xray/cns をテンプレートにして作成
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開始行:
本家 [[http://cns-online.org/>+http://cns-online.org/]]
[[xray/Phenix]]を使う方が多いようですが、たまに使われる方...
&size(10){以前の記事[[xray/cns160402]]};
***パッケージインストール [#x4e27204]
#code(nonumber){{
[root@c ~]# cd /Appl/src/
[root@c src]# ls -lh cns_solve_1.3_all_intel-mac_linux.ta...
-rw-r--r-- 1 root root 72M 4月 2 09:23 cns_solve_1.3_al...
[root@c src]#
}}
このパッケージを展開する場所がインストールする場所になる...
&color(red){*};&size(10){「./configure --prefix=...」に慣...
#code(nonumber){{
[root@c src]# cd /Appl/Linux
[root@c Linux]# gzip -cd ../src/cns_solve_1.3_all_intel-m...
[root@c Linux]# chown -R root:root ./cns_solve_1.3
}}
&color(magenta){cns_solve_env};ファイルを修正
#code(diff,nonumber){{
--- cns_solve_env.orig 2010-07-23 07:31:11.000000000 +0900
+++ cns_solve_env 2016-04-02 09:47:32.431765514 +0900
@@ -15,7 +15,7 @@
#
# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE C...
- setenv CNS_SOLVE '_CNSsolve_location_'
+ setenv CNS_SOLVE '/Appl/Linux/cns_solve_1.3'
#
# ======================================================...
}}
バイナリパッケージの実行ファイルを使用するならこれで完了
***使用方法 [#a66bab03]
&color(magenta){cns_solve_env};を読み込んで、cnsの各種コ...
ただし、(t)cshで&color(magenta){cns_solve_env};は書かれて...
#code(nonumber){{
[illya@c ~]$ echo $SHELL
/bin/bash
[illya@c ~]$ csh
[illya@c ~]$ echo $0 *現在使っているSHELLの確認
csh
[illya@c ~]$
[illya@c ~]$ source /Appl/Linux/cns_solve_1.3/cns_solve_env
}}
そして、プログラムを実行する
#code(nonumber){{
[illya@c ~]$ cns
===============================================...
| ...
| Crystallography & NMR System (CNS)...
| CNSsolve ...
| ...
===============================================...
Version: 1.3
Status: General release
===============================================...
Written by: A.T.Brunger, P.D.Adams, G.M.Clore,...
P.Gros, R.W.Grosse-Kunstleve,J.-S....
J.Kuszewski, M.Nilges, N.S.Pannu, ...
L.M.Rice, G.F.Schroeder, T.Simonso...
Copyright (c) 1997-2010 Yale University
===============================================...
Running on machine: c.sybyl.local (x86_64/Linu...
with 2 threads
Program started by: illya
Program started at: 10:01:05 on 02-Apr-2016
===============================================...
FFT3C: Using FFTPACK4.1
CNSsolve>stop
===============================================...
Maximum dynamic memory allocation: 8201488...
Maximum dynamic memory overhead: 208...
Program started at: 10:01:05 on 02-Apr-2016
Program stopped at: 10:01:07 on 02-Apr-2016
CPU time used: 0.0146 seconds
===============================================...
[illya@c ~]$
}}
&color(red){*};bashの場合は、こちら[[xray/cns/cns_solve_e...
***CNSsolveのwebをローカルに [#jd4772d5]
web画面を使ってインプットファイルを作れるが、その際、cns...
これをやめさせて、内部(研究室)のwebサーバで完結させてみる。
まず、&color(orangered){bin/www_cns_setup};を実行する。主...
-作る内部サイトのサイト名
-webコンテンツのコピー先(&color(orange){bin/www_server_se...
-cgiディレクトリの名称(中間ディレクトリ名といっていいかも)
の３つ。このスクリプトの中身は、$CNS_SOLVE/doc/html/local...
では実行してみる
#code(nonumber){{
[root@c ~]# echo $0
-bash
[root@c ~]# source /Appl/Linux/cns_solve_1.3/cns_solve_en...
[root@c ~]#
root@c ~]# /Appl/Linux/cns_solve_1.3/bin/www_cns_setup
name of WWW server [default: c.sybyl.local ]->
path to the start of WWW tree [default: /home/httpd/html ...
name of WWW CGI directory [default: cgi-bin ]-> .
full path to PERL on WWW server [default: /usr/bin/perl ]->
=========================================================...
location of CNSsolve directory is: /Appl/Linux/cns_solve_...
version of CNSsolve is: 1.3
name of WWW server is: c.sybyl.local
path to the start of the WWW tree is: /var/www
name of the CGI directory is: .
location of the PERL program is: /usr/bin/perl
=========================================================...
continue with these parameters? [y/n]-> y
proceeding with CNSsolve HTML interface installation
making directory /Appl/Linux/cns_solve_1.3/doc/html/local
:
:
Ask your WWW server administrator to run:
/Appl/Linux/cns_solve_1.3/bin/www_server_setup
to modify your local WWW server for the CNSsolve HTML int...
[root@c ~]#
}}
次に、www_server_setupを実行する
#code(nonumber){{
[root@c ~]# /Appl/Linux/cns_solve_1.3/bin/www_server_setup
location of CNSsolve directory [default: /Appl/Linux/cns_...
path to the start of WWW tree [default: /home/httpd/html ...
full path to CGI directory [default: /home/httpd/cgi-bin ...
=========================================================...
location of the CNSsolve directory is: /Appl/Linux/cns_so...
version of CNSsolve is: 1.3
path to the start of the WWW tree is: /var/www
location of the CGI directory is: /var/www
=========================================================...
continue with these parameters? [y/n]-> y
proceeding with CNSsolve HTML interface installation
making directory /var/www/cns_solve_1.3
making Apache/Httpd authentication file /var/www/cns_solv...
adding link from /Appl/Linux/cns_solve_1.3/inputs to /var...
adding link from /Appl/Linux/cns_solve_1.3/modules to /va...
adding link from /Appl/Linux/cns_solve_1.3/libraries to /...
adding link from /Appl/Linux/cns_solve_1.3/utils to /var/...
making directory /var/www/cns_solve_1.3/doc
making directory /var/www/cns_solve_1.3/doc/html
making Apache/Httpd authentication file /var/www/cns_solv...
adding link: /Appl/Linux/cns_solve_1.3/doc/html/icons to ...
a CNSsolve CGI directory already exists: /var/www/cns_sol...
overwrite the files in this directory? [y/n]-> y
overwriting contents of /var/www/cns_solve_1.3
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_defa...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_form...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_info...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_inpu...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_jsed...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_libr...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_menu...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_modu...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_save...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_util...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_view...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns.lib ...
Server side of CNSsolve HTML interface installation compl...
[root@c ~]#
}}
これでコンテンツの準備は完了と思ったのだが、doc/html配下...
なので、
#code(nonumber){{
[root@c ~]# cd /var/www/cns_solve_1.3/doc
[root@c doc]# rsync -av /Appl/Linux/cns_solve_1.3/doc/htm...
}}
としてコピーさせた。次にhttpdの設定。
上記作業でコンテンツの基点は「/var/www/cns_solve_1.3」と...
&color(red){*};&size(10){もしcgi-binのディレクトリを「.」...
httpdに読ませる設定ファイルは、
#code(nonumber){{
[root@c ~]# vi /etc/httpd/conf.d/cns.conf
Alias /cns /var/www/cns_solve_1.3/doc/html
Alias /cns_solve_1.3 /var/www/cns_solve_1.3
<Directory "/var/www/cns_solve_1.3">
Options +ExecCGI
AddHandler cgi-script .pl .cgi
<RequireAny>
Require ip 192.168.0.
Require all denied
</RequireAny>
</Directory>
[root@c ~]#
}}
とした。httpdを再起動させる
#code(nonumber){{
[root@c ~]# systemctl restart httpd
}}
ブラウザで「http://c.sybyl.local/cns」にアクセスして、inp...
あと、下記ファイルを削除しないと動かなかった..
#code(nonumber){{
[root@c ~]# mv /var/www/cns_solve_1.3/.htaccess /var/www...
}}
終了行:
本家 [[http://cns-online.org/>+http://cns-online.org/]]
[[xray/Phenix]]を使う方が多いようですが、たまに使われる方...
&size(10){以前の記事[[xray/cns160402]]};
***パッケージインストール [#x4e27204]
#code(nonumber){{
[root@c ~]# cd /Appl/src/
[root@c src]# ls -lh cns_solve_1.3_all_intel-mac_linux.ta...
-rw-r--r-- 1 root root 72M 4月 2 09:23 cns_solve_1.3_al...
[root@c src]#
}}
このパッケージを展開する場所がインストールする場所になる...
&color(red){*};&size(10){「./configure --prefix=...」に慣...
#code(nonumber){{
[root@c src]# cd /Appl/Linux
[root@c Linux]# gzip -cd ../src/cns_solve_1.3_all_intel-m...
[root@c Linux]# chown -R root:root ./cns_solve_1.3
}}
&color(magenta){cns_solve_env};ファイルを修正
#code(diff,nonumber){{
--- cns_solve_env.orig 2010-07-23 07:31:11.000000000 +0900
+++ cns_solve_env 2016-04-02 09:47:32.431765514 +0900
@@ -15,7 +15,7 @@
#
# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE C...
- setenv CNS_SOLVE '_CNSsolve_location_'
+ setenv CNS_SOLVE '/Appl/Linux/cns_solve_1.3'
#
# ======================================================...
}}
バイナリパッケージの実行ファイルを使用するならこれで完了
***使用方法 [#a66bab03]
&color(magenta){cns_solve_env};を読み込んで、cnsの各種コ...
ただし、(t)cshで&color(magenta){cns_solve_env};は書かれて...
#code(nonumber){{
[illya@c ~]$ echo $SHELL
/bin/bash
[illya@c ~]$ csh
[illya@c ~]$ echo $0 *現在使っているSHELLの確認
csh
[illya@c ~]$
[illya@c ~]$ source /Appl/Linux/cns_solve_1.3/cns_solve_env
}}
そして、プログラムを実行する
#code(nonumber){{
[illya@c ~]$ cns
===============================================...
| ...
| Crystallography & NMR System (CNS)...
| CNSsolve ...
| ...
===============================================...
Version: 1.3
Status: General release
===============================================...
Written by: A.T.Brunger, P.D.Adams, G.M.Clore,...
P.Gros, R.W.Grosse-Kunstleve,J.-S....
J.Kuszewski, M.Nilges, N.S.Pannu, ...
L.M.Rice, G.F.Schroeder, T.Simonso...
Copyright (c) 1997-2010 Yale University
===============================================...
Running on machine: c.sybyl.local (x86_64/Linu...
with 2 threads
Program started by: illya
Program started at: 10:01:05 on 02-Apr-2016
===============================================...
FFT3C: Using FFTPACK4.1
CNSsolve>stop
===============================================...
Maximum dynamic memory allocation: 8201488...
Maximum dynamic memory overhead: 208...
Program started at: 10:01:05 on 02-Apr-2016
Program stopped at: 10:01:07 on 02-Apr-2016
CPU time used: 0.0146 seconds
===============================================...
[illya@c ~]$
}}
&color(red){*};bashの場合は、こちら[[xray/cns/cns_solve_e...
***CNSsolveのwebをローカルに [#jd4772d5]
web画面を使ってインプットファイルを作れるが、その際、cns...
これをやめさせて、内部(研究室)のwebサーバで完結させてみる。
まず、&color(orangered){bin/www_cns_setup};を実行する。主...
-作る内部サイトのサイト名
-webコンテンツのコピー先(&color(orange){bin/www_server_se...
-cgiディレクトリの名称(中間ディレクトリ名といっていいかも)
の３つ。このスクリプトの中身は、$CNS_SOLVE/doc/html/local...
では実行してみる
#code(nonumber){{
[root@c ~]# echo $0
-bash
[root@c ~]# source /Appl/Linux/cns_solve_1.3/cns_solve_en...
[root@c ~]#
root@c ~]# /Appl/Linux/cns_solve_1.3/bin/www_cns_setup
name of WWW server [default: c.sybyl.local ]->
path to the start of WWW tree [default: /home/httpd/html ...
name of WWW CGI directory [default: cgi-bin ]-> .
full path to PERL on WWW server [default: /usr/bin/perl ]->
=========================================================...
location of CNSsolve directory is: /Appl/Linux/cns_solve_...
version of CNSsolve is: 1.3
name of WWW server is: c.sybyl.local
path to the start of the WWW tree is: /var/www
name of the CGI directory is: .
location of the PERL program is: /usr/bin/perl
=========================================================...
continue with these parameters? [y/n]-> y
proceeding with CNSsolve HTML interface installation
making directory /Appl/Linux/cns_solve_1.3/doc/html/local
:
:
Ask your WWW server administrator to run:
/Appl/Linux/cns_solve_1.3/bin/www_server_setup
to modify your local WWW server for the CNSsolve HTML int...
[root@c ~]#
}}
次に、www_server_setupを実行する
#code(nonumber){{
[root@c ~]# /Appl/Linux/cns_solve_1.3/bin/www_server_setup
location of CNSsolve directory [default: /Appl/Linux/cns_...
path to the start of WWW tree [default: /home/httpd/html ...
full path to CGI directory [default: /home/httpd/cgi-bin ...
=========================================================...
location of the CNSsolve directory is: /Appl/Linux/cns_so...
version of CNSsolve is: 1.3
path to the start of the WWW tree is: /var/www
location of the CGI directory is: /var/www
=========================================================...
continue with these parameters? [y/n]-> y
proceeding with CNSsolve HTML interface installation
making directory /var/www/cns_solve_1.3
making Apache/Httpd authentication file /var/www/cns_solv...
adding link from /Appl/Linux/cns_solve_1.3/inputs to /var...
adding link from /Appl/Linux/cns_solve_1.3/modules to /va...
adding link from /Appl/Linux/cns_solve_1.3/libraries to /...
adding link from /Appl/Linux/cns_solve_1.3/utils to /var/...
making directory /var/www/cns_solve_1.3/doc
making directory /var/www/cns_solve_1.3/doc/html
making Apache/Httpd authentication file /var/www/cns_solv...
adding link: /Appl/Linux/cns_solve_1.3/doc/html/icons to ...
a CNSsolve CGI directory already exists: /var/www/cns_sol...
overwrite the files in this directory? [y/n]-> y
overwriting contents of /var/www/cns_solve_1.3
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_defa...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_form...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_info...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_inpu...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_jsed...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_libr...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_menu...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_modu...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_save...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_util...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns_view...
copying /Appl/Linux/cns_solve_1.3/doc/html/local/cns.lib ...
Server side of CNSsolve HTML interface installation compl...
[root@c ~]#
}}
これでコンテンツの準備は完了と思ったのだが、doc/html配下...
なので、
#code(nonumber){{
[root@c ~]# cd /var/www/cns_solve_1.3/doc
[root@c doc]# rsync -av /Appl/Linux/cns_solve_1.3/doc/htm...
}}
としてコピーさせた。次にhttpdの設定。
上記作業でコンテンツの基点は「/var/www/cns_solve_1.3」と...
&color(red){*};&size(10){もしcgi-binのディレクトリを「.」...
httpdに読ませる設定ファイルは、
#code(nonumber){{
[root@c ~]# vi /etc/httpd/conf.d/cns.conf
Alias /cns /var/www/cns_solve_1.3/doc/html
Alias /cns_solve_1.3 /var/www/cns_solve_1.3
<Directory "/var/www/cns_solve_1.3">
Options +ExecCGI
AddHandler cgi-script .pl .cgi
<RequireAny>
Require ip 192.168.0.
Require all denied
</RequireAny>
</Directory>
[root@c ~]#
}}
とした。httpdを再起動させる
#code(nonumber){{
[root@c ~]# systemctl restart httpd
}}
ブラウザで「http://c.sybyl.local/cns」にアクセスして、inp...
あと、下記ファイルを削除しないと動かなかった..
#code(nonumber){{
[root@c ~]# mv /var/www/cns_solve_1.3/.htaccess /var/www...
}}
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