CentOS6.5 へのインストールレポート
国立天文台 天文シミュレーションプロジェクト 共同利用計算機 計算サーバ (w999.cfca.nao.ac.jp)にインストールした際の記録
基本的なインストール方法は install_guide に従った
事前準備
必要なqt3-develとfreeglut-develをyumで管理者に追加してもらい、pgplotはlocalにinstallを行った
[wakitasg@w999 ~]$ tar zxf pgplot5.2.tar.gz [wakitasg@w999 ~]$ mkdir -p ./local/pgplot [wakitasg@w999 ~]$ cd -p ./local/pgplot [wakitasg@w999 pgplot]$ cp ~/pgplot/drivers.list ./ [wakitasg@w999 pgplot]$ vi drivers.list 19 GIDRIV 1 /GIF GIF-format file, landscape 20 GIDRIV 2 /VGIF GIF-format file, portrait [wakitasg@w999 pgplot]$ ~/pgplot/makemake ~/pgplot linux g77_gcc [wakitasg@w999 pgplot]$ vi makefile 25 FCOMPL=gfortran 891 pndriv.o : /usr/include/png.h /usr/include/pngconf.h /usr/include/zlib.h /usr/include/zconf.h [wakitasg@w999 pgplot]$ make *** Finished compilation of PGPLOT *** Note that if you plan to install PGPLOT in a different directory than the current one, the following files will be needed. libpgplot.a libpgplot.so grfont.dat rgb.txt Also note that subsequent usage of PGPLOT programs requires that the full path of the chosen installation directory be named in an environment variable named PGPLOT_DIR.
- 参考サイト
- http://www.isale-code.de/redmine/projects/isale/wiki/ISALE_on_Fedora
- http://www.isale-code.de/redmine/projects/isale/wiki/Installing_pgplot
iSALE-chicxulub の install
ソースの取得
天文シミュレーションプロジェクトのネットワークの都合上、svnの実行の際は少し特殊である
[shigeru@localhost:~]$ssh -R 10080:earth.naturkundemuseum-berlin.de:3690 wakitasg@w999 [wakitasg@w999 ~]$ svn co --username shigeru svn://localhost:10080/iSALE/tags/chicxulub ./iSALE-Chicxulub Authentication realm: <svn://localhost:10080> iSALE Password for 'shigeru': (mailで送られてきたものを入れる:redmineのパスワードとは別物) ----------------------------------------------------------------------- ATTENTION! Your password for authentication realm: <svn://localhost:10080> iSALE can only be stored to disk unencrypted! You are advised to configure your system so that Subversion can store passwords encrypted, if possible. See the documentation for details. You can avoid future appearances of this warning by setting the value of the 'store-plaintext-passwords' option to either 'yes' or 'no' in '/home/wakitasg/.subversion/servers'. ----------------------------------------------------------------------- Store password unencrypted (yes/no)? no (noを選択した) (ファイル名が多数表示される) Checked out revision 1544.
configureとmake
localにinstallしたpgplotにPATHを通すために、少し長めとなる
[wakitasg@w999 iSALE-Chicxulub]$ ./configure --prefix=/home/wakitasg/mwork2/isale --with-isaleplot --with-vimod --with-pgplot-lib="/home/wakitasg/local/pgplot/libpgplot.a -L/usr/lib64 -lpng -lz -lX11" --------- TESTING PERMISSIONS ---------------------------------- checking existence or writing permissions of /home/wakitasg/mwork2/isale... does not exist, will be created ---------------------------------------------------------------- --------- CONFIGURATION PROCESS SUMMARY ------------------------ ---------------------------------------------------------------- Version flag........................................... -DREV=1544 Make command for external packages..................... make --silent Make flags............................................. --no-print-directory --silent Debugging kernel enabled............................... no Debugging libraries enabled............................ no Profiling enabled...................................... no Kinematic description of motion........................ EULER Advection mode......................................... MAS ANEOS library.......................................... Fortran compiler....................................... gfortran Fortran flags.......................................... -O3 -DREV=1544 -ffree-form Fortran77 compiler..................................... gfortran Fortran77 flags........................................ -O3 -DREV=1544 Fortran additional flags............................... -Dlinux -Dgfortran -DARCH_x86_64 Fortran flags for iSALE3D.............................. -DEULER -DADV_MAS -DFRONTFIX Fortran compiler for parallel compilation.............. gfortran Fortran compiler for iSALE-2D.......................... gfortran Fortran flag for invocation of CPP..................... -x f95-cpp-input C compiler............................................. gcc C flags (debugging and optimization) .................. -O3 -DREV=1544 C++ compiler........................................... g++ C++ flags (debugging and optimization) ................ -O3 -DREV=1544 VIMoD-path............................................. ${datarootdir}/vimod qt3 support required................................... yes qt3 support available.................................. yes qt3 includes........................................... -I/usr/lib64/qt-3.3/include qt3 libraries.......................................... -L/usr/lib64/qt-3.3/lib -lqt-mt OpenGL support required................................ yes OpenGL support available............................... yes OpenGL includes........................................ -I/usr/include -I/usr/include OpenGL libraries....................................... -L/lib -lGL -lGLU pgplot support required................................ yes pgplot support available............................... yes pgplot libraries....................................... /home/wakitasg/local/pgplot/libpgplot.a -L/usr/lib64 -lpng -lz -lX11 -L/usr/lib64 -lpng -lz -L/usr/lib64 -lX11 LaTeX required......................................... no ---------------------------------------------------------------- --------------------------------------------- DESIRED / AVAILABLE / ENABLED iSALE-2D..................................... yes / yes / yes iSALE-3D..................................... yes / no / no iSALE-tests.................................. yes / yes / yes docsrc....................................... no / yes / no compression libraries (libjc)................ yes / yes / yes vimod........................................ yes / yes / yes jtools....................................... no / no / no tools........................................ yes / no / no iSALEPlot.................................... yes / yes / yes ANEOS........................................ yes / no / no everything seems to be OK - installation into.......... /home/wakitasg/mwork2/isale ---------------------------------------------------------------- ---------------------------------------------------------------- ---------------------------------------------------------------- [wakitasg@w999 iSALE-Chicxulub]$ time make(すぐに終わる) real 1m7.057s user 0m45.170s sys 0m5.710s [wakitasg@w999 iSALE-Chicxulub]$ time make install(すぐに終わる) real 0m6.635s user 0m0.487s sys 0m0.409s
デモを実行
計算サーバでは実行ファイルをその場では実行することは許可されていないため、ジョブスクリプトを書いてから実行することになる
[wakitasg@w999 iSALE-Chicxulub]$ cd ~/mwork2/isale/ [wakitasg@w999 isale]$ cd share/examples/demo2D/ [wakitasg@w999 demo2D]$ vi isale.pbs (ジョブスクリプトの作成) #! /bin/sh #PBS -r y #PBS -o Log.out #PBS -e Log.err #PBS -N iSALE # Go to this job's working directory cd $PBS_O_WORKDIR # Run your executable time ./iSALE2D [wakitasg@w999 demo2D]$ qsub isale.pbs (ジョブの投入) [wakitasg@w999 demo2D]$ cat Log.err (かかった計算時間) real 0m22.168s user 0m20.069s sys 0m0.560s
計算結果を描画
こちらも同様にジョブの投入を行う
[wakitasg@w999 demo2D]$ cd demo2D [wakitasg@w999 demo2D]$ cp ../isale.pbs ./isaleplot.pbs # Run your executable time ../iSALEPlot -f ../iSALEPlot.inp -m jdata.dat [wakitasg@w999 demo2D]$ cat Log.out %PGPLOT, Unable to read font file: grfont.dat %PGPLOT, Use environment variable PGPLOT_FONT to specify the location of the PGPLOT grfont.dat file.
エラーの通り、結果のグラフに文字がなかったので、暫定的に以下を実行して解決
[wakitasg@w999 demo2D]$ ln -s ~/local/pgplot/grfont.dat grfont.dat
これで無事に文字が表示されるようになった
おまけで動画を作成
[wakitasg@w999 demo2D]$ cd DamPre/ [wakitasg@w999 DamPre]$ convert -delay 10 -loop 0 00*.png iSALE2D-demo.gif
Keyword(s):
References:[3. インストール]