iSALE - CentOS6.5 へのインストールレポート Diff
- Added parts are displayed like this.
- Deleted parts are displayed
like this.
((<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|URL:http://www.cfca.nao.ac.jp/mseries>)) （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|URL:http://www.isale-code.de/redmine/projects/isale/wiki/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
基本的なインストール方法は ((<install_guide|URL:http://www.isale-code.de/redmine/projects/isale/wiki/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