17と19のリビジョン間の差分 (その間の編集: 2回)

Using Cluster Systems

This section explains the usage methods common among the Computer Systems for the Next Generation Simulation Technology Education and the Wide-Area Coordinated Cluster System for Education and Research. See the page for each system for details of specific functions.

Using Cluster Systems

Logging in

Wide-Area Coordinated Cluster System for Education and Research

Setting Up the Developmental Environment

To compile a program, it is necessary to set environment variables depending on the parallel processing MPI and the compiler. For example, if you plan to use an Intel MPI as the parallel computing MPI and an Intel compiler as the compiler, set the environment variables using the following commands shown below. Note that the Intel MPI and the Intel compiler are set as the session defaults.

$ module load intelmpi.intel

You can also use the following commands to set the environment variables.

Parallel computing MPI	Compiler	Environment variable setting command
Intel MPI	Intel compiler	module load intelmpi.intel
Open MPI	Intel compiler	module load openmpi.intel
MPICH2	Intel compiler	module load mpich2.intel
MPICH1	Intel compiler	module load mpich.intel
-	Intel compiler	module load intel
-	PGI compiler	module load pgi
-	gcc compiler	module load gcc
-	nvcc compiler	module load cuda-5.0

To change the environmental settings, execute the following command to delete the current settings and set the new environment variables.

$ module unload environmental_settings

For example, if you change the Intel MPI and the Intel compiler to the Open MPI and the Intel compiler, execute as follows.

$ module unload intelmpi.intel
$ module load openmpi.intel

Setting Up the Software Usage Environment

When using software, it is necessary to change the environment variables depending on the software package to be used. For example, use the following command to set the environment variables to use Gaussian.

$ module load gaussian09-C.01

You can also use the following commands to set the environment variables.

Software name	Version	Environment variable setting command
Structural analysis
ANSYS Multiphysics, CFX, Fluent, LS-DYNA	14.5	module load ansys14.5
ABAQUS	6.12	module load abaqus-6.12-3
Patran	2012.2	module load patran-2012.2
DEFORM-3D	10.2	module loadd deform-3d-10.2
Computational materials science
PHASE (Serial version)	11.00	module load phase-11.00-serial
PHASE (Parallel version)	11.00	module load phase-11.00-parallel
PHASE-Viewer	3.2.0	module load phase-viewer-v320
UVSOR (Serial version)	3.42	module load uvsor-v342-serial
UVSOR (Parallel version)	3.42	module load uvsor-v342-parallel
OpenMX (Serial version)	3.6	module load openmx-3.6-serial
OpenMX (Parallel version)	3.6	module load openmx-3.6-parallel
Computational Science
Gaussian	09 Rev.C.01	module load gaussian09-C.01
NWChem (Serial version)	6.1.1	module load nwchem-6.1.1-serial
NWChem (Parallel version)	6.1.1	module load nwchem-6.1.1-parallel
GAMESS (Serial version)	2012.R2	module load gamess-2012.r2-serial
GAMESS (Parallel version)	2012.R2	module load gamess-2012.r2-parallel
MPQC	3.0-alpha	module load mpqc-2.4-4.10.2013.18.19
Amber, AmberTools (Serial version)	12	module load amber12-serial
Amber, AmberTools (Parallel version)	12	module load amber12-parallel
CONFLEX (Serial version & Parallel version)	7	module load conflex7
Technical processing
MATLAB	R2012a	module load matlab-R2012a

You must be a Type A user to use ANSYS, ABAQUS, Patran, DEFORM-3D, GAUSSIAN, CHEMKIN-PRO, and MATLAB.
To apply for registration as a Type A user, see: http://imc.tut.ac.jp/en/research/form.

To cancel the software environment, execute the following command.

$ module unload environmental_settings

For example, to discard the Gaussian environmental setting, use the following command.

$ module unload gaussian09-C.01

Setting Up the Session Environment

Editing the following files automatically sets up the session environment after logging in.

When using sh: ~/.profile
When using bash: ~/.bash_profile
When using csh: ~/.cshrc

Example 1: To use ansys, gaussian, and conflex in your session through bash, add the following codes to ~/.bashrc.

eval `modulecmd bash load ansys14.5`
eval `modulecmd bash load gaussian09-C.01`
eval `modulecmd bash load conflex7`

Example 2: To use OpenMPI, Intel Compiler, gaussian, and conflex in your session through csh, add the following codes to ~/.cshrc.

eval `modulecmd tcsh unload intelmpi.intel`
eval `modulecmd tcsh load openmpi.intel`
eval `modulecmd tcsh load gaussian09-C.01`
eval `modulecmd tcsh load conflex7`

The following command displays the currently loaded modules.

$ module list

The following command displays the available modules.

$ module avail

Compiling

Intel Compiler

To compile a C/C++ program, execute the following command.

$ icc source_file_name –o output_program_name

To compile a FORTRAN program, execute the following command.

$ ifort source_file_name –o output_program_name

PGI Compiler

To compile a C/C++ program, execute the following command.

$ pgcc source_file_name –o output_program_name

To compile a FORTRAN program, execute the following command.

$ pgf90 source_file_name –o output_program_name

$ pgf77 source_file_name –o output_program_name

GNU Compiler

To compile a C/C++ program, execute the following command.

$ gcc source_file_name –o output_program_name

Intel MPI

To compile a C/C++ program, execute the following command.

$ mpiicc source_file_name –o output_program_name

To compile a FORTRAN program, execute the following command.

$ mpiifort source_file_name –o output_program_name

OpenMPI, MPICH2, and MPICH1

To compile a C/C++ program, execute the following command.

$ mpicc source_file_name –o output_program_name

To compile a FORTRAN program, execute the following command.

$ mpif90 source_file_name –o output_program_name

$ mpif77 source_file_name –o output_program_name

Executing Jobs

The job management system, Torque, is used to manage jobs to be executed. Always use Torque to execute jobs.

Queue Configuration

Wide-Area Coordinated Cluster System for Education and Research

Submitting Jobs

Create the Torque script and submit the job as follows using the qsub command.

$ qsub –q quque_name script_name

For example, enter the following to submit a job to rchq, a research job queue.

$ qsub -q rchq script_name

In the script, specify the number of processors per node to request as follows.

#PBS -l nodes=no_of_nodes:ppn=processors_per_node

Example: To request 1 node and 16 processors per node

#PBS -l nodes=1:ppn=16

Example: To request 4 nodes and 16 processors per node

#PBS -l nodes=4:ppn=16

To execute a job with the specified memory capacity, add the following codes to the script.

#PBS -l nodes=no_of_nodes:ppn=processors_per_node,mem=memory_per_job

Example: To request 1 node, 16 processors per node, and 16GB memory per job

#PBS -l nodes=1:ppn=16,mem=16gb

To execute a job with the specified calculation node, add the following codes to the script.

#PBS -l nodes=nodeA:ppn=processors_for_nodeA+nodeB:ppn= processors_for_nodeB，・・・

Example: To request csnd00 and csnd01 as the nodes and 16 processors per node

#PBS -l nodes=csnd00:ppn=16+csnd01:ppn=16

* From csnd00 to csnd27 are the calculation nodes (see Hardware Configuration under System Configuration).

* csnd00 and csnd01 are equipped with Tesla K20X.

To execute a job on a calculation node with GPGPU, add the following codes to the script.

#PBS -l nodes=1:GPU:ppn=1

To execute a job in a specified duration of time, add the following codes to the script.

#PBS -l walltime=hh:mm:ss

Example: To request a duration of 336 hours to execute a job

#PBS -l walltime=336:00:00

The major options of the qsub command are as follows.

Option	Example	Description
-e	-e filename	Outputs the standard error to a specified file. When the -e option is not used, the output file is created in the directory where the qsub command was executed. The file name convention is job_name.ejob_no.
-o	-o filename	Outputs the standard output to the specified file. When the -o option is not used, the output file is created in the directory where the qsub command was executed. The file name convention is job_name.ojob_no.
-j	-j join	Specifies whether to merge the standard output and the standard error to a single file or not. -j oe: Merges the standard error into the standard output file. -j eo: Merges the standard output into the standard error file. -j n: Does not merge the standard error file and the standard output file (Default).
-q	-q destination	Specifies the queue to submit a job.
-l	-l resource_list	Specifies the resources required for job execution.
-N	-N name	Specifies the job name (up to 15 characters). If a job is submitted via a script, the script file name is used as the job name by default. Otherwise, STDIN is used.
-m	-m mail_events	Notifies the job status by an email. -m n: Does not send an email. -m a: Sends an email if the job terminates abnormally. -m b: Sends an email when the job execution starts. -m e: Sends an email when the job execution ends.
-M	-M user_list	Specifies the email address to receive the notice.

Sample Script: When Using an Intel MPI and an Intel Compiler

### sample
#!/bin/sh
#PBS -q rchq
#PBS -l nodes=1:ppn=16
MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`
cd $PBS_O_WORKDIR

mpirun -np $MPI_PROCS ./a.out

* The target queue (either eduq or rchq) to submit the job can be specified in the script.

Sample Script: When Using an OpenMPI and an Intel Compiler

### sample
#!/bin/sh
#PBS -q rchq
#PBS -l nodes=1:ppn=16
MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

module unload intelmpi.intel
module load openmpi.intel

cd $PBS_O_WORKDIR

mpirun -np $MPI_PROCS ./a.out

* The target queue (either eduq or rchq) to submit the job can be specified in the script.

Sample Script: When Using an MPICH2 and an Intel Compiler

### sample
#!/bin/sh
#PBS -q rchq
#PBS -l nodes=1:ppn=16
MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

module unload intelmpi.intel
module load mpich2.intel

cd $PBS_O_WORKDIR

mpirun -np $MPI_PROCS -iface ib0 ./a.out

* When using MPICH2, always specify the -iface option.

* The target queue (either eduq or rchq) to submit the job can be specified in the script.

Sample Script: When Using an OpenMP Program

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=8
#PBS -q eduq

export OMP_NUM_THREADS=8

cd  $PBS_O_WORKDIR

./a.out

Sample Script: When Using an MPI/OpenMP Hybrid Program

### sample
#!/bin/sh
#PBS -l nodes=4:ppn=8
#PBS -q eduq

export OMP_NUM_THREADS=8

cd  $PBS_O_WORKDIR

sort -u $PBS_NODEFILE > hostlist

mpirun -np 4 -machinefile ./hostlist ./a.out

Sample Script: When Using a GPGPU Program

### sample
#!/bin/sh
#PBS -l nodes=1:GPU:ppn=1
#PBS -q eduq

cd  $PBS_O_WORKDIR

module load cuda-5.0

./a.out

ANSYS Multiphysics Jobs

Single Job

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

ansys145 -b nolist -p AA_T_A -i vm1.dat -o vm1.out -j vm1

* vm1.dat exists in /common/ansys14.5/ansys_inc/v145/ansys/data/verif.

Parallel Jobs

The sample script is as follows.

Example: When using Shared Memory ANSYS

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=4
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

ansys145 -b nolist -p AA_T_A -i vm141.dat -o vm141.out -j vm141 -np 4

Example: When using Distributed ANSYS

### sample
#!/bin/sh
#PBS -l nodes=2:ppn=2
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

ansys145 -b nolist -p AA_T_A -i vm141.dat -o vm141.out -j vm141 -np 4 -dis

* vm141.dat exists in /common/ansys14.5/ansys_inc/v145/ansys/data/verif

ANSYS CFX Jobs

Single Job

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

cfx5solve -def StaticMixer.def

* StaticMixer.def exists in /common/ansys14.5/ansys_inc/v145/CFX/examples.

Parallel Jobs

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=4
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

cfx5solve -def StaticMixer.def -part 4 -start-method 'Intel MPI Local Parallel'

*StaticMixer.def exits in /common/ansys14.5/ansys_inc/v145/CFX/examples.

ANSYS Fluent Jobs

Single Job

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

fluent 3ddp -g -i input-3d > stdout.txt 2>&1

Parallel Jobs

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=4
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

fluent 3ddp -g -i input-3d -t4 -mpi=intel > stdout.txt 2>&1

ANSYS LS-DYNA Jobs

Single Job

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load ansys14.5

cd $PBS_O_WORKDIR

lsdyna145 i=hourglass.k memory=100m

* For hourglass.k, see LS-DYNA Examples (http://www.dynaexamples.com/).

ABAQUS Jobs

Single Job

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load abaqus-6.12-3

cd $PBS_O_WORKDIR

abaqus job=1_mass_coarse

*1_mass_coarse.inp exits in /common/abaqus-6.12-3/6.12-3/samples/job_archive/samples.zip.

PHASE Jobs

Parallel Jobs (phase command: SCF calculation)

The sample script is as follows.

### sample
#!/bin/sh
#PBS -q eduq
#PBS -l nodes=2:ppn=2

cd $PBS_O_WORKDIR

module load phase-11.00-parallel
mpirun -np 4 phase

* For PHASE jobs, a set of I/O files are defined as file_names.data.

* Sample input files are available at /common/phase-11.00-parallel/sample/Si2/scf/.

Single Job (ekcal command: Band calculation)

The sample script is as follows.

### sample
#!/bin/sh
#PBS -q eduq
#PBS -l nodes=1:ppn=1

cd $PBS_O_WORKDIR

module load phase-11.00-parallel
ekcal

* For ekcal jobs, a set of I/O files are defined as file_names.data.

* Sample input files are available at /common/phase-11.00-parallel/sample/Si2/band/.

* (Prior to using the sample files under Si2/band/, execute the sample file in ../scf/ to create nfchgt.data.)

UVSOR Jobs

Parallel Jobs (epsmain command: Dielectric constant calculation)

The sample script is as follows.

### sample
#!/bin/sh
#PBS -q eduq
#PBS -l nodes=2:ppn=2

cd $PBS_O_WORKDIR

module load uvsor-v342-parallel
mpirun -np 4 epsmain

* For epsmain jobs, a set of I/O files are defined as file_names.data.

* Sample input files are available at /common/uvsor-v342-parallel/sample/electron/Si/eps/.

* (Prior to using the sample files under Si/eps/, execute the sample file in ../scf/ to create nfchgt.data.)

OpenMX Jobs

Parallel Jobs

The sample script is as follows.

### sample
#!/bin/bash
#PBS -l nodes=2:ppn=2

cd $PBS_O_WORKDIR

module load openmx-3.6-parallel
export LD_LIBRARY_PATH=/common/intel-2013/composer_xe_2013.1.117/mkl/lib/intel64:$LD_LIBRARY_PATH
mpirun -4 openmx H2O.dat

* H2O.dat exists in /common/openmx-3.6-parallel/work/.

* The following line must be added to H2O.dat.

* DATA.PATH /common/openmx-3.6-parallel/DFT_DATA11.

GAUSSIAN Jobs

Sample input file (methane.com)

%NoSave
%Mem=512MB
%NProcShared=4
%chk=methane.chk
#MP2/6-31G opt

methane

0  1
 C                 -0.01350511    0.30137653    0.27071342
 H                  0.34314932   -0.70743347    0.27071342
 H                  0.34316773    0.80577472    1.14436492
 H                  0.34316773    0.80577472   -0.60293809
 H                 -1.08350511    0.30138971    0.27071342

Single Job

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load gaussian09-C.01

cd $PBS_O_WORKDIR

g09 methane.com

Parallel Jobs

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=4,mem=3gb,pvmem=3gb
#PBS -q eduq

cd $PBS_O_WORKDIR

module load gaussian09-C.01

g09 methane.com

NWChem Jobs

Sample input file (h2o.nw)

echo
start h2o
title h2o


geometry units au
 O 0       0        0
 H 0       1.430   -1.107
 H 0      -1.430   -1.107
end

basis
  * library 6-31g**
end
scf
  direct; print schwarz; profile
end
task scf

Parallel Jobs

The sample script is as follows.

### sample
#!/bin/sh
#PBS -q eduq
#PBS -l nodes=2:ppn=2

export NWCHEM_TOP=/common/nwchem-6.1.1-parallel
cd $PBS_O_WORKDIR

module load nwchem.parallel
mpirun -np 4 nwchem h2o.nw

GAMESS Jobs

Single Job

The sample script is as follows.

### sample
#!/bin/bash
#PBS -q eduq
#PBS -l nodes=1:ppn=1

module load gamess-2012.r2-serial
mkdir -p /work/$USER/scratch/$PBS_JOBID
mkdir -p $HOME/scr
rm -f $HOME/scr/exam01.dat
rungms exam01.inp 00 1

* exam01.inp exists in /common/gamess-2012.r2-serial/tests/standard/.

MPQC Jobs

Sample input file (h2o.in)

% HF/STO-3G SCF water
method: HF
basis: STO-3G
molecule:
    O    0.172   0.000   0.000
    H    0.745   0.000   0.754
    H    0.745   0.000  -0.754

Parallel Jobs

The sample script is as follows.

### sample
#!/bin/sh
#PBS -q rchq
#PBS -l nodes=2:ppn=2

MPQCDIR=/common/mpqc-2.4-4.10.2013.18.19

cd $PBS_O_WORKDIR

module load mpqc-2.4-4.10.2013.18.19
mpirun -np 4 mpqc -o h2o.out h2o.in

AMBER Jobs

Sample input file (gbin-sander)

 short md, nve ensemble
 &cntrl
   ntx=5, irest=1,
   ntc=2, ntf=2, tol=0.0000001,
   nstlim=100, ntt=0,
   ntpr=1, ntwr=10000,
   dt=0.001,
 /
 &ewald
   nfft1=50, nfft2=50, nfft3=50, column_fft=1,
 /
EOF

Sample input file (gbin-pmemd)

 short md, nve ensemble
 &cntrl
   ntx=5, irest=1,
   ntc=2, ntf=2, tol=0.0000001,
   nstlim=100, ntt=0,
   ntpr=1, ntwr=10000,
   dt=0.001,
 /
 &ewald
   nfft1=50, nfft2=50, nfft3=50,
 /
EOF

Single Job

The sample script is as follows.

Example: To use sander

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load amber12-serial

cd $PBS_O_WORKDIR

sander -i gbin-sander -p prmtop -c eq1.x

* prmtop and eq1.x exists in /common/amber12-parallel/test/4096wat.

Example: To use pmemd

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load amber12-serial

cd $PBS_O_WORKDIR

pmemd -i gbin-pmemd -p prmtop -c eq1.x

* prmtop and eq1.x exists in /common/amber12-parallel/test/4096wat.

Parallel Jobs

The sample script is as follows.

Example: To use sander

### sample
#!/bin/sh
#PBS -l nodes=2:ppn=4
#PBS -q eduq

module unload intelmpi.intel
module load openmpi.intel
module load amber12-parallel

cd $PBS_O_WORKDIR

mpirun -np 8 sander.MPI -i gbin-sander -p prmtop -c eq1.x

* prmtop and eq1.x exists in /common/amber12-parallel/test/4096wat.

Example: To use pmemd

### sample
#!/bin/sh
#PBS -l nodes=2:ppn=4
#PBS -q eduq

module unload intelmpi.intel
module load openmpi.intel
module load amber12-parallel

cd $PBS_O_WORKDIR

mpirun -np 8 pmemd.MPI -i gbin-pmemd -p prmtop -c eq1.x

* prmtop and eq1.x exists in /common/amber12-parallel/test/4096wat.

CONFLEX Jobs

Sample input file (methane.mol)

  Sample
  Chem3D Core 13.0.009171314173D

  5  4  0  0  0  0  0  0  0  0999 V2000
    0.1655    0.7586    0.0176 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2324   -0.3315    0.0062 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7729   -0.7586    0.0063 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7729   -0.6729    0.8919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7648   -0.6523   -0.8919 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0
  2  3  1  0
  2  4  1  0
  2  5  1  0
M  END

Single Job

The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=1
#PBS -q eduq

c
cd $PBS_O_WORKDIR

flex7a1.ifc12.Linux.exe -par /common/conflex7/par methane

Parallel Jobs

Create the script and submit the job using the qsub command. The sample script is as follows.

### sample
#!/bin/sh
#PBS -l nodes=1:ppn=8
#PBS -q eduq

module load conflex7

cd $PBS_O_WORKDIR

mpirun -np 8 flex7a1.ifc12.iMPI.Linux.exe -par /common/conflex7/par methane

MATLAB Jobs

Sample input file (matlabdemo.m)

% Sample

n=6000;X=rand(n,n);Y=rand(n,n);tic; Z=X*Y;toc

% after finishing work
switch getenv('PBS_ENVIRONMENT')
  case {'PBS_INTERACTIVE',''}
    disp('Job finished. Results not yet saved.');
  case 'PBS_BATCH'
    disp('Job finished. Saving results.')
    matfile=sprintf('matlab-%s.mat',getenv('PBS_JOBID'));
    save(matfile);
    exit
  otherwise
    disp([ 'Unknown PBS environment ' getenv('PBS_ENVIRONMENT')]);
end

Single Job

The sample script is as follows.

### sample
#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -q eduq

module load matlab-R2012a

cd $PBS_O_WORKDIR

matlab -nodisplay -nodesktop -nosplash -nojvm -r "maxNumCompThreads(1); matlabdemo"

Parallel Jobs

The sample script is as follows.

### sample
#!/bin/bash
#PBS -l nodes=1:ppn=4
#PBS -q eduq

module load matlab-R2012a

cd $PBS_O_WORKDIR

matlab -nodisplay -nodesktop -nosplash -nojvm -r "maxNumCompThreads(4); matlabdemo"

CASTEP/DMol3 Jobs

There are two ways to run Materials Studio CASTEP/DMol3 using the University’s supercomputer:

(1) Submit the job from Materials Studio Visualiser to the supercomputer (only Materials Studio 2016 is supported).

(2) Transfer the input file to the supercomputer using Winscp etc. and submit the job using the qsub command.

This section explains about the method (2).　To submit the job in the method (2), the parameters to pass the job scheduler can be changed.　The following is an example using CASTEP.

1. Create an input file using Materials Studio Visualizer.

In the CASTEP Calculation window, click Files….

In the CASTEP Job Files window, click Save Files.

The input file is stored at:

specified_path\project_name_Files\Documents\folder_created_in_above_step

For example, when performing an energy calculation using acetanilide.xsd in CASTEP following the above steps, the folder is created with the name of acetanilide CASTEP Energy.

The above specified_path is usually C:\Users\account_name\Documents\Materials Studio Projects.

The folder name contains a blank character. Delete the blank character or replace it with underscore (_). The folder name must not contain Japanese characters.

2. Using file transfer software such as Winscp, transfer the created folder and the file it contains to the supercomputer.

3. Create a script as follows in the transferred folder and submit the job using the qsub command.

### sample

#!/bin/sh
#PBS -l nodes=1:ppn=8,mem=24gb,pmem=3gb,vmem=24gb,pvmem=3gb
#PBS -l walltime=24:00:00
#PBS -q rchq

MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

cd $PBS_O_WORKDIR

cp /common/accelrys/cdev0/MaterialsStudio8.0/etc/CASTEP/bin/RunCASTEP.sh .
perl -i -pe 's/\r//' *

./RunCASTEP.sh -np $MPI_PROCS acetanilide

* Specify the file name without an extension in the transferred folder as the third argument in RunCASTEP.sh.

* Specify a value of 8 or less in =ppn.

* The values for the duration of job execution and the permitted memory capacity can be changed as necessary.

* Specifications in the Gateway location, Queue, and Run in parallel on fields in the Job Control tab in the CASTEP Calculation window will be ignored in job execution from the command line. The settings specified in the script used with the qsub command will be used.

* The script contents vary depending on the computer and calculation modules to be used. See the following Example Scripts.

4. After the job is completed, transfer the result file to your client PC and view the results using Materials studio Visualizer.

Notes on Joint Research

There are eight Materials Studio licenses owned by the University for CASTEP and a further eight for Dmol3. One job with eight or less parallel executions can be conducted under a single license. These licenses are shared. Avoid exclusively occupying the licenses and consider other users.

Example Scripts

Running Materials Studio 8.0 CASTEP in the Wide-Area Coordinated Cluster System for Education and Research

### sample

#!/bin/sh
#PBS -l nodes=1:ppn=8,mem=50000mb,pmem=6250mb,vmem=50000mb,pvmem=6250mb
#PBS -l walltime=24:00:00
#PBS -q wLrchq

MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

cd $PBS_O_WORKDIR

cp /common/accelrys/wdev0/MaterialsStudio8.0/etc/CASTEP/bin/RunCASTEP.sh .
perl -i -pe 's/\r//' *

./RunCASTEP.sh -np $MPI_PROCS acetanilide

Running Materials Studio 8.0 DMOL3 in the Wide-Area Coordinated Cluster System for Education and Research

### sample

#!/bin/sh
#PBS -l nodes=1:ppn=8,mem=50000mb,pmem=6250mb,vmem=50000mb,pvmem=6250mb
#PBS -l walltime=24:00:00
#PBS -q wLrchq

MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

cd $PBS_O_WORKDIR

cp /common/accelrys/wdev0/MaterialsStudio8.0/etc/DMol3/bin/RunDMol3.sh .
perl -i -pe 's/\r//' *

./RunDMol3.sh -np $MPI_PROCS acetanilide

Running Materials Studio 2016 CASTEP in the Wide-Area Coordinated Cluster System for Education and Research

### sample

#!/bin/sh
#PBS -l nodes=1:ppn=8,mem=50000mb,pmem=6250mb,vmem=50000mb,pvmem=6250mb
#PBS -l walltime=24:00:00
#PBS -q wLrchq

MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

cd $PBS_O_WORKDIR

cp /common/accelrys/wdev0/MaterialsStudio2016/etc/CASTEP/bin/RunCASTEP.sh .
perl -i -pe 's/\r//' *

./RunCASTEP.sh -np $MPI_PROCS acetanilide

Running Materials Studio 2016 DMOL3 in the Wide-Area Coordinated Cluster System for Education and Research

### sample

#!/bin/sh
#PBS -l nodes=1:ppn=8,mem=50000mb,pmem=6250mb,vmem=50000mb,pvmem=6250mb
#PBS -l walltime=24:00:00
#PBS -q wLrchq

MPI_PROCS=`wc -l $PBS_NODEFILE | awk '{print $1}'`

cd $PBS_O_WORKDIR

cp /common/accelrys/wdev0/MaterialsStudio2016/etc/DMol3/bin/RunDMol3.sh .
perl -i -pe 's/\r//' *

./RunDMol3.sh -np $MPI_PROCS acetanilide

Viewing Job Status

Use the qstat command to view the job or queue status.

(1) Viewing the job status

qstat -a

(2) Viewing the queue status

qstat -Q

Major options for the qstat command are as follows.

Options	Usage	Description
-a	-a	Displays all jobs in the queue and jobs being executed.
-Q	-Q	Displays the statuses of all queues in an abbreviated form.
-Qf	-Qf	Displays the statuses of all queues in a detailed form.
-q	-q	Displays the limitation values of the queues.
-n	-n	Displays the calculation node name assigned to the job.
-r	-r	Displays a list of running jobs.
-i	-i	Displays a list of idle jobs.
-u	-u user_name	Displays the jobs owned by the specified user.
-f	-f job_ID	Displays details of the job that has the specified job ID.

Canceling a Submitted Jobs

Use the qdel command to cancel the submitted job.

qdel jobID

Check the job ID beforehand using the qstat command.

-  ⇤ ← 2017-08-20 14:22:10時点のリビジョン17 → 
  サイズ: 29851
  編集者: intergroup01
  コメント:
+   ← 2017-08-24 13:32:58時点のリビジョン19 → ⇥
  サイズ: 29914
  編集者: intergroup01
  コメント:
-削除された箇所はこのように表示されます。
+追加された箇所はこのように表示されます。
 行 26:
-||- ||compiler ||module load cuda-5.0 ||
+||- ||nvcc compiler ||module load cuda-5.0 ||
 行 31:
-$ module unload '''''environmental_settings'''''
+$ module unload environmental_settings
 行 74:
- * To apply for registration as a Type A user, see:
http://imc.tut.ac.jp/en/research/form.
+ * To apply for registration as a Type A user, see: http://imc.tut.ac.jp/en/research/form.
-行 162:
+行 161:
-=== OpenMPI, MPICH2, MPICH1 ===
+=== OpenMPI, MPICH2, and MPICH1 ===
-行 182:
+行 181:
-Create the Torque script and submit the job as follows using the qsub command.
+Create the Torque script and submit the job as follows using the '''qsub''' command.
-行 247:
+行 246:
-||-e ||-e filename ||Outputs the standard error to a specified file. When the '''-e''' option is not used, the output file is created in the directory where the '''qsub''' command was executed. The file name convention is job_name.ejob_no. ||
||-o ||-o filename ||Outputs the standard output to the specified file. When the '''-o''' option is not used, the output file is created in the directory where the '''qsub''' command was executed. The file name convention is job_name.ojob_no. ||
+||-e ||-e filename ||Outputs the standard error to a specified file. When the '''-e''' option is not used, the output file is created in the directory where the '''qsub''' command was executed. The file name convention is ''job_name.ejob_no.'' ||
||-o ||-o filename ||Outputs the standard output to the specified file. When the '''-o''' option is not used, the output file is created in the directory where the '''qsub''' command was executed. The file name convention ''is job_name.ojob_no.'' ||
-行 372:
+行 371:
-=== ANSYS Multiphysics Job ===
+=== ANSYS Multiphysics Jobs ===
-行 430:
+行 429:
-=== ANSYS CFX Job ===
+=== ANSYS CFX Jobs ===
-行 471:
+行 470:
-=== ANSYS Fluent Job ===
+=== ANSYS Fluent Jobs ===
-行 507:
+行 506:
-=== ANSYS LS-DYNA Job ===
+=== ANSYS LS-DYNA Jobs ===
-行 528:
+行 527:
-=== ABAQUS Job ===
+=== ABAQUS Jobs ===
-行 549:
+行 548:
-=== PHASE Job ===
+=== PHASE Jobs ===
-行 567:
+行 566:
-* For PHASE jobs, a set of I/O files are defined as file_names.data.
+* For PHASE jobs, a set of I/O files are defined as ''file_names.''data.
-行 588:
+行 587:
-* For ekcal jobs, a set of I/O files are defined as file_names.data.
+* For ekcal jobs, a set of I/O files are defined as ''file_names.''data.
-行 594:
+行 593:
-=== UVSOR Job ===
+=== UVSOR Jobs ===
-行 611:
+行 610:
-* For epsmain jobs, a set of I/O files are defined as file_names.data.
+* For epsmain jobs, a set of I/O files are defined as ''file_names.''data.
-行 617:
+行 616:
-=== OpenMX Job ===
+=== OpenMX Jobs ===
-行 641:
+行 640:
-=== GAUSSIAN Job ===
+=== GAUSSIAN Jobs ===
-行 643:
+行 642:
-e
-行 695:
+行 694:
-=== NWChem Job ===
+=== NWChem Jobs ===
-行 736:
+行 735:
-=== GAMESS Job ===
+=== GAMESS Jobs ===
-行 756:
+行 755:
-=== MPQC Job ===
+=== MPQC Jobs ===
-行 788:
+行 787:
-=== AMBER Job ===
+=== AMBER Jobs ===
-行 908:
+行 907:
-=== CONFLEX Job ===
+=== CONFLEX Jobs ===
-行 961:
+行 960:
-=== MATLAB Job ===
+=== MATLAB Jobs ===
-行 1018:
+行 1017:
-=== CASTEP/DMol3 Job ===
+=== CASTEP/DMol3 Jobs ===
-行 1039:
+行 1038:
-specified_path\project_name_Files\Documents\folder_created_in_above_step
+''specified_path\project_name''_Files\Documents\''folder_created_in_above_step''
-行 1043:
+行 1042:
-The above specified_path is usually
C:\Users\account_name\Documents\Materials Studio Projects.

The folder name contains a blank character. Delete the blank character or replace it with underscore (_). The folder name must not contain Japanese characters.
+The above ''specified_path'' is usually
C:\Users\''account_name''\Documents\Materials Studio Projects.

The folder name contains a blank character. Delete the blank character or replace it with underscore (_). The folder name must not contain Japanese characters.
-行 1080:
+行 1079:
-* The script contents vary depending on the computer and calculation modules to be used. See the following Example Scripts.
+* The script contents vary depending on the computer and calculation modules to be used. See the following ''Example Scripts''.
-行 1086:
+行 1085:
-There are eight Materials Studio licenses owned by the University for CASTEP and a further eight for Dmol3. 1One job with eight or less parallel executions can be conducted under a single license. These licenses are shared. Avoid exclusively occupying the licenses and consider other users.
+There are eight Materials Studio licenses owned by the University for CASTEP and a further eight for Dmol3. One job with eight or less parallel executions can be conducted under a single license. These licenses are shared. Avoid exclusively occupying the licenses and consider other users.
-行 1204:
+行 1203:
-||-u ||-u user_name ||Displays the jobs owned by the specified user. ||
||-f ||-f job_ID ||Displays details of the job that has the specified job ID. ||


== Canceling a Submitted Job ==
+||-u ||-u ''user_name'' ||Displays the jobs owned by the specified user. ||
||-f ||-f ''job_ID'' ||Displays details of the job that has the specified job ID. ||


== Canceling a Submitted Jobs ==

TUT HPC Cluster Wiki: "en / ClusterSystemUsage"の差分

Using Cluster Systems

Logging in

Setting Up the Developmental Environment

Setting Up the Software Usage Environment

Setting Up the Session Environment

Compiling

Intel Compiler

PGI Compiler

GNU Compiler

Intel MPI

OpenMPI, MPICH2, and MPICH1

Executing Jobs

Queue Configuration

Submitting Jobs

Sample Script: When Using an Intel MPI and an Intel Compiler

Sample Script: When Using an OpenMPI and an Intel Compiler

Sample Script: When Using an MPICH2 and an Intel Compiler

Sample Script: When Using an OpenMP Program

Sample Script: When Using an MPI/OpenMP Hybrid Program

Sample Script: When Using a GPGPU Program

ANSYS Multiphysics Jobs

Single Job

Parallel Jobs

ANSYS CFX Jobs

Single Job

Parallel Jobs

ANSYS Fluent Jobs

Single Job

Parallel Jobs

ANSYS LS-DYNA Jobs

Single Job

ABAQUS Jobs

Single Job

PHASE Jobs

Parallel Jobs (phase command: SCF calculation)

Single Job (ekcal command: Band calculation)

UVSOR Jobs

Parallel Jobs (epsmain command: Dielectric constant calculation)

OpenMX Jobs

Parallel Jobs

GAUSSIAN Jobs

Single Job

Parallel Jobs

NWChem Jobs

Parallel Jobs

GAMESS Jobs

Single Job

MPQC Jobs

Parallel Jobs

AMBER Jobs

Single Job

Parallel Jobs

CONFLEX Jobs

Single Job

Parallel Jobs

MATLAB Jobs

Single Job

Parallel Jobs

CASTEP/DMol3 Jobs

Viewing Job Status

Canceling a Submitted Jobs