In your job script, you can set up environmental variable and options using setenv command. However, when you execute parallel job at multiple nodes, they are not reflected to all slave nodes.
In this case, please use the NQSII option '-v' in the job script as follows.
#PBS -v [environment variable or options]=[value]
We introduce tuning examples by CMC in cooperation with NEC. Please refer the following pages. Please note that needs authentication by user account.
Yes, you can use it.
A login shell is set to csh by default on SX-ACE and VCC. How to change shell is the following.
$ bash
If you want to change login shell from csh to bash, please describe the following in ".cshrc" file on home directory.
exec bash
It is necessary to prepare ".bashrc" file by yourself When you set an alias to bash.
A login shell is set to bash by default on OCTOPUS.
Yes.
When you outputted the binary data on SX-9 with unformatted WRITE statement,etc, SX-ACE can read this binary data.
We provide the command for checking disk usage.
Please see the following page.
How to check resource usage
You do not have to do anything. If you would not apply for continue service to the next fiscal year, we end your account at the end of fiscal year.
You can check your job status with the following command.
sstat
If the system decide when your job starts, STT will change status to ASG(Assigned) and PlannedStartTime will show what time your job starts.
Please see the following page about the detail.
You can use these libraries on our all system.
We are providing the library, MathKeisan, for SX-ACE user. This library include Blas and Lapack and other library. Please see the following page about the detail of use.
How to use MathKeisan
And we are providing the library, IntelMKL, for OCTOPUS user. This library include Lapack and Blas also. Please see the following page about the detail of use.
It probably has a problem with a character/line feed code in your job script. Our system's character encoding is UTF-8 and the line feed code is LF. When you copy a file to our system, you should do it by ASCII or convert codes using the command like iconv.
The scheduler is scheduling jobs by requested resources and user's priority. Therefore, you may have to wait depending on your request.
You can see the scheduling status of your job using the command below.
sstat
When the status(STT) is ASG(Assigned), it indicates that the job is scheduled already. PlannedStartTime shows actually execution start time of it.
For further information, please see below.
If you wait a very long time, the job request might be exceeded resource limit. Or there might be any problem with the system. In that case, Please contact us.
system{at}hpc.cmc.osaka-u.ac.jp
「qwait」コマンドを使用することで、実現可能です。
このコマンドは引数で与えたリクエストID(例：12345.cmc)を待ち合わせするというものです。
指定のリクエストIDのジョブが終了するとメッセージ終了と共にコマンドが終了します。
コマンドの詳細についてはポータルで公開されておりますマニュアル
「NQS利用の手引」のリファレンス編 第1章 ユーザコマンドをご参照頂けますようお願い致します。
NQSII利用の手引き(要認証)
NQSV利用の手引き
※ man qwait でもヘルプを参照できます。
qwait については下記のような使い方が可能です。
監視スクリプトをバックグラウンド実行し、スクリプト内で qwaitを実行します。
exitコード(上記のマニュアルに記載があります)で判定し、その後の動作を分岐させています。
参考にしてください。
-----------
$ qsub job1-1
Request 12345.cmc submitted to queue: Pxx.
$ (./chkjob >& log &)
----- chkjob
#!/bin/sh
while :
do
qwait 12345.cmc #リクエストIDを任意のものに変更して下さい
case $? in
0) qsub job1-2;exit;;
1) qsub job2-1;exit;;
2) qsub job3-1;exit;;
3) echo NQS error | mail xxxx@yyyy.ac.jp;exit;;#メールアドレスを任意のものに変更してください
7) continue;;
*) ;;
esac
done
------------
以上です。
このエラーの原因は基本的に以下の２つのどちらかとなります。
改行コードがCRLFのファイルはエディタ(vi,emacsなど)で開いた際、画面下に[DOS]と表記されます。
アップロードする前の対処方法としては下記の通りです。
またアップロード後であっても、フロントエンドノード上で以下のコマンドを実行することで、
改行コードがCRLFからLFに変換されたsample2.shが生成されます。
sed 's/r//g' sample.sh > sample2.sh
In the case of SX cross compiler, you can compile in the following procedure.
% sxc++ -S a.c
% sxf90 b.f90 a.s
In the case of intel compiler, you can compile in the following procedure.
% icc -c a.c
% ifort b.f90 a.o
You can use commands written the Users's Reference. Please write this command to the job script file and submit.
Utility Programs
[Example] If "water.chk" on current directory changes "water.fchk", please write following script to the job script file.
${g09root}/g09/formchk water.chk water.fchk
