2019.12.05

Can I submit many jobs at once while setting other input files/execution files per job?

If your file name includes a sequential number, you can do it with a "parametric job" on our system.
An environmental value "$PBS_$SUBREQNO" store a sequential number that you specified with "qsub -t" option (1 - 5 number in the following example).
When you submit a "parametric job", our system receives a few jobs (5 jobs in the following example) set different input files per job (input1 - input5 in the following example). 

example: job script file

 

example: how to submit a job

 

example: qstat result: in the case of a "parametric job", qstat display one record per one qsub

 

example: sstat result: in the case of "parametric job", sstat display record as much as a number that you specified with "qsub -t" option

2019.04.11

Could I run some jobs at the same time?

If our system resource is not crowded, you can run some jobs at the same time with the following procedure.

qsub A.nqs
qsub B.nqs

2018.12.20

When I submit a job-request, we get a error message, "NQScrereq: [BSV ELIMEXCEED] Global submit limit has exceeded."

This error is for exceeding a limit number of submitting job per user or per system. We set this limit for preventing an accident. Please inform us from the following form.

Inquiry form

2017.11.27

When I execute "qsub" and "qstat" command, it is printed the error message, "Setting locale failed.".

Our frontend server takes over a locale setting of your terminal for ssh client, Mac OS. "SendEnv" setting of your terminal occur it. Please try the following two ways.
 

Modify on "/etc/ssh_config"

Please comment out "SendEnv" setting by # mark on "/etc/ssh_config" as following.
Make sure that it must be done before connecting to frontend server.

    Host *
    # SendEnv LANG LC_*

 

write a locale setting on profile

If you want that ssh server take over a locale setting from your terminal but you want to resolve this problem, please write in bash_profile as following

    LC_ALL=en.US UTF=8

 

2017.06.06

If I run parallel computing by MPI, can I specify using nodes that are near each other on network topology?

No, you can't. Our scheduler will choose appropriated node on automatically for your job.
Thank you for your understanding.

2017.01.20

We want to re-direct standard output of MPI result on vector node of SQUIDto the other file.

If you want to re-direct standard output of MPI result on vector node of SQUID, please use the script "/opt/nec/ve/bin/mpisep.sh".
 
How to use this script is the following:

In the case, the standard output is output to stdout.0:(MPI process ID), and the standard error output is output to stderr.0:(MPI process ID) in real time.
 

Please see "3.3" of the following manual about the detail:
NEC MPI User's guide
 

If you modified mpisep.sh, you change stdout/stderr filename into whatever you want to name.

2016.09.16

Can I specify any permissions for standard output file and standard error output file ?

On SX-ACE and VCC, the permission of standard output file and standard error output file depend on "umask". Please specify the permission with "umask" command on front-end server.

2016.08.24

Could I run some jobs in my specified order?

Yes. You can do it by "Workflow" or "Request Connection Function".
 

Please see the following manual 7.Workflow an 1.2.22. Request Connection Function about how to use.
NQSII User's Guide
 

The different between Workflow and Request Connection Function

The different is the timing of running request. In the case of Workflow, all request become an object for assign immediately after submitting. In the case of Request Connection Function, next request become an object for assign after the previous request finished . Therefore, you should choose the workflow, if system is crowded,.

2016.08.24

Could I specify PATH for MPI slave node in the job script file ?

You can specify for MPI slave node almost all environment value by "#PBS -v option". But you can not specify some environment value on NQSII. Path is one of those. Please see the following manual, the end of 1.16.qsub(1).
NQSII User's Guide
 

You can specify PATH for slave node by the MPI runtime option.

2015.07.13

I got the error message "/var/spool/nqsII/jsv/jobfile/0.10989.11/user_script: 実行形式エラー. 間違ったアーキテクチャです." during the runtime of job.

Your job script file's file-format could be BOM(Byte Order Mark) format. Therefore, it is possible that the first line which you indicate to use specific shell is not interpreted. The job script should be non-BOM format.
 

Please check your file using the command below.

% file nqs.sh

 

You can change the file-format by a text-editor like vi. Please submit it again after changing the file-format.
 

We will show an example to edit BOM-format by using vi editor.
 

Open the file by vi, add the option '-b'.

% vi -b nqs.sh

<feff>#!/bin/csh

At the beginning of the first line, <feff>, this is BOM character. Delete these letters and save it.
 

2015.05.25

I got the error message "Request could not be routed.Request deleted." when i submitted a job request.

You might mistake the jobclass submitted.
Please confirm your job-script again. If your job-script is right, please contact us on the following page.
 
Inquiry form

2015.03.12

When I execute "qsub" and "qstat" command, it is printed the error message, "NQSconnect: [BSV ELICENSE] nqscui license was exceeded.".

This error message means that these commands exceeded license number limit already.
 
We have readied a enough number of license. But, in the case that executing these commands are concentrated in same time, it may exceeded license number limit. If you see this message, please inform us.
 
Form for Inquiries

2015.03.04

What will become my submitted job before maintenance or during the maintenance ?

20150304
 
Basically, the job will run correctly. But that action differs depending on your submitted time or your specified elapse-time.

* Please note that your job might not run depending on situation of jobs the other users submitted, in the case of shared use.
 
Please see the following about the detail.
 

If you submitted a job before the maintenance

If Planned End Time of your submitted job exceed the beginning time of the maintenance, your job will not run till the maintenance finished. Planned End Time is calculated from submit-time and elapse-time which you specified elapstim_req at job-script.
 
For example, if you specified "elapstime_req=5:00:00" at your job-script and you submitted your job on 1:00 p.m., Planned End Time become 6:00 p.m.
* Without depending on the above, please note that your job might not run depending on situation of jobs the other users submitted, in the case of shared use.

 

If Planned End Time of your submitted job doesn't exceed the beginning time of the maintenance

Your job will run correctly without waiting the maintenance finished.
 

If Planned End Time of your submitted job exceed the beginning time of the maintenance

As mentioned above, your job will not run till the maintenance finished. The submitted job is received as QUE status, and will run after the maintenance except the maintenance held in the end of the fiscal year. All jobs will be deleted in the maintenance held in the end of the fiscal year. If you re-adjust the elapsed-time (elapstime_req) so as not to exceed the beginning time of maintenance and if re-submit, your job might be run soon. When you are in a hurry, please try it.
 

From before planning the maintenance, if you have ran the job that Planned End Time exceed the beginning time of the maintenance

Maybe this situation will be in the case of dedicated use only. Your job will run correctly till the beginning maintenance. We're afraid that you must stop during the maintenance. If your job corresponds to this situation, we would contact you.

 

If you submit a job during the maintenance

Your job will not run till the maintenance finished. The submitted job is received as QUE status, and will run after the maintenance.
 

If you submit a job after the maintenance

Your job will run correctly.
 

2015.02.10

Environmental variable and options specified in my job script are not reflected to my computation.

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]

2014.07.24

Can I check when my job starts?

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.

About scheduler command

2014.07.14

I got the error message "No request queue specified, and no local default has been defined." when I submitted a job request.

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.

2014.07.14

My job request has been in waiting queue for long time..

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.

 

About scheduler command

 

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

2014.07.14

実行中のジョブが終了したことを合図に、次のジョブを自動で投入したい。 その際、実行中のjobが成功したかどうかで、投入するジョブを変えたい。

「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。

2014.07.14

ジョブを実行しても、エラーメッセージに 「/var/spool/nqsII/jsv/jobfile/****/user_script: コマンドが見つかりません.」 と出力され実行されない。

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。
 

    1.先頭行の "#!" で指定されているコマンド名(通常はシェル名)の絶対パスが誤っている可能性があります。
     パスが正しいか、入力ミスが無いかをご確認ください。
     
    2.ジョブスクリプトファイルの改行コードが CRLF (Windows)になっている可能性があります。
     スクリプトファイルは、文字コードを "UTF-8"、改行コードを "LF" で作成してください。
     

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。
 

    ・文字コードや改行コードを指定できるテキストエディタを利用する。
     (秀丸エディタ[シェアウェア] や サクラエディタ 等いろいろあります)
      ※ 文字コードは "UTF-8"、改行コードは "LF" を指定
     
    ・WinSCP でファイルをアップロードする時に転送モードを"テキスト" に設定するか、
     ファイルの拡張子をテキストだと自動判別されるもの(.txt , .sh 等)にする。
     ※ この方法では文字コードには対応できません

 
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