\u308b\u72b6\u614b\u3002<\/code><\/pre>\n
qsub, qstat, qdel\u3067\u30b8\u30e7\u30d6\u3092\u7ba1\u7406\u3067\u304d\u308b\u3002<\/p>\n
Open-MPI 3.1.5\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u53c2\u8003\u30b5\u30a4\u30c8: 
\nFAQ: Building CUDA-aware Open MPI<\/a><\/p>\n
gdrcopy\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
$ wget https:\/\/github.com\/NVIDIA\/gdrcopy\/archive\/master.zip\n$ unzup master.zip\n$ cd gdrcopy-master\n$ sudo make PREFIX=\/usr\/local\/gdrcopy CUDA=\/usr\/local\/cuda all install\n$ sudo .\/insmod.sh<\/code><\/pre>\n
UCX\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
$ sudo yum install numactl-devel\n$ wget https:\/\/github.com\/openucx\/ucx\/releases\/download\/v1.7.0\/ucx-1.7.0.tar.gz\n$ tar xvzf ucx-1.7.0.tar.gz\n$ cd ucx-1.7.0\n$ .\/configure --prefix=\/usr\/local\/ucx\/1.7.0 --with-cuda=\/usr\/local\/cuda --with-gdrcopy=\/usr\/local\/gdrcopy\n$ make\n$ sudo make install<\/code><\/pre>\n
Gromacs2019\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3067\u306fOpenmpi\u306eversion 1.6\u4ee5\u4e0a\u304c\u63a8\u5968\u3055\u308c\u3066\u3044\u308b\u3002\u5f8c\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3059\u308bORCA\u306e\u305f\u3081\u306bOpen-MPI 3.1.4\u3082\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\u3002configure\u6642\u306b\u306f “tm.h” \u3092\u30c7\u30d5\u30a9\u30eb\u30c8\u3067\u63a2\u3059\u304c\u3001–with-tm\u30d5\u30e9\u30c3\u30b0\u3092\u4ed8\u3051\u3066\u304a\u304f\u3068 “tm.h” \u304c\u898b\u3064\u304b\u3089\u306a\u3044\u6642\u306b\u30a8\u30e9\u30fc\u3068\u306a\u308b\u3002<\/p>\n
$ wget https:\/\/download.open-mpi.org\/release\/open-mpi\/v3.1\/openmpi-3.1.4.tar.gz\n$ tar xvzf openmpi-3.1.4.tar.gz\n$ cd openmpi-3.1.4\n$ .\/configure --prefix=\/usr\/local\/open-mpi\/3.1.4_gcc6.3.1 --with-tm CPPFLAGS=-I\/usr\/include\/torque\n$ make all\n$ sudo su\n# make install<\/code><\/pre>\n
\u4ee5\u4e0b\u3092 ~\/.bashrc \u306b\u8ffd\u8a18\u3002<\/p>\n
#open-mpi\u7528\u8a2d\u5b9a\nMPIROOT=/usr/local/open-mpi/3.1.4_gcc6.3.1\nexport PATH=$MPIROOT/bin:$PATH\nexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPIROOT/lib\n#export MANPATH=$MANPATH:$MPIROOT/share/man\n<\/pre>\n
<\/p>\n
Gromacs2019.5\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u5206\u5b50\u52d5\u529b\u5b66\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30d7\u30ed\u30b0\u30e9\u30e0\u3002
\n\u516c\u5f0f\u30b5\u30a4\u30c8: Gromacs.org<\/a><\/p>\n
Gromacs\u306e\u30d3\u30eb\u30c9\u306b\u306fcmake (3.4.3 or higher) \u304c\u5fc5\u8981\u3002yum\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3067\u304d\u308bcmake\u306f2.8.12\u306e\u305f\u3081\u81ea\u5206\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\u3002Gromacs2020\u306esource\u306echecksum\u306e\u8a08\u7b97\u306e\u305f\u3081\u306bpython3\u3092yum\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f ($ sudo yum install python3)\u3002<\/p>\n
$ wget https:\/\/github.com\/Kitware\/CMake\/releases\/download\/v3.16.4\/cmake-3.16.4.tar.gz\n$ tar xvzf cmake-3.16.4.tar.gz\n$ cd cmake-3.16.4\n$ .\/bootstrap --prefix=\/usr\/local\/cmake --no-system-libs\n$ make\n$ sudo make install<\/code><\/pre>\n
CPU\u7248<\/h4>\n
$ wget http:\/\/ftp.gromacs.org\/pub\/gromacs\/gromacs-2019.5.tar.gz\n$ tar xvzf gromacs-2019.5.tar.gz\n$ cd gromacs-2019.5\n$ mkdir build\n$ cd build\n$ scl enable devtoolset-6 bash\n$ export VMDDIR=\/usr\/local\/vmd193\/lib\n$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON \\\n-DGMX_GPU=OFF -DCMAKE_INSTALL_PREFIX=\/usr\/local\/gromacs\/2019.5\n$ make\n$ make check\n$ sudo make install\n~\/.bashrc\u306b source \/usr\/local\/gromacs\/2019.5\/bin\/GMXRC \u3092\u8ffd\u52a0\u3002<\/code><\/pre>\n
CPU-MPI\u7248<\/h4>\n
$ cmake .. -DGMX_GPU=OFF -DCMAKE_INSTALL_PREFIX=\/usr\/local\/gromacs\/2019.5 -DGMX_BUILD_MDRUN_ONLY=ON \\\n-DGMX_BUILD_SHARED_LIBS=OFF -DGMX_MPI=ON\n$ make\n$ make check\n$ sudo make install<\/code><\/pre>\n
GPU\u7248<\/h4>\n
$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON \\\n-DCMAKE_INSTALL_PREFIX=\/usr\/local\/gromacs\/2019.5_cuda\n$ make\n$ make check\n$ sudo make install<\/code><\/pre>\n
GPU-MPI\u7248<\/h4>\n
$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=\/usr\/local\/gromacs\/2019.5_cuda \\\n-DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BUILD_SHARED_LIBS=OFF -DGMX_MPI=ON\n$ make\n$ make check\n$ sudo make install<\/code><\/pre>\n
<\/p>\n
\u5b9f\u884c\u901f\u5ea6\u306e\u6bd4\u8f03<\/h4>\n
\u30aa\u30d7\u30b7\u30e7\u30f3\u306f “-pin on -resethway -noconfout”\u3002<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Version<\/th>\nCompiler\u7b49<\/th>\nprocs<\/th>\nthread<\/th>\nGPU<\/th>\nGPU tasks<\/th>\nparalleli-<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
zation<\/p>\n<\/th>\n
ns\/day<\/th>\n<\/tr>\n
2019.5<\/td>\nGCC 6.3.1 (AVX2-256)<\/td>\n1<\/td>\n1<\/td>\n0<\/td>\n\u2013<\/td>\n–<\/td>\n1.688<\/td>\n<\/tr>\n
Intel Compiler  19.1.0.20191121<\/td>\n1<\/td>\n1<\/td>\n0<\/td>\n–<\/td>\n2.094<\/td>\n<\/tr>\n
GCC 8.3.1<\/td>\n1<\/td>\n1<\/td>\n0<\/td>\n–<\/td>\n2.096<\/td>\n<\/tr>\n
GCC 6.3.1 (AVX512)<\/td>\n1<\/td>\n1<\/td>\n0<\/td>\n–<\/td>\n2.102<\/td>\n<\/tr>\n
1<\/td>\n2<\/td>\n0<\/td>\nOpenMP<\/td>\n3.976<\/td>\n<\/tr>\n
1<\/td>\n4<\/td>\n0<\/td>\n7.813<\/td>\n<\/tr>\n
1<\/td>\n8<\/td>\n0<\/td>\n14.876<\/td>\n<\/tr>\n
8<\/td>\n8<\/td>\n0<\/td>\nthread MPI<\/td>\n13.713<\/td>\n<\/tr>\n
GCC 6.3.1 (AVX512)<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
OpenMPI 4.0.2<\/p>\n<\/td>\n
8<\/td>\n8<\/td>\n0<\/td>\nMPI<\/td>\n13.417<\/td>\n<\/tr>\n
GCC 6.3.1 (AVX512)<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
CUDA 10.2<\/p>\n<\/td>\n
1<\/td>\n1<\/td>\n1<\/td>\nPP (non-bonded)<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
PME<\/p>\n<\/td>\n
–<\/td>\n24.279<\/td>\n<\/tr>\n
1<\/td>\n2<\/td>\n1<\/td>\nOpenMP<\/td>\n46.275<\/td>\n<\/tr>\n
1<\/td>\n4<\/td>\n1<\/td>\n86.828<\/td>\n<\/tr>\n
1<\/td>\n8<\/td>\n1<\/td>\n113.155<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Version<\/th>\nCompiler\u7b49<\/th>\nprocs<\/th>\nthread<\/th>\nGPU<\/th>\nGPU tasks<\/th>\nparalleli-<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
zation<\/p>\n<\/th>\n
ns\/day<\/th>\n<\/tr>\n
2020.1<\/td>\nGCC 6.3.1<\/td>\n1<\/td>\n1<\/td>\n0<\/td>\n–<\/td>\n–<\/td>\n2.121<\/td>\n<\/tr>\n
1<\/td>\n2<\/td>\n0<\/td>\nOpenMP<\/td>\n4.017<\/td>\n<\/tr>\n
1<\/td>\n4<\/td>\n0<\/td>\n7.915<\/td>\n<\/tr>\n
1<\/td>\n8<\/td>\n0<\/td>\n15.026<\/td>\n<\/tr>\n
GCC 6.3.1<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
CUDA 10.2<\/p>\n<\/td>\n
1<\/td>\n1<\/td>\n1<\/td>\nPP (non-bonded)<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
PME<\/p>\n<\/td>\n
–<\/td>\n25.996<\/td>\n<\/tr>\n
1<\/td>\n2<\/td>\n1<\/td>\nOpenMP<\/td>\n49.437<\/td>\n<\/tr>\n
1<\/td>\n4<\/td>\n1<\/td>\n87.792<\/td>\n<\/tr>\n
1<\/td>\n8<\/td>\n1<\/td>\n114.822<\/td>\n<\/tr>\n
GCC 6.3.1<\/td>\n1<\/td>\n1<\/td>\n0<\/td>\n–<\/td>\n–<\/td>\n2.141*<\/td>\n<\/tr>\n
1<\/td>\n2<\/td>\n0<\/td>\nOpenMP<\/td>\n4.012*<\/td>\n<\/tr>\n
1<\/td>\n4<\/td>\n0<\/td>\n7.831*<\/td>\n<\/tr>\n
1<\/td>\n8<\/td>\n0<\/td>\n14.490*<\/td>\n<\/tr>\n
GCC 6.3.1<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
CUDA 10.2<\/p>\n<\/td>\n
1<\/td>\n1<\/td>\n1<\/td>\nPP (non-bonded, update)<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
PME<\/p>\n<\/td>\n
–<\/td>\n28.802*<\/td>\n<\/tr>\n
1<\/td>\n2<\/td>\n1<\/td>\nOpenMP<\/td>\n55.383*<\/td>\n<\/tr>\n
1<\/td>\n4<\/td>\n1<\/td>\n100.179*<\/td>\n<\/tr>\n
1<\/td>\n8<\/td>\n1<\/td>\n126.110*<\/td>\n<\/tr>\n
2<\/td>\n2<\/td>\n2<\/td>\nPP (non-bonded, update, bonded)<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
PME<\/p>\n<\/td>\n
thread-MPI + OpenMP<\/td>\n38.852*<\/td>\n<\/tr>\n
2<\/td>\n4<\/td>\n2<\/td>\n59.652*<\/td>\n<\/tr>\n
2<\/td>\n8<\/td>\n2<\/td>\n82.539*<\/td>\n<\/tr>\n
2<\/td>\n2<\/td>\n1<\/td>\nP2P\u2020<\/sup>, PP (non-bonded, update, bonded)<\/p>\n
 <\/p>\n
 <\/p>\n
 <\/p>\n
PME,<\/p>\n<\/td>\n
123.466*\u2020<\/sup><\/td>\n<\/tr>\n
2<\/td>\n2<\/td>\n2<\/td>\n121.744*\u2020<\/sup><\/td>\n<\/tr>\n
2<\/td>\n4<\/td>\n2<\/td>\n143.346*\u2020<\/sup><\/td>\n<\/tr>\n
4<\/td>\n4<\/td>\n2<\/td>\n149.603*\u2020<\/sup><\/td>\n<\/tr>\n
4<\/td>\n4<\/td>\n2<\/td>\n155.283*\u2020\u2021<\/sup><\/td>\n<\/tr>\n
2<\/td>\n8<\/td>\n2<\/td>\n156.652*\u2020<\/sup><\/td>\n<\/tr>\n
4<\/td>\n8<\/td>\n2<\/td>\n160.870*\u2020<\/sup><\/td>\n<\/tr>\n
4<\/td>\n8<\/td>\n2<\/td>\n187.990*\u2020\u2021<\/sup><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
* constraints = h-bonds.<\/p>\n
\u2020 <\/sup>export GMX_GPU_DD_COMMS=true && export GMX_GPU_PME_PP_COMMS=true && export GMX_FORCE_UPDATE_DEFAULT_GPU=true  \uff08\u53c2\u8003: Gray, Alan (2020-02-25) Creating Faster Molecular Dynamics Simulations with GROMACS 2020. NVIDIA Developer Blog<\/a>.\uff09<\/p>\n
\u2021<\/sup> PP:0,PP:0,PP:1,PME:1.<\/span><\/p>\n
GRACE\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
Gromacs\u30d7\u30ed\u30b0\u30e9\u30e0\u306b\u3088\u308b\u89e3\u6790\u3067\u51fa\u529b\u3055\u308c\u305fxvg\u30d5\u30a1\u30a4\u30eb\u306e\u8868\u793a\u7528\u3002<\/p>\n
$ sudo yum install --enablerepo=epel grace<\/code><\/pre>\n
\u3067\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\u3082\u306e\u306f “Broken or incomplete installation – read the FAQ!”\u3068\u8868\u793a\u3055\u308c\u8d77\u52d5\u3057\u306a\u304b\u3063\u305f\u3002
\n\u95a2\u9023\u30e9\u30a4\u30d6\u30e9\u30ea<\/p>\n
$ wget http:\/\/li.nux.ro\/download\/nux\/dextop\/el7\/x86_64\/\/pdflib-lite-7.0.5-5.el7.nux.x86_64.rpm\n$ wget http:\/\/li.nux.ro\/download\/nux\/dextop\/el7\/x86_64\/\/pdflib-lite-devel-7.0.5-5.el7.nux.x86_64.rpm\n$ sudo rpm -ihv pdflib-lite*\n$ sudo yum --enablerepo=epel install fftw2-devel\n$ sudo yum install libXpm-devel motif-devel<\/code><\/pre>\n
$ wget ftp:\/\/plasma-gate.weizmann.ac.il\/pub\/grace\/src\/grace-latest.tar.gz\n$ tar xvzf grace-latest.tar.gz\n$ cd grace-5.1.25\/\n$ scl enable devtoolset-6 bash\n$ .\/configure --prefix=\/usr\/local\n$ make\n$ make check\n$ sudo make install<\/code><\/pre>\n
\/usr\/local\/grace\/bin \u306bPATH\u3092\u901a\u3059\u3002<\/p>\n
PLUMED\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u5206\u5b50\u52d5\u529b\u5b66\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u305f\u3081\u306e\u62e1\u5f35\u30b5\u30f3\u30d7\u30ea\u30f3\u30b0\u30a2\u30eb\u30b4\u30ea\u30ba\u30e0\u30e9\u30a4\u30d6\u30e9\u30ea\u3002GROMACS\u306b\u30d1\u30c3\u30c1\u3092\u5f53\u3066\u308b\u3068\u3001\u30cf\u30df\u30eb\u30c8\u30cb\u30a2\u30f3\u30ec\u30d7\u30ea\u30ab\u4ea4\u63db\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u306e\u6a5f\u80fd\u304c\u8ffd\u52a0\u3055\u308c\u308b\u3002<\/p>\n
PLUMED 2.6.0\u306e\u30b3\u30f3\u30d1\u30a4\u30eb<\/h4>\n
$ tar xvzf plumed-src-2.6.0.tgz\n$ cd plumed-2.6.0\/\n$ .\/configure --prefix=\/usr\/local\/plumed\/2.6.0\n$ sudo make install<\/code><\/pre>\n
PLUMED-patched GROMACS 2019.4 \u306e\u30b3\u30f3\u30d1\u30a4\u30eb<\/h4>\n
$ wget http:\/\/ftp.gromacs.org\/pub\/gromacs\/gromacs-2019.4.tar.gz\n$ tar xvzf gromacs-2019.4.tar.gz\n$ cd gromacs-2019.4\n$ plumed patch -p\n$ mkdir build\n$ cd build\n$ cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=\/usr\/local\/gromacs\/2019.4_plumed\/ -DBUILD_SHARED_LIBS=OFF -DBUILD_TESTING=OFF -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON\n$ make\n$ sudo make install<\/code><\/pre>\n
VMD 1.9.3\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
GROMACS\u30c8\u30e9\u30b8\u30a7\u30af\u30c8\u30ea\u306e\u53ef\u8996\u5316\u3002NAMD\u306e\u5b9f\u884c\u306a\u3069\u3002<\/p>\n
\u95a2\u9023\u30e9\u30a4\u30d6\u30e9\u30ea\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
$ sudo yum install libXi-devel libXinerama-devel tbb tbb-devel libXrandr-devel libXcursor-devel fltk-devel<\/code><\/pre>\n
NVIDIA-OptiX-SDK-7.0.0-linux64.sh – \/opt\u306b\u5c55\u958b\u3002<\/p>\n
$ tar xvzf v2.0.1.tar.gz\n$ cd ospray-2.0.1\n$ mkdir build\n$ cd build\n$ ccmake ..\/scripts\/superbuild\/ -DCMAKE_INSTALL_PREFIX=\/usr\/local\/ospray-2.0.1\n$ sudo su\n# make<\/code><\/pre>\n
$ sudo yum --enablerepo=epel install netcdf netcdf-static netcdf-devel netcdf-cxx* netcdf-fortran* netcdf-mpi* netcdf-mpich*<\/code><\/pre>\n
VMD\u306e\u30b3\u30f3\u30d1\u30a4\u30eb<\/h4>\n
\u53c2\u8003\u30b5\u30a4\u30c8: VMD-1.9.3 for LX – \u8a08\u7b97\u79d1\u5b66\u7814\u7a76\u30bb\u30f3\u30bf\u30fc<\/a><\/p>\n
$ export work=PATH_TO_WORKINGDIRECTORY\n$ export VMDINSTALLBINDIR=\/usr\/local\/vmd193\/bin\n$ export VMDINSTALLLIBRARYDIR=\/usr\/local\/vmd193\/lib\n$ export CPATH=\/usr\/include\/python2.7:$work\/vmd-1.9.3\/lib\/tachyon\/src:$CPATH\n$ export TCLINC=-I\/usr\/include\n$ export TCLLIB=-L\/usr\/lib64\n$ export PLUGINDIR=$work\/vmd-1.9.3\/plugins\n$ tar xvzf vmd-1.9.3.src.tar.gz\n$ tar xvzf vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz vmd-1.9.3\/lib\/surf\/surf_LINUXAMD64 vmd-1.9.3\/lib\/stride\/stride_LINUXAMD64\n$ cd plugins\/\n$ make LINUXAMD64\n$ make distrib\n$ cd ..\/vmd-1.9.3\/lib\/\n$ tar xvzf ..\/..\/tachyon-0.99b6.tar.gz\n$ cd tachyon\/unix\/\n$ make linux-64-thr\n$ cd ..\/compile\/linux-64-thr\/\n$ cp libtachyon.a ..\/..\/\n$ cp tachyon ..\/..\/tachyon_LINUXAMD64\n$ cd $work\/vmd-1.9.3\n$ sed -i '2iunsetenv XMODIFIERS' bin\/vmd.csh\n$ sed -i '2iunset XMODIFIERS' bin\/vmd.sh\n$ sed -i 's\/python2.5\/python2.7\/g' .\/configure\n$ sed -i 's\/-ltachyon\/..\\\/lib\\\/tachyon\\\/libtachyon.a\/' .\/configure\n$ .\/configure LINUXAMD64 OPENGL FLTK TK LIBTACHYON NETCDF COLVARS TCL PYTHON PTHREADS NUMPY SILENT NOSTATICPLUGINS\n$ cd src\n$ make \n$ sudo make install\n~\/.bashrc \u306b "export PATH=\/usr\/local\/vmd193\/bin:$PATH" \u3092\u8ffd\u52a0\u3002\n<\/code><\/pre>\n
macOS\u5074\u306eXQuartz\u3067Indirect GLX\u3092\u4f7f\u3063\u3066OpenGL\u30a2\u30d7\u30ea\u30b1\u30fc\u30b7\u30e7\u30f3\u3092\u4f7f\u3046\u306f\u4ee5\u4e0b\u306e\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3059\u308b\u3002<\/p>\n
$ defaults write org.macosforge.xquartz.X11 enable_iglx -bool true<\/code><\/pre>\n
AmberTools19\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u5206\u5b50\u52d5\u529b\u5b66\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u30d1\u30c3\u30b1\u30fc\u30b8\u3002AmberTools\u306f\u7121\u6599\u3002Amber\u306f\u6709\u6599\uff08AmberTools\u306b\u542b\u307e\u308c\u308bsander\u3088\u308a\u9ad8\u901f\u306apmemd\u3092\u4f7f\u3048\u308b\uff09\u3002<\/p>\n
\u516c\u5f0f\u30b5\u30a4\u30c8: ambermd.org<\/a>
\n\u53c2\u8003\u30b5\u30a4\u30c8:Installing Amber – The Amber Project<\/a><\/p>\n
$ sudo yum install libXt-devel<\/code><\/pre>\n
\u901a\u5e38\u7248\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
http:\/\/ambermd.org\/GetAmber.php<\/a>\u304b\u3089AmberTools19.tar.bz2\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9<\/p>\n
$ cd \/usr\/local\/\n$ sudo tar xvjf \/path-to\/AmberTools19.tar.bz2\n$ sudo chown -R USER:USER amber18\n$ export AMBERHOME=\/usr\/local\/amber18\n$ cd $AMBERHOME\n$ scl enable devtoolset-6 bash\n$ .\/configure gnu\nThere are patches available. Do you want to apply them now? [y\/N] \u2014 Y + enter\u3067\u30d1\u30c3\u30c1\u3092\u5f53\u3066\u308b\u3002\nShould I download and install Miniconda for you? [y\/n] \u2014 y\u3002AmberTools\u5c02\u7528\u306ePython\u74b0\u5883\u3092\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3002\n$ echo "test -f \/usr\/local\/amber18\/\/amber.sh && source \/usr\/local\/amber18\/\/amber.sh" >> ~\/.bashrc\n$ source  ~\/.bashrc\n$ make install\n$ make test \uff08\u3068\u3066\u3082\u6642\u9593\u304c\u304b\u304b\u308b\uff09<\/code><\/pre>\n
2444 file comparisons passed\n0 file comparisons failed (0 ignored)\n0 tests experienced errors\nTest log file saved as /usr/local/amber18/logs/test_at_serial/2020-02-10_10-06-35.log\nNo test diffs to save!\n<\/pre>\n
MPI\u7248\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
\u4e0a\u3068\u540c\u3058\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u5185\u3067\u305d\u306e\u307e\u307e\u4f5c\u696d\u3002<\/p>\n
$ .\/configure -mpi gnu\n$ make install<\/code><\/pre>\n
GPU\u7248\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
$ export CUDA_HOME=\/usr\/local\/cuda\n$ .\/configure -cuda gnu\n$ make install<\/code><\/pre>\n
cpptraj.cuda\u3068pbsa.cuda\u304c\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u305f\u3002<\/p>\n
GPU-MPI\u7248\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
CUDA 10.2\u3092\u4f7f\u7528\u3002<\/p>\n
$ export CUDA_HOME=\/usr\/local\/cuda\n$ .\/configure -cuda -mpi gnu\n$ make install<\/code><\/pre>\n
cpptraj.MPI.cuda\u304c\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u305f\u3002<\/p>\n
GENESIS\u306e\u30b3\u30f3\u30d1\u30a4\u30eb<\/h3>\n
\u4e3b\u306b\u7406\u5316\u5b66\u7814\u7a76\u6240\u6749\u7530\u30b0\u30eb\u30fc\u30d7<\/a>\u306b\u3088\u3063\u3066\u958b\u767a\u3055\u308c\u3066\u3044\u308b\u5206\u5b50\u52d5\u529b\u5b66\u3001\u5206\u5b50\u30e2\u30c7\u30ea\u30f3\u30b0\u30bd\u30d5\u30c8\u30a6\u30a7\u30a2\u3002<\/p>\n
\u901a\u5e38\u7248<\/h4>\n
$ tar xvjf genesis-1.4.0.tar.bz2\n$ cd genesis-1.4.0\/\n$ scl enable devtoolset-6 bash\n$ export LD_LIBRARY_PATH=\/opt\/intel_user\/parallel_studio_xe_2020\/compilers_and_libraries_2020\/linux\/mkl\/lib\/intel64_lin:$LD_LIBRARY_PATH\n$ .\/configure --prefix=\/usr\/local\/genesis\/1.4.0\n$ make\n$ sudo make install\n$ cd ..\/\n$ tar xvjf tests-1.4.0.tar.bz2\n$ cd tests-1.4.0\/regression_test\/\n$ export OMP_NUM_THREADS=1\n$ python2 .\/test.py "mpirun -np 8 \/usr\/local\/genesis\/1.4.0\/bin\/spdyn"<\/code><\/pre>\n
PME_VSHIFT_DISP\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3067\u306f “IEEE_INVALID_FLAG IEEE_DIVIDE_BY_ZERO”\u3001PME\u30c7\u30a3\u30ec\u30af\u30c8\u30ea\u3067\u306f “IEEE_DENORMAL” \u30a8\u30e9\u30fc\u3067aborted\u3057\u305f\u3002
\n<\/p>\n
AutoDock\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u30bf\u30f3\u30d1\u30af\u8cea-\u30ea\u30ac\u30f3\u30c9\u30c9\u30c3\u30ad\u30f3\u30b0\u30d7\u30ed\u30b0\u30e9\u30e0\u3002<\/p>\n
Single thread\u7248\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
\u516c\u5f0f\u30b5\u30a4\u30c8: CCSB AutoDock SUITE<\/a><\/p>\n
$ wget http:\/\/autodock.scripps.edu\/downloads\/autodock-registration\/tars\/dist426\/autodocksuite-4.2.6-x86_64Linux3.tar\n$ tar xvf autodocksuite-4.2.6-x86_64Linux3.tar\n$ sudo cp x86_64Linux3\/autodock4 x86_64Linux3\/autogrid4 \/usr\/local\/bin<\/code><\/pre>\n
AutoDock-GPU\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u516c\u5f0f\u30b5\u30a4\u30c8: Home – ccsb-scripps \/ AutoDock-GPU<\/a><\/p>\n
$ unzip AutoDock-GPU-master.zip\n$ cd AutoDock-GPU-master\n$ export CPU_INCLUDE_PATH=\/usr\/local\/cuda\/include\n$ export CPU_LIBRARY_PATH=\/usr\/local\/cuda\/lib64\n$ export gpu_include_path=\/usr\/local\/cuda\/include\n$ export gpu_library_path=\/usr\/local\/cuda\/lib64\n$ (for i in 16 32 64 128 256; do make device="CPU" numwi=$i; do make device="GPU" numwi=$i; done)\n$ sudo cp .\/bin\/autodock_gpu_* \/usr\/local\/bin<\/code><\/pre>\n
CPU\u7248\u306f “Error: clGetDevices(): -1” \u3067\u30af\u30e9\u30c3\u30b7\u30e5\u3057\u3066\u52d5\u304b\u306a\u304b\u3063\u305f\u3002<\/p>\n
\u30c6\u30b9\u30c8<\/h4>\n
1PTR.pdb\u3078\u306eATX\u306e\u30c9\u30c3\u30ad\u30f3\u30b0\u306b\u5fc5\u8981\u306a\u30d5\u30a1\u30a4\u30eb\u3092PMV\u3067\u4f5c\u6210\u3057\u305f\u3002\u8a2d\u5b9a\u306flong\uff08ga_num_evals 25000000\uff09\u3002Number of GA Runs = 2\u3067\u6bd4\u8f03\u3002<\/p>\n
$ autodock4 -p ATX.dpf -l legacy.dlg\n$ autodock_gpu_16wi -ffile .\/1ptr.maps.fld -lfile .\/ATX.pdbqt -nev 25000000 -nrun 2 -resnam "gpu-16wi"\n$ autodock_gpu_256wi -ffile .\/1ptr.maps.fld -lfile .\/ATX.pdbqt -nev 25000000 -nrun 2 -resnam "gpu-256wi_ADADELTA" -lsmet ad<\/code><\/pre>\n\n\n\n\n\n\n\n\n
Version<\/th>\nProgram run time (s)<\/th>\nLocal search method<\/th>\n<\/tr>\n
Autodock 4.2.6 (single thread)<\/td>\n542.06<\/td>\nSolis-Wets<\/td>\n<\/tr>\n
GPU_16wi<\/td>\n114.939<\/td>\nSolis-Wets (default)<\/td>\n<\/tr>\n
GPU_64wi<\/td>\n49.633<\/td>\n<\/tr>\n
GPU_256wi<\/td>\n32.03<\/td>\n<\/tr>\n
107.523<\/td>\nADADELTA<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
MGLTools 1.5.7\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
\u516c\u5f0f\u30b5\u30a4\u30c8: MGLTools<\/a>
\nAutoDock\u306e\u305f\u3081\u306e\u30d5\u30a1\u30a4\u30eb\u751f\u6210\u3068\u53ef\u8996\u5316\u3002<\/p>\n
$ chmod +x mgltools_Linux-x86_64_1.5.7_install\n$ sudo .\/mgltools_Linux-x86_64_1.5.7_install<\/code><\/pre>\n
GUI\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u30a6\u30a3\u30b6\u30fc\u30c9\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3002\u8d77\u52d5\u306f \/usr\/local\/MGLTools-1.5.7\/bin\/pmv \u3002<\/p>\n
GAMESS(US) \u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u30d7\u30ed\u30b0\u30e9\u30e0\u3002\u516c\u5f0f\u30a6\u30a7\u30d6\u30b5\u30a4\u30c8\u304b\u3089\u30bd\u30fc\u30b9\u30b3\u30fc\u30c9\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3059\u308b\u3002
\n.\/lked \u6642\u306b “libmkl_gf_ilp64.a” \u304c\u306a\u3044\u3068\u6012\u3089\u308c\u305f\u306e\u3067\uff08libmkl_gf_ilp64.so\u306f\u3042\u3063\u305f\uff09\u3001intel MKL\u3092\u81ea\u5206\u3067\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u518d\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3057\u305f\u3002<\/p>\n
$ cd \/usr\/local\n$ sudo tar xvzf \/path-to-source-file\/gamess-current.tar.gz\n$ cd gamess\n$ sudo su\n# .\/config\nlinux64\n30Sep2019R2\ngfortran\n6.3\nmkl\n\/opt\/intel_user\/parallel_studio_xe_2020\/compilers_and_libraries_2020\/linux\/mkl\nproceed\nsockets\nno\nno\n# cd ddi\ncompddi\u3092\u30a8\u30c7\u30a3\u30bf\u3067\u958b\u304dMAXCPUS\u306e\u5024\u3092\u5909\u66f4\uff08\u30c7\u30d5\u30a9\u30eb\u30c8\u306f32\uff09\u3002\n# .\/compddi >& compddi.log &\n# mv ddikick.x ..\n# cd ..\n# .\/compall >& compall.log &\n# .\/lked gamess 30Sep2019R2 >& lked.log &\n\nrungms\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u9069\u5b9c\u7de8\u96c6\u3057\u305f\uff08SCR=$HOME\/scr\u3001USERSCR=$HOME\/scr\uff09\u3002<\/code><\/pre>\n
$ cd tests\/standards\n$ mkdir $HOME\/scr\n$ ..\/runtest ..\/..\/rungms 30Sep2019R2 4\nchecktst\u30b9\u30af\u30ea\u30d7\u30c8\u3092\u7de8\u96c6\uff08set ext=log \u2192set ext=gamess\uff09\u3002\n$ .\/checktst<\/code><\/pre>\n
OpenMP\u3092\u6709\u52b9\u5316\u3059\u308b\u5834\u5408\u306fInstallation of GAMESS for OpenMP and MPI protocols<\/a>\u3092\u53c2\u8003\u306b\u3057\u305f\u3002OpenMP\u3092\u5229\u7528\u3059\u308b\u306b\u306fDIRECT SCF\uff082\u96fb\u5b50\u7a4d\u5206\u3092HDD\u306b\u66f8\u304d\u8fbc\u307e\u305a\u306b\u6bce\u56de\u8a08\u7b97\u3059\u308b\uff09\u3092\u5229\u7528\u3059\u308b\u3002\u305d\u306e\u305f\u3081\u306b\u306f\u3001GAMESS\u306einput\u30d5\u30a1\u30a4\u30eb\u4e2d\u306b<\/p>\n
 $SCF DIRSCF=.TRUE. $END<\/pre>\n
\u306e1\u884c\u304c\u5fc5\u8981\u3002\u30b9\u30ec\u30c3\u30c9\u6570\u306f<\/p>\n
$  export OMP_NUM_THREADS=8<\/code><\/pre>\n
\u3067\u6307\u5b9a\u3059\u308b\u3002<\/p>\n
Firefly\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u30d7\u30ed\u30b0\u30e9\u30e0\u3002\u65e7\u79f0PC GAMESS\u3002<\/p>\n
\u30e1\u30fc\u30eb\u3092\u9001\u3063\u305f\u3068\u3053\u308d\u3002<\/p>\n
MOPAC2016\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u516c\u5f0f\u30b5\u30a4\u30c8: MOPAC2016 – openmopac.net<\/a>
\nMOPAC2016 for CentOS 7\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066\u5c55\u958b\u3002\u7121\u6599\uff08Academic\uff09\u306eLicense Key\u3092\u53d6\u5f97\u3057\u3066\u304a\u304f\u3002<\/p>\n
$ unzip MOPAC2016_for_CentOS-7.zip\n$ sudo mkdir \/opt\/mopac\n$ sudo chmod 777 \/opt\/mopac\n$ cp MOPAC2016.exe libiomp5.so \/opt\/mopac\n$ chmod +x \/opt\/mopac\/MOPAC2016.exe<\/code><\/pre>\n
“alias mopac=”\/opt\/mopac\/MOPAC2016.exe” \u3068 “export LD_LIBRARY_PATH=\/opt\/mopac:$LD_LIBRARY_PATH” \u3092 $HOME\/.bashrc\u306b\u8ffd\u52a0\u3002<\/p>\n
$ source ~\/.bashrc\n$ mopac LICENSE_KEY\n$ mopac Example\\ data\\ set.mop<\/code><\/pre>\n
<\/p>\n
WebMO\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u516c\u5f0f\u30b5\u30a4\u30c8:webmo.net<\/a>
\nApache\u30b5\u30fc\u30d0\u304c\u81ea\u52d5\u3067\u8d77\u52d5\u3059\u308b\u3088\u3046\u306b\u3057\u3066\u304a\u304f\u3002<\/p>\n
NWChem\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u516c\u5f0f\u30b5\u30a4\u30c8: NWChem: Open Source High-Performance Computational Chemistry<\/a>
\n\u53c2\u8003\u30b5\u30a4\u30c8\uff1a NWChem v.6.8.1 – \u7b2c\u4e00\u539f\u7406\u8a08\u7b97\u5165\u9580<\/a><\/p>\n
DFT\u8a08\u7b97\u3060\u3063\u305f\u3089\u3001Firefly\u3084GAMESS\u3088\u308a\u901f\u3044\u3089\u3057\u3044\uff08\u7121\u6599\u306e\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u30bd\u30d5\u30c8\u30fb\u30d7\u30ed\u30b0\u30e9\u30e0\u306f\u3069\u308c\u304c\u3044\u3044\u306e\u304b” – in-silico notebook<\/a>\uff09\u3002<\/p>\n
OpenMPI 2.0.2\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h4>\n
OpenMPI\u306e\u30d0\u30fc\u30b8\u30e7\u30f3\u304c3\u4ee5\u4e0a\u3060\u3068\u30a8\u30e9\u30fc\u304c\u51fa\u308b\u305f\u3081\u3002<\/p>\n
$ wget https:\/\/download.open-mpi.org\/release\/open-mpi\/v2.0\/openmpi-2.0.4.tar.gz\n$ tar xvzf openmpi-2.0.4.tar.gz\n$ cd openmpi-2.0.4\n$ scl enable devtoolset-6 bash\n$ .\/configure --prefix=\/usr\/local\/open-mpi\/2.0.4_gcc6.3.1\n$ make \n$ sudo make install<\/code><\/pre>\n
NWChem 6.8.1\u306e\u30b3\u30f3\u30d1\u30a4\u30eb<\/h4>\n
$ wget https:\/\/github.com\/nwchemgit\/nwchem\/archive\/6.8.1-release.tar.gz\n$ tar xvzf 6.8.1-release.tar.gz\n$ sudo cp -r nwchem-6.8.1-release\/ \/usr\/local\/nwchem-6.8.1\n$ sudo chown -R USER:USER \/usr\/local\/nwchem-6.8.1\n$ cd \/usr\/local\/nwchem-6.8.1\n$ scl enable devtoolset-6 bash\n$ export NWCHEM_TOP=\/usr\/local\/nwchem-6.8.1\n$ export NWCHEM_TARGET=LINUX64\n$ export USE_MPI=y\n$ export USE_PYTHONCONFIG=y\n$ export PYTHONVERSION=2.7\n$ export PYTHONHOME=\/usr\n$ export MKLROOT=\/opt\/intel_user\/parallel_studio_xe_2020\/compilers_and_libraries_2020\/linux\/mkl\n$ export BLASOPT="-L$MKLROOT\/lib\/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"\n$ export USE_OPENMP=T\n$ export MPIROOT=\/usr\/local\/open-mpi\/2.0.4_gcc6.3.1\n$ export PATH=$MPIROOT\/bin:$PATH\n$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MPIROOT\/lib\n$ cd src\/\n$ make nwchem_config NWCHEM_MODULES="all python"\n$ make -jN (N\u306f\u30b9\u30ec\u30c3\u30c9\u6570)<\/code><\/pre>\n
~\/.bashrc \u306b<\/p>\n
export PATH=/usr/local/nwchem-6.8.1/bin/LINUX64:$PATH<\/pre>\n
\u3068\u8ffd\u8a18\u3002nwchem\u306e\u5b9f\u884c\u524d\u306f<\/p>\n
$ export PATH=\/usr\/local\/open-mpi\/2.0.4_gcc6.3.1\/bin:$PATH\n$ export LD_LIBRARY_PATH=\/usr\/local\/open-mpi\/2.0.4_gcc6.3.1\/lib:\/opt\/intel_user\/parallel_studio_xe_2020\/compilers_and_libraries_2020\/linux\/mkl\/lib\/intel64_lin:$LD_LIBRARY_PATH<\/code><\/pre>\n
\u3068\u3059\u308b\u3002<\/p>\n
\u4e26\u5217\u8a08\u7b97: “export OMP_NUM_THREADS=N\uff08\u30b9\u30ec\u30c3\u30c9\u6570\uff09” \uff08OpenMP\u30b9\u30ec\u30c3\u30c9\u6570\uff09\u3068 “mpirun -np N\uff08\u30d7\u30ed\u30bb\u30b9\u6570\uff09 input.nw <& output.out &” \uff08MPI\u30d7\u30ed\u30bb\u30b9\u6570\uff09\u3067\u5236\u5fa1\u3059\u308b\u3002<\/p>\n
$ mpirun -np 4 nwchem h2o.nw >& h2o.nwout &<\/code><\/pre>\n
WebMO\u3067\u306e\u5b9f\u884c\u306e\u305f\u3081\u3001\/home\/webadmin\/cgi-bin\/webmo\/run_nwchem.cgi \u3092\u7de8\u96c6\u3057\u3066\u3001$ENV{‘LD_LIBRARY_PATH’}.=”:$LD_LIBRARY_PATH”; \u306e\u884c\u306bMKL\u3068OpenMPI\u306ePATH\u3092\u8ffd\u52a0\u3057\u305f\u3002
\nWebMO\u3067\u6307\u5b9a\u3057\u306a\u3044\u3068\u3044\u3051\u306a\u3044nwchemrc\u30d5\u30a1\u30a4\u30eb\u306e\u4e2d\u8eab\u306f\u4ee5\u4e0b\u306e\u3088\u3046\u306b\u66f8\u304f\u3002<\/p>\n
nwchem_basis_library /usr/local/nwchem-6.8.1/src/basis/libraries/\nnwchem_nwpw_library /usr/local/nwchem-6.8.1/src/nwpw/libraryps/\nffield amber\namber_1 /usr/local/nwchem-6.8.1/src/data/amber_s/\namber_2 /usr/local/nwchem-6.8.1/src/data/amber_x/\n#amber_3 /usr/local/nwchem-6.8.1/src/data/amber_q/\n#amber_4 /usr/local/nwchem-6.8.1/src/data/amber_u/\nspce /usr/local/nwchem-6.8.1/src/data/solvents/spce.rst\ncharmm_s /usr/local/nwchem-6.8.1/src/data/charmm_s/\ncharmm_x /usr/local/nwchem-6.8.1/src/data/charmm_x/\n# scratch_dir /scratch\n# permanent_dir /data\n# memory_total  50000000 # 400 MB, double precision words only\n# memory_heap   12500000 # 100 MB, double precision words only\n# memory_stack  12500000 # 100 MB, double precision words only\n# memory_global 25000000 # 200 MB, double precision words only<\/pre>\n
ORCA\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u30dc\u30f3\u5927\u5b66\u306e\u516c\u5f0f\u30a6\u30a7\u30d6\u30d5\u30a9\u30fc\u30e9\u30e0<\/a>\u304b\u3089\u30d0\u30fc\u30b8\u30e7\u30f34.2.1\uff08ORCA 4.2.1, Linux, x86-64, shared, .tar.xz Archive, 380 MB\uff09\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u3066 \/opt \u306b\u5c55\u958b\u3002<\/p>\n
#!/bin/bash\nPREFIX=/usr/local/open-mpi/3.1.4_gcc6.3.1\n \nif [ -z "`echo $PATH | grep $PREFIX/bin`" ]; then\n        export PATH=$PREFIX/bin:$PATH\nfi\n \nif [ -z "`echo $LD_LIBRARY_PATH | grep $PREFIX/lib`" ]; then\n        if [ -n "$LD_LIBRARY_PATH" ]; then\n                export LD_LIBRARY_PATH=$PREFIX/lib:$LD_LIBRARY_PATH\n        else\n                export LD_LIBRARY_PATH=$PREFIX/lib\n        fi\nfi<\/pre>\n
WebMO\u304b\u3089\u4e26\u5217\u3067\u5b9f\u884c\u3059\u308b\u306b\u306f\u3001
\nPreview\u30bf\u30d6\u3067Generate\u30dc\u30bf\u30f3\u3092\u62bc\u3057\u3066\u5165\u529b\u30d5\u30a1\u30a4\u30eb\u3092\u8868\u793a\u3057\u3066<\/p>\n
! B3LYP cc-pVDZ \n%pal\nnprocs 4\nend\n\n* internal 0 1\nC 0 0 0 0.0000000 0.0000000 0.0000000\nC 1 0 0 1.5453030 0.0000000 0.0000000\n.....<\/pre>\n
\u306e\u3088\u3046\u306b %pal \u30d6\u30ed\u30c3\u30af\u3092\u633f\u5165\u3059\u308b\u3002
\n\u30bf\u30fc\u30df\u30ca\u30eb\u304b\u3089\u5b9f\u884c\u3059\u308b\u306b\u306f<\/p>\n
$ source \/opt\/orca\/mpivars.sh\n$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:\/opt\/orca\/orca_4_2_1_linux_x86-64_shared_openmpi314\n$ \/opt\/orca\/orca_4_2_1_linux_x86-64_shared_openmpi314\/orca input.inp > output.out \n\u203b MPI\u3067\u4e26\u5217\u8a08\u7b97\u3059\u308b\u306b\u306forca\u30d7\u30ed\u30b0\u30e9\u30e0\u3078\u306e\u30d5\u30eb\u30d1\u30b9\u304c\u5fc5\u8981\u3002\n$ orca_2mkl input -molden<\/code><\/pre>\n
\u6700\u5f8c\u306e\u30b3\u30de\u30f3\u30c9\u3067GBW\u30d0\u30a4\u30ca\u30ea\u30d5\u30a1\u30a4\u30eb\u304cgmolden\u306a\u3069\u3067\u8aad\u307f\u8fbc\u3080\u7528\u306eASCII\u30d5\u30a1\u30a4\u30eb\u306b\u5909\u63db\u3055\u308c\u308b\u3002<\/p>\n
Gabedit\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u69d8\u3005\u306a\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u30d7\u30ed\u30b0\u30e9\u30e0\u306eGUI\u30d5\u30ed\u30f3\u30c8\u30a8\u30f3\u30c9\u3002\u5206\u5b50\u8ecc\u9053\u306e\u53ef\u8996\u5316\u3002<\/p>\n
$ sudo yum --enablerepo=epel install pangox-compat\n$ sudo yum install gtk2-devel\n$ sudo yum --enablerepo=epel install gtkglext-devel gtkglext-libs openbabel\n$ tar xvzf GabeditSrc250.tar.gz\n$ cd GabeditSrc250\n$ make\n$ sudo cp .\/gabedit \/usr\/local\/bin<\/code><\/pre>\n
MOLDEN\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u69d8\u3005\u306a\u91cf\u5b50\u5316\u5b66\u8a08\u7b97\u30d7\u30ed\u30b0\u30e9\u30e0\u306eGUI\u30d5\u30ed\u30f3\u30c8\u30a8\u30f3\u30c9\u3002\u5206\u5b50\u8ecc\u9053\u306e\u53ef\u8996\u5316\u3002<\/p>\n
$ sudo yum install imake #provides "makedepend"\n$ wget ftp:\/\/ftp.cmbi.umcn.nl\/pub\/molgraph\/molden\/molden5.9.tar.gz\n$ tar xvzf molden5.9.tar.gz\n$ cd molden5.9\n$ make\n$ cd ..\/\n$ sudo cp -r .\/molden5.9 \/usr\/local\/\n$ cd \/usr\/local\/molden5.9\n$ sudo chmodrm .\/*.o .\/*.f .\/*.c .\/makefile*<\/code><\/pre>\n
IboView<\/a>\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
Intrinsic Atomic Orbitals\uff08IAOs\uff09\u306b\u57fa\u3065\u304f\u5206\u5b50\u306e\u96fb\u5b50\u69cb\u9020\u89e3\u6790\u30d7\u30ed\u30b0\u30e9\u30e0\u3002\u30d0\u30fc\u30b8\u30e7\u30f320150427\u3002<\/p>\n
$ wget http:\/\/www.iboview.org\/bin\/ibo-view.20150427.tar.bz2\n$ scl enable devtoolset-6 bash\n$ tar xvjf ibo-view.20150427.tar.bz2\n$ cd ibo-view.20150427\n$ export MKLROOT=\/opt\/intel_user\/parallel_studio_xe_2020\/compilers_and_libraries_2020\/linux\/mkl\n$ qmake-qt4 main.pro QMAKE_INSTALL_DIR=\/usr\/local\/ibo-view\n$ make\n$ iboview examples\/c2h4.xyz<\/code><\/pre>\n
OpenGL\u306e\u30d0\u30fc\u30b8\u30e7\u30f3 >3.2\u3092\u8981\u6c42\u3059\u308b\u3002Mac\u5074\u306eXquartz\u3067\u306f\u8868\u793a\u3067\u304d\u306a\u304b\u3063\u305f\u3002
\n<\/p>\n
Open-source PyMOL\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u5206\u5b50\u69cb\u9020\u53ef\u8996\u5316\u30d7\u30ed\u30b0\u30e9\u30e0\u3002
\n\u53c2\u8003\u30b5\u30a4\u30c8:Linux Install – PyMOLwiki<\/a>
\nmacOS\/CentOS 7\/Ubuntu 18.04\u3078\u306e\u30aa\u30fc\u30d7\u30f3\u30bd\u30fc\u30b9\u7248PyMOL\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u65b9\u6cd5 – Qiita<\/a><\/p>\n
$ sudo yum install glew-devel glm-devel python3-devel\n$ sudo yum --enablerepo=epel install python-pmw python36-numpy msgpack-devel\n$ sudo pip3.6 install --upgrade pip\n$ sudo pip3.6 install sip pyqt5 pmw mmtf-python\n$ chmodgit clone https:\/\/github.com\/schrodinger\/pymol-open-source.git\n$ chmodgit clone https:\/\/github.com\/rcsb\/mmtf-cpp.git\n$ mv mmtf-cpp\/include\/mmtf* pymol-open-source\/include\/\n$ cd pymol-open-source\n$ sudo su\n# prefix=\/usr\/local\/pymol\n# python3 setup.py install --home=$prefix<\/code><\/pre>\n
\/usr\/local\/pymol\/bin \u306bPATH\u3092\u901a\u3059\u3002<\/p>\n
MODELLER\u306e\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/h3>\n
\u30bf\u30f3\u30d1\u30af\u8cea\u30db\u30e2\u30ed\u30b8\u30fc\u30e2\u30c7\u30ea\u30f3\u30b0\u30d7\u30ed\u30b0\u30e9\u30e0<\/a>\u3002<\/p>\n
$ conda config --add channels salilab\n$ conda install modeller<\/code><\/pre>\n
\u30d7\u30ea\u30f3\u30bf\u30fc\u306e\u30bb\u30c3\u30c8\u30a2\u30c3\u30d7<\/h3>\n
FUJI XEROX\u306e\u30a6\u30a7\u30d6\u30b5\u30a4\u30c8<\/a>\u304b\u3089Linux\u7528\u30c9\u30e9\u30a4\u30d0\u3092\u30c0\u30a6\u30f3\u30ed\u30fc\u30c9\u3057\u305f\u3002<\/p>\n
$ sudo rpm -ivh Fuji_Xerox-DocuPrint_C2110-1.0-1.i386.rpm<\/code><\/pre>\n
CUPS\u306f\u8d77\u52d5\u3057\u3066\u3044\u305f\u306e\u3067\u3001Firefox\u304b\u3089 http:\/\/localhost:631\/ \u306b\u30a2\u30af\u30bb\u30b9\u3002\u5370\u5237\u30c6\u30b9\u30c8\u3059\u308b\u3068\u3001<\/p>\n
(/usr/lib/cups/filter/FX_DocuPrint_C2110/FXM_PF) stopped with status 102 (No such file or directory)<\/pre>\n
\u3068\u3044\u3046\u30a8\u30e9\u30fc\u3067\u6b62\u307e\u308b\u3002”\/usr\/lib\/cups\/filter\/FX_DocuPrint_C2110\/FXM_PF” \u3092\u5b9f\u884c\u3057\u3088\u3046\u3068\u3059\u308b\u3068\u3001”\/lib\/ld-linux.so.2″ \u304c\u306a\u3044\u3068\u8a00\u308f\u308c\u308b\u3002”64bit\u74b0\u5883\u3067\u300132bit\u3067\u30d3\u30eb\u30c9\u3055\u308c\u305f\u30b3\u30de\u30f3\u30c9\u3092\u5b9f\u884c\u3059\u308b\u3068\u4e0a\u8a18\u30a8\u30e9\u30fc” \u304c\u51fa\u308b\u3089\u3057\u3044\u3002<\/p>\n
$ sudo yum install ld-linux.so.2<\/code><\/pre>\n
\u3068\u3059\u308b\u3068<\/p>\n
  glibc.i686 0:2.17-292.el7                                                                   \n  nss-softokn-freebl.i686 0:3.44.0-8.el7_7<\/pre>\n
\u304c\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u305f\u3002\u6b21\u306f “libcups.so.2” \u304c\u306a\u3044\u3068\u8a00\u308f\u308c\u305f\u306e\u3067\u540c\u69d8\u306byum\u304b\u3089\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb<\/p>\n
$ sudo yum install libcups.so.2<\/code><\/pre>\n
\u3057\u305f\u3068\u3053\u308d\u5927\u91cf\u306b\u30d1\u30c3\u30b1\u30fc\u30b8\u304c\u30a4\u30f3\u30b9\u30c8\u30fc\u30eb\u3055\u308c\u305f\u3002\u5370\u5237\u306f\u3067\u304d\u308b\u3088\u3046\u306b\u306a\u3063\u305f\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
“Great Red Oystrich Make …<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"om_disable_all_campaigns":false,"_uag_custom_page_level_css":"","_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"_uf_show_specific_survey":0,"_uf_disable_surveys":false,"_locale":"ja","_original_post":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/?p=1931","footnotes":""},"categories":[5],"tags":[],"class_list":["post-1931","post","type-post","status-publish","format-standard","hentry","category-5","ja"],"aioseo_notices":[],"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false,"onepress-blog-small":false,"onepress-small":false,"onepress-medium":false},"uagb_author_info":{"display_name":"RCY","author_link":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/author\/charlesy\/"},"uagb_comment_info":3,"uagb_excerpt":"“Great Red Oystrich Make ...","_links":{"self":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1931","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/comments?post=1931"}],"version-history":[{"count":123,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1931\/revisions"}],"predecessor-version":[{"id":2960,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/posts\/1931\/revisions\/2960"}],"wp:attachment":[{"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/media?parent=1931"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/categories?post=1931"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ag.kagawa-u.ac.jp\/charlesy\/wp-json\/wp\/v2\/tags?post=1931"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}