4と7のリビジョン間の差分 (その間の編集: 3回)

Using Cluster Systems

This section explains the usage methods common among 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
-	nnvcc 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/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, 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

/* * Computer Systems for the Next Generation Simulation Technology Education

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 Job

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 Job

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 Job

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 Job

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 Job

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 Job

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 Job

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 Job

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 Job

Sample input file (methane.com) e

%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 Job

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 Job

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 Job

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 Job

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, eq1.xは/common/amber12-parallel/test/4096watにあります．

例：pmemdを用いる場合

### 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, eq1.xは/common/amber12-parallel/test/4096watにあります．

並列ジョブ

以下に，実行スクリプト例を示します．

例：sanderを用いる場合

### 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, eq1.xは/common/amber12-parallel/test/4096watにあります．

例：pmemd を用いる場合

### 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, eq1.xは/common/amber12-parallel/test/4096watにあります．

CONFLEXジョブ

サンプル入力ファイル(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

シングルジョブ

以下に，実行スクリプト例を示します．

### 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

並列ジョブ

実行スクリプトを作成しqsubコマンドよりジョブを投入します．以下に，実行スクリプト例を示します．

### 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ジョブ

サンプル入力ファイル(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

シングルジョブ

以下に，実行スクリプト例を示します．

### 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"

並列ジョブ

以下に，実行スクリプト例を示します．

### 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ジョブ

本学スパコンを利用してMaterials Studio CASTEP/DMol3を実行する場合，

①　Materials Studio Visualiserからスパコンに対しジョブを投入する(Materials Studio2016のみ対応)

②　入力ファイルをWinscp等でスパコンに転送し「qsub」コマンドによりジョブを投入する

の二通りがあります．ここでは②について説明します．②で実行する場合，ジョブスケジューラに与えるパラメータを変更することができます．以下では，CASTEPを例に説明します．

1. Materials Studio Visualizerで入力ファイルを作成します．

「CASTEP Calculation」ウィンドウの「Files...」をクリックします．

次に，「CASTEP Job Files」ウィンドウの「Save Files」をクリックします．

入力ファイルは

(任意のパス)\(プロジェクト名)_Files\Documents\（上記操作において作成されたフォルダ）\

に保存されます．例えば，acetanilide.xsdに対してCASTEPによりエネルギー計算を行う場合、「（上記操作において作成されたフォルダ）」は「acetanilide CASTEP Energy」となります．

また，「(任意のパス)」は，通常，「C:\Users\(アカウント名)\Documents\Materials Studio Projects」です．

作成されるフォルダの名前にはスペースが含まれます．スペースを削除するか，”_”などで置換してください．また，フォルダ名に日本語が含まれてはいけません．

2. Winscp等のファイル転送ソフトを利用し,作成した入力ファイルをフォルダごと本学スパコンへ転送してください．

3. 転送したフォルダ内に下記のような実行スクリプトを作成し，「qsub」コマンドによりジョブを投入してください．

### 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

* RunCASTEP.shの第3引数は，転送したフォルダ内のファイル名を指定してください．拡張子は必要ありません．

* 「ppn=」は，8以下，の値を指定してください．

* 経過時間制限値，メモリ利用容量制限値は必要に応じて変更できます．

* 「CASTEP Calculation」ウィンドウの”Job Control”タブにおける「Gateway location」「Queue」「Run in parallel on」の設定はコマンドライン実行に対し意味を持ちません．qsubコマンド時に利用する実行スクリプト内の設定が用いられます．

* 実行スクリプトは利用する計算機や計算モジュールにより異なります．下記の「実行スクリプト例」をご参照ください．

4. ジョブ終了後、計算結果ファイルをクライアントPCに転送し，Materials studio Visualizerを利用して閲覧してください．

共同利用に関する注意事項

Materials Studioのライセンスは，CASTEP：8本，Dmol3：8本，を所有しています．1ライセンスで8並列以下のジョブを1つ実行することができます．本ライセンスは共用です．他のユーザーと競合しないように留意の上，ご利用をお願いします．

実行スクリプト例

広域連携教育研究用クラスタシステムでMaterials Studio 8.0 CASTEPを実行する場合：

### 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

広域連携教育研究用クラスタシステムでMaterials Studio 8.0 DMOL3を実行する場合：

### 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

広域連携教育研究用クラスタシステムでMaterials Studio 2016 CASTEPを実行する場合：

### 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

広域連携教育研究用クラスタシステムでMaterials Studio 2016 DMOL3を実行する場合：

### 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

ジョブの状態を確認する

ジョブ，キューの状態確認にはqstatコマンドを利用します．

(1) ジョブの状態表示

qstat -a

(2) キューの状態表示

qstat -Q

qstatコマンドの主なオプションを以下に示します．

オプション	使用例	意味
-a	-a	すべてのキューイング・実行中のジョブを表示する．
-Q	-Q	すべてのキューの状態を簡易表示する．
-Qf	-Qf	すべてのキューの状態を詳細表示する．
-q	-q	キューの制限値を表示する．
-n	-n	ジョブに割り当てた計算ノードのホスト名を表示する．
-r	-r	実行中のジョブのリストを表示させます．
-i	-i	非実行中のジョブのリストを表示する．
-u	-u ユーザ名	指定したユーザのジョブのリストを表示する．
-f	-f ジョブID	指定したジョブIDの詳細情報を表示する．

投入したジョブをキャンセルする

ジョブのキャンセルにはqdelコマンドを使用します．

qdel jobID

job IDはqstatコマンドより確認してください．

-  ⇤ ← 2017-04-21 21:45:29時点のリビジョン4 → 
  サイズ: 31809
  編集者: intergroup01
  コメント:
+   ← 2017-04-22 07:29:34時点のリビジョン7 → ⇥
  サイズ: 30825
  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 472:
-=== ANSYS Fluentジョブ ===
==== シングルジョブ ====
以下に，実行スクリプト例を示します．
+=== ANSYS Fluent Job ===
==== Single Job ====
The sample script is as follows.
 行 491:
-==== 並列ジョブ ====
以下に，実行スクリプト例を示します．
+==== Parallel Jobs ====
The sample script is as follows.
-行 509:
+行 508:
-=== ANSYS LS-DYNAジョブ ===
==== シングルジョブ ====
以下に，実行スクリプト例を示します．
+=== ANSYS LS-DYNA Job ===
==== Single Job ====
The sample script is as follows.
-行 528:
+行 527:
-*hourglass.kはLS-DYNA Examples(http://www.dynaexamples.com/)を参照してください．

=== ABAQUSジョブ ===
==== シングルジョブ ====
以下に，実行スクリプト例を示します．
+* For hourglass.k, see LS-DYNA Examples (http://www.dynaexamples.com/).

=== ABAQUS Job ===
==== Single Job ====
The sample script is as follows.
-行 549:
+行 548:
-*1_mass_coarse.inpは/common/abaqus-6.12-3/6.12-3/samples/job_archive/samples.zipにあります．

=== PHASEジョブ ===
==== 並列ジョブ (phaseコマンド:SCF計算) ====
以下に，実行スクリプト例を示します．
+*1_mass_coarse.inp exits in /common/abaqus-6.12-3/6.12-3/samples/job_archive/samples.zip.

=== PHASE Job ===
==== Parallel Jobs (phase command: SCF calculation) ====
The sample script is as follows.
-行 569:
+行 568:
-* phaseの場合、入出力ファイル一式はfile_names.dataという名前のファイルで記述されます.

* 入力ファイル一式として例えば、/common/phase-11.00-parallel/sample/Si2/scf/下のサンプルなどを利用できます.

==== シングルジョブ (ekcalコマンド:Band計算) ====
以下に，実行スクリプト例を示します．
+* 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.
-行 590:
+行 589:
-* ekcalの場合、入出力ファイル一式はfile_names.dataという名前のファイルで記述されます.

* 入力ファイル一式として例えば、/common/phase-11.00-parallel/sample/Si2/band/下のサンプルなどを利用できます.

* (Si2/band/のサンプルを使用するには、予め../scf/のサンプルを実行してnfchgt.dataを用意しておく必要があります。).

=== UVSORジョブ ===
==== 並列ジョブ (epsmainコマンド:誘電率計算) ====
以下に，実行スクリプト例を示します．
+* 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 Job ===
==== Parallel Jobs (epsmain command: Dielectric constant calculation) ====
The sample script is as follows.
-行 614:
+行 612:
-* epsmainの場合、入出力ファイル一式はfile_names.dataという名前のファイルで記述されます.

* 入力ファイル一式として例えば、/common/uvsor-v342-parallel/sample/electron/Si/eps/下のサンプルなどを利用できます.

* (Si/eps/のサンプルを使用するには、予め、../scf/のサンプルを実行してnfchgt.dataを用意しておく必要があります。).

=== OpenMXジョブ ===
==== 並列ジョブ ====
以下に，実行スクリプト例を示します．
+* 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 Job ===
==== Parallel Jobs ====
The sample script is as follows.
-行 638:
+行 636:
-* H2O.datは/common/openmx-3.6-parallel/work/にあります.

* ただし、H2O.datに以下の一行を追加しておく必要があります.
+* H2O.dat exists in /common/openmx-3.6-parallel/work/.

* The following line must be added to H2O.dat.
-行 644:
+行 642:
-=== GAUSSIANジョブ ===
サンプル入力ファイル(methane.com)
+=== GAUSSIAN Job ===
Sample input file (methane.com)
e
-行 663:
+行 661:
-==== シングルジョブ ====
以下に，実行スクリプト例を示します．
+==== Single Job ====
The sample script is as follows.
-行 681:
+行 679:
-==== 並列ジョブ ====
以下に，実行スクリプト例を示します．
+==== Parallel Jobs ====
The sample script is as follows.
-行 699:
+行 696:
-=== NWChemジョブ ===
サンプル入力ファイル(h2o.nw)
+=== NWChem Job ===
Sample input file (h2o.nw)
-行 723:
+行 720:
-==== 並列ジョブ ====
以下に，実行スクリプト例を示します．
+==== Parallel Jobs ====
The sample script is as follows.
-行 741:
+行 737:
-=== GAMESSジョブ ===
==== シングルジョブ ====
以下に，実行スクリプト例を示します．
+=== GAMESS Job ===
==== Single Job ====
The sample script is as follows.
-行 760:
+行 756:
-* exam01.inpは/common/gamess-2012.r2-serial/tests/standard/にあります.

=== MPQCジョブ ===
サンプル入力ファイル(h2o.in)
+* exam01.inp exists in /common/gamess-2012.r2-serial/tests/standard/.
=== MPQC Job ===
Sample input file (h2o.in)
-行 775:
+行 770:
-==== 並列ジョブ ====
以下に，実行スクリプト例を示します．
+==== Parallel Jobs ====
The sample script is as follows.
-行 794:
+行 789:
-=== AMBERジョブ ===
サンプル入力ファイル(gbin-sander)
+=== AMBER Job ===
Sample input file (gbin-sander)
-行 811:
+行 806:
-サンプル入力ファイル(gbin-pmemd)
+Sample input file (gbin-pmemd)
-行 828:
+行 823:
-==== シングルジョブ ====
以下に，実行スクリプト例を示します．

例：sanderを用いる場合
+==== Single Job ====
The sample script is as follows.

Example: To use sander

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, 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 Job

Single Job

Parallel Jobs

ANSYS CFX Job

Single Job

Parallel Jobs

ANSYS Fluent Job

Single Job

Parallel Jobs

ANSYS LS-DYNA Job

Single Job

ABAQUS Job

Single Job

PHASE Job

Parallel Jobs (phase command: SCF calculation)

Single Job (ekcal command: Band calculation)

UVSOR Job

Parallel Jobs (epsmain command: Dielectric constant calculation)

OpenMX Job

Parallel Jobs

GAUSSIAN Job

Single Job

Parallel Jobs

NWChem Job

Parallel Jobs

GAMESS Job

Single Job

MPQC Job

Parallel Jobs

AMBER Job

Single Job

並列ジョブ

CONFLEXジョブ

シングルジョブ

並列ジョブ

MATLABジョブ

シングルジョブ

並列ジョブ

CASTEP/DMol3ジョブ

ジョブの状態を確認する

投入したジョブをキャンセルする