2022.12.09

Can I install and use uniquely MPI on SQUID?

Yes, you can install OpenMPI. In the case, you have to make module file as the following:

You specify module file in job script as the following:

2022.10.13

I would like to know how to address the following error: Runtime Error: Cannot allocate memory for environment variable VE_FORT_UFMTENDIAN.

This error occurs when an array is specified as a sequence of unformatted input/output statements and the array size is large.
It can be identified by specifying the following compiler options and runtime environment variables.
* The error file and the number of lines will be displayed as shown below:

example)
$ nfort main.f90 -g -traceback=verbose
$ export VE_TRACEBACK=VERBOSE
$ ./a.out
Runtime Error: Cannot allocate memory for environment variable VE_FORT_UFMTENDIAN.
Program terminated by fatal error
[ 0] 0x600c00a58910 ? ?:?
[ 1] 0x600c00a51b38 ? ?:?
[ 2] 0x600c00cd4c78 ? ?:?
[ 3] 0x60000001f850 MAIN main.f90:28 *
[ 4] 0x60000001fc80 ? ?:?
[ 5] 0x600c02a407a8 ? ?:?
[ 6] 0x600000002d00 ? ?:?

2022.10.13

Can I use wandb on SQUID?

You can install wandb with pip command.

pip install wandb
wandb login "XXXX"

 
SQUID can not access to internet on computational nodes, however, we permitted only for "wandb".
Please describe a job script file as the following:

#!/bin/bash
#PBS -q SQUID
#PBS --group=[group name]
#PBS -l elapstim_req=1:00:00
cd $PBS_O_WORKDIR
export http_proxy="http://ibgw1f-ib0:3128"
export https_proxy="https://ibgw1f-ib0:3128"
python test.py

 
Please use requests-2.24. Versions such as 2.26 will not work properly with SQUID.

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

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

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

2017.06.06

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)

2016.09.16

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 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.

2016.08.24

How could I make the independent random number generation ?

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.

2016.05.06

What limitation is there on the trial use ?

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.

2016.02.25

How can I check the congestion information of jobs ?

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.

2015.11.10

How can I apply adding the resource (Point or Storage).

You can apply adding the resource on the following web-system.
利用者管理システム(要認証)
 
Please see the following page about how to apply.
一般利用(学術利用) 資源追加申請

2015.11.10

Could I use GROMACS on SX-AXE ?

No, you can't use. You can use GROMACS on only VCC.
We have not planed to install to SX-ACE. Thank you for your understanding.

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