7. Script language

At Supercomputer Fugaku , preparing the OSS script language to the computing node.

Note

The OSS delivery has moved to Spack. The articles in this chapter are old OSS information before moving to Spack.

See Using OSS.

7.1. Overview

The following OSS compiled by the Fujitsu compiler is available for the compute nodes.

  • Python2

  • Python3

  • Ruby

Attention

  • When constructing these OSS environment, some modifications necessary for compiling with the Fujitsu compiler have been made, but no other special settings have been made.

  • OSS, basically, offers only environment information such as install path.

  • For setting the installation path required for OSS execution, modulefile is prepared for each OSS. Please use by refering to the following sob script example.

7.2. Python

Python2 and Pythn3 are available to use.

7.2.1. Python2

Note

Sunsetting Python 2

See https://www.python.org/doc/sunset-python-2/.

This indicates how to use Python2.

7.2.1.1. Package

To Python2, the following packages are added.

Versuon

Added package

Python 2.7.15

  • NumPy

  • SciPy

  • mpi4py

  • virtualenv

See also

For NumPy and SciPy, fjlapackexsve (BLAS, LAPACK thread parallel version Fujitsu library is used.

7.2.1.2. Environment variable and use direction

Environment variable setting for executing Python2 uses module file (Python2-CN/2.7.15). Here indicates the job script example.

  • Execution by Python2 command

#!/bin/bash
#PJM -L "node=1"
#PJM -L "elapse=10:00"
#PJM -x PJM_LLIO_GFSCACHE=/vol000N
#PJM -g groupname
#PJM -S

module load Python2-CN
export FLIB_CNTL_BARRIER_ERR=FALSE

# execute job
python2 sample.py

  • If execute by using mpi4py (Uses mpiexec command)

#!/bin/bash
#PJM -L "node=2"
#PJM -L "elapse=10:00"
#PJM --mpi "proc=8"
#PJM -x PJM_LLIO_GFSCACHE=/vol000N
#PJM -g groupname
#PJM -S

module load Python2-CN
export FLIB_CNTL_BARRIER_ERR=FALSE

# execute job
mpiexec -n 8 python2 mpi-sample.py

7.2.2. Python3

Note

A new version of Python is available in Spack.

The package provided by Spack (py-*) should be used in conjunction with the Python provided by Spack.

See Using OSS.

This indicates how to use Python3.

7.2.2.1. Package

To Python3, the following packages are added.

Version

Added package

Python 3.6.8

  • NumPy

  • SciPy

  • mpi4py

See also

For NumPy and SciPy, fjlapackexsve (BLAS, LAPACK thread parallel version Fujitsu library is used.

7.2.2.2. Environment variable and use direction

Environment variable setting for executing Python2 uses module file (Python3-CN/3.6.8). Here indicates the job script example.

  • Execution by Python3 command

#!/bin/bash
#PJM -L "node=1"
#PJM -L "elapse=10:00"
#PJM -x PJM_LLIO_GFSCACHE=/vol000N
#PJM -g groupname
#PJM -S

module load Python3-CN
export FLIB_CNTL_BARRIER_ERR=FALSE

# execute job
python3 sample.py

  • If execute by using mpi4py (Uses mpiexec command)

#!/bin/bash
#PJM -L "node=2:noncont"
#PJM -L "elapse=10:00"
#PJM --mpi "proc=8"
#PJM -x PJM_LLIO_GFSCACHE=/vol000N
#PJM -g groupname
#PJM -S

module load Python3-CN
export FLIB_CNTL_BARRIER_ERR=FALSE

# execute job
mpiexec -n 8 python3 mpi-sample.py

7.3. Ruby

Installing the following version Ruby.

Version

Ruby 2.6.5

7.3.1. Environment variable

Environment variable setting for executing Ruby uses module file (Ruby-CN/2.6.5). Here indicates the job script example

  • Execution by Ruby command

#!/bin/bash
#PJM -L "node=1"
#PJM -L "elapse=10:00"
#PJM -x PJM_LLIO_GFSCACHE=/vol000N
#PJM -g groupname
#PJM -S

module load Ruby-CN

# execute job
ruby sample.rb

7.4. Java

Here indicates the use of Java compiler.

7.4.1. Compiler environment setting

Use environment of Java compiler is set using modulefile.

To use, execute the following before executing translation.

  • Compiling on the login node

    Use the openjdk provided by Spack. For more information on using Spack, please refer to the “Fugaku Spack Users Guide” on the Fugaku website.

[_LNlogin]$ . /vol0004/apps/oss/spack/share/spack/setup-env.sh # Environment setting of Spack
[_LNlogin]$ spack load openjdk arch=linux-rhel8-skylake_avx512 # Environment setting of OpenJDK

  • Compiling on the compute node

[_LNlogin]$ module load OpenJDK-CN

The usable environment is as following.

Node

Software name

Language

Version

Command

Login node

OpenJDK

Java

11.0.2

javac/mpijavac

Compute Node

OpenJDK

Java

11u

javac/mpijavac

7.4.2. Compile command

Here is an example of compiling a Java program using mpijavac.

Normally, use javac for Java program translation, but about MPI program translation, use mpijavac command for MPI program translation command.

  • If use MPI library

[_LNlogin]$ mpijavac [compile option] source file name

  • If not use MPI library

[_LNlogin]$ javac [compile option] source file name

The translation command name of the command used on the login node and the command used on the compute node is the same.

  • Translation command

Type

Command name

MPI library

Cross compiler

mpijavac

Use

javac

Not use

Native compiler

mpijavac

Use

javac

Not use

Note

When using mpijavac, execution is possible only on compute node. Cannot execute on login node.

Here indicates main compile option.

Compile option

Description

---showme

Displays the calling line when the translation command of the MPI program calls the javac command. Actually does not proceed translation.

---verbose

Displays the calling line when the translation command of the MPI program calls the javac command. Proceeds translation.

---help,-help,-h

Displays help message. Actually does not proceed translation.

avac_arguments

Specifies an option giving to javac command.

See also

  • mpijavac command is javac command’s wrapper command and calls JDK’s javac command internally.Thus, mpijavaccommand can specify javac command option directly.

  • mpijavac command can translate Java program without specifying MPI library’s class path.

  • When Java program translation, to use jar file that the user prepares, it is requried to set the target jar file path with the environment variable CLASSPATH or javac command’s -classpath option.

  • If specified both of environment variable CLASSPATH and -classpath option, -classpath option has priority.

7.4.3. Execution direction

Shows how to execute a Java program “javasample.class” compiled with javac and mpijavac.

[Sequential execution]

#!/bin/bash
#PJM -L "node=1"
#PJM -L "rscgrp=small"
#PJM -L "elapse=10:00"
#PJM -x PJM_LLIO_GFSCACHE=/vol000N
#PJM -g groupname
#PJM -s

module load OpenJDK-CN

numactl --cpunodebind 4 --membind 4 java javasample

[MPI Execution]

#!/bin/bash
#PJM -L "node=2"
#PJM -L "rscgrp=small"
#PJM -L "elapse=10:00"
#PJM -x PJM_LLIO_GFSCACHE=/vol000N
#PJM -g groupname
#PJM --mpi "proc=8"
#PJM -s

module load OpenJDK-CN

export PLE_MPI_STD_EMPTYFILE=off # Do not create a file if there is no output to stdout/stderr at execution time.
export OMPI_MCA_plm_ple_memory_allocation_policy=bind_local
mpiexec java javasample