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GRRM20 with Matlantis Integration Package Announcement

  • Updated

 

Contents

  1. Introduction
    1. Handouts
  2. Installation of GRRM20
  3. Instllation of Interface programs
  4. Functional test
    1. How to run from notebook environment
    2. How to run from terminal environment
  5. TIPS
    1. Notes on Executing GRRM20 on Matlantis
    2. Contact
  6. FAQ

 

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1. Introduction

The GRRM20 with Matlantis integration package provides the following.

  • Files required to run “GRRM20 with Matlantis”
  • Technical support on how to run GRRM20 on Matlantis

Note : Please follow the instructions in sections 2 to 4 of this manual for installation.

 

1. 1 Handouts

We will provide a zip file from Matlantis' Package Launcher. Please expand it on Matlantis and check the file structure.

  • Click the icon in the red frame shown below to launch the Matlantis Package launcher.




  • There is GRRM Packages in the middle section of Package Launcher.



     
  • grrm-pfp-packages-v0.2.1 Folder structure
    It consists of three parts: GRRM20_install, grrm_pfp_interface, and GRRM20_testjobs.

    The notebooks you mainly use are as follows.
    • install_grrm20.ipynb: Used to install GRRM20.
    • install.ipynb: Installs the interface (step 3).
    • kickGRRM.ipynb: Runs GRRM20s from the notebook for testing.
    • GRRM20_test_jobs: Contains GRRM20 test jobs.

      Note : In addition, HPC Systems will provide the GRRM20 main unit package files. Please perform the installation work described in the following sections after you have the main unit package and the associated package on hand.

      🗂grrm-pfp-packages-v0.2.1

              ∟🗂GRRM20_install

                      ∟install_grrm20.ipynb (Installation of GRRM20)

                         * GRRM20 with Matlantis main files stored here.(Section 2)

              ∟🗂grrm_pfp_interface

                      ∟🗂 example

                              ∟install.ipynb (Instllation of interface programs)(Section 3)

                              ∟🗂 grrm_from_notebook

                                      ∟kickGRRM.ipynb (Run GRRM20s from Notebook)(Section 4)

                              ∟🗂 grrm_from_terminal
                                      ∟ job1.com (Test file for execution from Terminal)

              ∟🗂GRRM20_testjobs



2. Instration of GRRM20

You need the file provided by HPC Systems, Inc.（GRRM20withMatlantis_FL_yyyymmddxxxxxxxxx.tar.bz2）

  1. Extract grrm-pfp-packages-vx.x.x.zip on Matlantis. (Right-click on the zip file > extract archive)

  2. GRRM20 with Matlantis main package Place the tar.bz2 file in the GRRM20_install directory.

  3. Open the install_grrm20.ipynb file in the GRRM20_install directory. Follow the instructions in install_grrm20.ipynb.

  4. Once the installation is complete, the “GRRM20p” command will be executable.

    • There will be operations to modify the .bashrc and .env files. If you have already created these files yourself, please be careful. The original files will be saved in the .evacuation_dir directory in your home directory.
    • The following settings will be added to the .bashrc and .env files after configuration.


    • ~/.bashrc. 
      # Set up aliases
      alias ll='ls -alF'
      alias grep='grep --color=auto'
      alias ls='ls --color=auto'

      # Set up Python environment
      # use_venv python38
      use_venv python39

      source /home/jovyan/programs/GRRM20/GRRM20setting.sh

      # Set up command history
      export HISTSIZE=10000


    • ~/.env
      PATH="/home/jovyan/GRRM20:${PATH}"
      LD_LIBRARY_PATH="/home/jovyan/GRRM20:${LD_LIBRARY_PATH}"
      GRRMroot="/home/jovyan/programs/GRRM20"
      subgrr="GRRM20.out"
      subgau=""
      subchk=""
      subuchk=""
      submol=""
      subsiesta=""
      submpi=""
      I_MPI_FABRICS="shm:tcp"
      I_MPI_FALLBACK=0
      I_MPI_HYDRA_BOOTSTRAP="ssh"
      STLM_SERVER_ADDRESS="xxxxxxx(This is the server URL. It is kept private for security reasons.)"
      STLM_SERVER_PORT= NNNNN

      Note : The port number (NNNNN) is different for each tenant.

 

 

3. Instllation of interface programs

Install the interface for running GRRM20 using PFP on Matlantis. Once the installation is complete, the GRRM20s command will be enabled, allowing you to run GRRM20 using PFP.。

 

Open /grrm_pfp_interface/examples/install.ipynb and follow the instructions in the notebook.

 

Notes：

  • When installing the integration package for the first time, skip the section at the beginning of the notebook labeled “(Note) For users who were using the interface prior to v0.1.1” and execute the following pip install command.
  • On the other hand, if you are using the interface prior to v0.1.1, uncomment the top cell and proceed with deleting the environment variable settings.


4. Functional test

Perform a functional test of GRRM20s. We have prepared two methods for running the test: from a notebook and from a terminal. Please use the method that you prefer.

 

4.1 How to run from Notebook environment

Please refer to the file /grrm_pfp_interface/examples/grrm_from_notebook/kickGRRM.ipynb. The results of executing from the notebook are stored in the grrm_work directory by default.

 

The steps performed in Notebook are as follows.

  •  Load the .env file
  •  Set arguments and run GRRM20s

Arguments can be used to set calc_mode, model_version, the output file destination directory name (grrm_work_dir), and other settings.

 

4.2 How to run from terminal environment

Move to the directory where the input file is located. In this example, we will explain how to execute the file examples/grrm_from_terminal/job1.com.

cd /grrm-pfp-package-v0.2.1/grrm_pfp_interface/examples/grrm_from_terminal/

 

Run GRRM20s. (To run in the background, use nohup & as follows.)

nohup GRRM20s &

 

When the calculation ends normally, multiple output files are generated according to the input file name. In the case of job1.com, the following message is output in job1_message_END.rrm: “Normal termination of the GRRM Program Ver. 23-3123 at Hokkaido Univ....”

cat job1_message_END.rrm

 

 

5. TIPS

5.1 Notes on Executing GRRM20 on Matlantis

  • The general usage of GRRM20 is based on the GRRM General Interface. Please refer to the manual at Hokkaido University AFIR Web.
  • Input file
    When running on Matlantis, the first line must contain “%link=non-supported” and the option specification line must contain “sublink=./kickpfp.py”. (kickpfp.py is created in the current directory when GRRM20s is executed, so you do not need to create it yourself.)


    Example：job1.com
     
    %link=non-supported
    # MIN

    0 1
    C         -0.079213112255          0.000038936045         -0.592031587948
    O          0.018800714554         -0.000018308130          0.717081381477
    H          0.322739833191          0.909186505065         -0.947006485140
    H          0.322739833191         -0.909359858691         -0.946723086445
    Options
    sublink = ./kickpfp.py

 

  • Executable job types
    Executable job types have sample input files in test_jobs. The following methods can be used.
    • MIN
    • Freq
    • Saddle
    • IRC
    • ADDF
    • SCW
    • 2PSHS
    • LUP
    • MC-AFIR
    • DS-AFIR
    • SC-AFIR
    • RePATH
    • ReStruct
    • ReEnergy
    • RCMC


On the other hand, the following methods cannot be used.

    • MESX, MECI
    • External atoms (Micro Iteration)

 

5.2 Contact

If you have any questions, please contact our technical support team via the Contact page on the Matlantis website. Please include the keyword “GRRM” in your inquiry so that we know it is related to GRRM.

For inquiries regarding methods available with GRRM20 with Matlantis, we will respond in collaboration with HPC Systems, Inc., so please note that it may take some time to respond. We appreciate your understanding.

 

6. FAQ

  • Calculation stopped due to an error during the operation test.
    • If the path is not accessible or GRRM20s is not running

      An error example of  job1_message_ERROR.rrm：
       
      The job1_message_CONTINUE.rrm file doesn't exist...
    • License authentication failed error
       An error example of job1_message_ERROR.rrm：
       
      ERROR!
      Please check job1...
    • When you execute GRRM before the contract start date
      nohup.out (when running in a terminal environment) or kickGRRM.ipynb (when running in a notebook environment)
       
      connect():Connection refused
    • If the license has expired
      nohup.out (when running in a terminal environment) or kickGRRM.ipynb (when running in a notebook environment)
       
      License error has occurred.
  • If you want to stop the calculation midway
    Please Create a file named {jobname}_message_STOP.rrm in the directory where the program is running. After a certain amount of time, GRRM20 will switch to calculation stop mode.

  • GRRM20s arguments (when running in terminal)
    If you are using a notebook, the arguments are listed in kickGRRM.ipynb.

    $ nohup GRRM20s {job_name} mode=CRYSTAL_U0 version=5.0.0 work="test" &
    • mode：Specify the PFP calculation mode.
    • version： Specify the PFP version
    • work： Specify the directory name for outputting calculation results (str format). If not specified, output files will be saved in the current directory.
      For more details, please refer to /grrm_pfp_packages/examples/grrm_from_terminal/README.md

 

 

 

 

 

 

 

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