In OCTOPUS and SQUID, the machinefile is automatically generated and set to MPI based on the value specified by PBS -l cpunum_job using the environment variable $NQSII_MPIOPTS / $NQSV_MPIOPT. Options such as ppn, rr, and prehost cannot be specified at the same time as the machinefile.
Even if we assume that we allocate 128 MPI processes / 64 processes per node, and specify them as follows, the ppn option will be invalid:

mpirun ${NQSV_MPIOPTS} -np 128 -ppn 64 ./a.out

Basically, 128 MPI processes can be created and 64 processes can be allocated per node by specifying the following.

#PBS -l cpunum_job=64
(...)
mpirun ${NQSV_MPIOPTS} -np 128 ./a.out

The environment variable $NQSV_MPIOPTS specifies the following options and files.

-machinefile /var/opt/nec/nqsv/jsv/jobfile/[a number of requestID and etc.]/mpinodes

The mpinodes file is a machine file, and in the above case, the host name and number of cores are specified as follows.

host001:64
host002:64

 
However, if you want to specify the process placement more precisely (e.g., if you want to set up pinning and compute without using processes on specific cores), the above options may not work in some cases. When using ppn, rr, and prehost options, specify the hostfile option and $PBS_NODEFILE environment variable instead of $NQSII_MPIOPTS / $NQSV_MPIOPT. 128 To create MPI processes and allocate 64 processes per node, specify as follows.

mpirun -hostfile ${PBS_NODEFILE} -np 128 -ppn 64 ./a.out

If you use PBS_NODEFILE, the value specified by #PBS -l cpunum_job will not be set to MPI. Please check the number of processes by yourself.

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

OCTOPUSには以下のGnuplotがインストールされています。

・4.6 (デフォルト)
・5.2.4 (/octfs/apl/Gnuplot/5.2.4)

Octaveから呼び出されるGnuplotのバージョンは、以下の２通りの方法で指定が可能です。
 
・呼び出したいバージョンのパスを設定する

下記のジョブスクリプト例の4行目のように、Octaveの実行の前にGnuplotのバージョンのパスを設定することで、呼び出すバージョンを指定することができます。（Gnuplot5.2.4を呼び出す場合の例です）
パスを設定しない場合、デフォルトのバージョンが呼び出されます。

1 2 3 4 5 6

#!/bin/bash #PBS -q OCTOPUS #PBS -l elapstim_req=1:00:00 export PATH=/octfs/apl/Gnuplot/5.2.4/bin:$PATH cd $PBS_O_WORKDIR /octfs/apl/Octave/5.1.0/bin/octave-5.1.0 file.m

・Octaveの設定ファイル「.octaverc」を作成する

ホームディレクトリにOctaveの設定ファイル「.octaverc」を作成し、下記の一文を記述してください。

gnuplot_binary="[Gnuplotの実行ファイルのパス]"

上記のように記述することで、Octaveから呼び出されるデフォルトのGnuplotの実行ファイルを設定できます。
例えば、5.2.4を呼び出す場合は「gnuplot_binary="/octfs/apl/Gnuplot/5.2.4/bin"」と記述してください。

If you did not specify "${NQSII_MPIOPTS}" when you execute MPI program, you will get the following error message:

[mpiexec@oct-***] HYDT_bscd_pbs_query_node_list (../../tools/bootstrap/external/pbs_query_node_list.c:23): No PBS nodefile found
[mpiexec@oct-***] HYDT_bsci_query_node_list (../../tools/bootstrap/src/bsci_query_node_list.c:19): RMK returned error while querying node list
[mpiexec@oct-***] main (../../ui/mpich/mpiexec.c:621): unable to query the RMK for a node list

Please see the following page about a sample job script for MPI program:
How to use Intel MPI on OCTOPUS

This error message notice that "nodefile" for MPI program does not exist. "nodefile" automatically is set by ${NQSII_MPIOPTS} on OCTOPUS.

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

Binary data is seldom written in an output file when each process is written to output data to the same name file.
 

Please use MPI-IO or write to output data to separate files for each process.
 

Please see the following page for MPI-IO
MPIの実行結果を1つのファイルに出力したい

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

Yes. Please apply "Adding usage resource" from User management system.
User management system
 

Please see the following page for the detail about "Adding usage resource".
How to add usage resource

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

When you specified OpenMP or Auto-Parallelization option on compile, the compiler links the library for parallelization whether parallel directive or not.
The functions of library for Parallelization differ from the normal functions in that have the lock routine for that other thread limit access to resources.

 
If it calls the functions of Library for parallelization on the un-parallelization part, it runs on one thread, of course. Therefore, it will not wait for other processes for lock routine. But, it needs a little bit processing time. Because the functions of library for parallelization have to make a decision for whether should do or do not the lock routine. Please note that.

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.

While executing qstat and sstat command, our system consume one license of them. A number of licenses is enough for normal usage. But, if many user execute at regular intervals, licenses may be shortage. In this case, many user will not be able to execute these command.
Please refrain from executing at regular intervals. If you have to do absolutely, please execute at 10 minute intervals.

You can use till the end of fiscal year you apply additional disk. If you want to use in the next year also, you have to re-apply for continue service.

Yes. Please see the following page.

User add/change/delete

Please contact us from the following WEB form.
Form for inquires

Users can not check the job status of other users. We appreciate your understanding.

If you install any library and application to your disk, our permits are not necessary.
 
If you expect that center install any library and application to a whole of system, please contact us from the following web form:
Inquiry / Request form
 

Please note that we may not permit or we may ask to install with yourself, depending on the kind of library and application.

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,.

Please see the following manual page.
HPCI Manuals
 

Note

In the following case, we will create same account for HPCI account and local account.
Primary center : Cybermedia Center, Osaka University
HPCI system provider : Cybermedia Center, Osaka University

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.

Many PRNG (pseudo random number generator) make random number from the specified random seed. If you specified same random seed, it will generate same random number. If you want to get the independent random number, you have to change random seed each time.

On trial use, you can not use over our ruled Point and 3 month. But there is not what limited besides these. You can use our system like normal use.
 
Please see this page about node hour.
Please see this page about trial use.

Users can not check the congestion information of jobs.
 
If the large scale computing system was not crowded, your submitting job will become "ASG" on job scheduler. Therefore, please judge whether congestion or not by "STT" on sstat command.
 
And, if your submitted job keeps “QUE” by any error of your job or any problem of our system, we will report you about it.

Please see the following page about our large-scale computer system.

System Introduction

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.
 

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

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

 
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.
 

We explain about the common basic to use all systems on the following page. Please see.

Basics to use system

This system has different compilers for each resource. Please see the following page about the detail.
 
How to use SQUID How to use OCTOPUS