2022.01.18

I want to use ppn, rr, and prehost options with Intel MPI

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.

2021.11.08

I can't use 2-step verification anymore due to a change of model, loss, or some other problem.

Please let us know through the contact form. In this case, please specify your name, user number, and e-mail address as they were at the time of registration.
Please note that your password will also be initialized at that time.
Inquery form

2020.03.10

I want to mount HPCI shared storage from a not-HPCI group. / I want to mount HPCI shared storage for a project not using Osaka University.

How to mount HPCI shared storage is the following. However, you have to prepare a mount point directory in advance.
Please contact us from this page.
 
1. store your proxy certificate in the repository on HPCI Certificate Issuing System.
 

2. login our login server and enter the following command:

myproxy-logon -s portal.hpci.nii.ac.jp -l hpciXXXX(HPCI-ID) -t168

 

3. mount HPCI shared storage to /gfarm/(project ID)/(user ID)directory (mount point).

mount.hpci

 

4. un-mount HPCI shared storage after use.

umount.hpci

 

please see "HPCI Shared Storage User Manual" on this page for a detail.

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

2019.11.25

Octaveから呼び出されるGnuplotのバージョンを設定したい

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。

 

・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。

2019.04.11

I get a runtime error message "No PBS nodefile found" on MPI program.

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.

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

2019.01.10

Binary data get into output file of MPI job

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

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

2018.11.16

Can I take over an account from Trial use to General (non-free) use?

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

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

 

2017.10.30

Could I use Gaussian for joint reserch with companies ?

Yes, you can use.
If you already use Gaussian, you don't have to apply for Gaussian any more.

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.

2017.05.29

Why it increase the processing time on un-parallelization part with OpenMP?

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.

2017.04.14

I get the compile error, " (****) is abnormally terminated by SIGSEGV".

In all likelihood, your compile exceed the limit of stack size on frontend server.
the limit of stack size is normally 10240 K bytes. Please change the limit number, and try to re-compile.
You can change the limit of stack size with the following command:

limit stacksize (anything number) kbytes

 

If you have got same error message on stack size changed, Please inquiry us from the following web form. We will investigate your compile.

2017.04.14

Can I see the documents about "sxar" or "sxld" ("ar" or "ld" command for SX-ACE) ?

We have not provided document file, but have provided "man" command for "sxar" or "sxld". Please input the following command:

sxman sxar

sxman sxld

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.

2016.12.02

How can I use "FFTW" library on SX ?

You can't use "FFTW" library on SX-ACE.
But you can use FFT by "MathKeisan" library that optimized for SX.
MathKeisan MathKeisan User's Guide(Authorization required)

2016.10.18

AVS/Express outputs the error of OpenGL and is closed automatically

[The detail of error]
Attempting to connect to license server
Received license from server
Checking hostid 0
OM(Root) -> X Error of failed request: BadValue (integer parameter out of range for operation)
Major opcode of failed request: 150 (GLX)
Minor opcode of failed request: 3 (X_GLXCreateContext)
Value in failed request: 0x0
Serial number of failed request: 4664
Current serial number in output stream: 4666

 
In the case of this error, please add -nohw option as the following and run AVS/Express with the software renderer mode.

avs -nohw

You can do it also with setting the following environment value.

XP_DEFAULT_RENDERER=SW

Please contact us on the following web form, if you did not avoid this error with this procedure.
contact form

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.

2016.08.25

May I execute qstat or sstat command at regular intervals?

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.

2016.08.25

Until when can I use additional disk , if I apply additional disk in the middle of the fiscal year ?

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.

2016.08.25

Can I add user account of my student or coworker in my group ?

Yes. Please see the following page.

User add/change/delete

2016.08.25

How can I change the item of expenditure or date of payment after application ?

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

2016.08.25

How can I check the job-status of other users ?

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

2016.08.24

I want to install an application and a library.

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.

2016.08.24

Could I use Python?

Yes. We provide Python on all system.

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

What is the different between HPCI account and local account ?

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

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.

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