Subsections


5.2 How to use software

This section introduces the software that requires attention when using it.
  1. AIPS
  2. CASA
  3. CASA Analysis Utilities
  4. GILDAS
  5. IDL
  6. IRAF
  7. Jupyter Notebook
  8. MCSRED
  9. Miriad
  10. NEWSTAR
  11. pLaTeX
  12. SDFRED
  13. xdvi
  14. Karma
  15. CARTA


1. AIPS

Application

For those who want to use AIPS, please inform us (consult(at-mark)ana.nao.ac.jp) of your MDAS account. We will allocate an AIPS ID to each user. AIPS users can only use their own allocated AIPS ID, but cannot use other user's AIPS ID.

If you do not have allocated AIPS IDs, only AIPS IDs between 2 and 9 can be used. Anyone can use these IDs, so someone may handle your data. We recommend that you get allocated AIPS IDs.

Data storage location

The AIPS user data directory is set up in the home directory as AIPS IDs are allocated. Since the home directory is NFS, you can access same data from any interactive data analysis servers.

If you do not have allocated AIPS IDs, AIPS user data is stored into “/lfs01/aips/DATA/LOCALHOST_1”. Since /lfs01 is a target of the periodic data deletion, the AIPS user data would be deleted.

How to start AIPS

Please input commands below. AIPS(31DEC19) should be started.
$ source /usr/local/aips/LOGIN.SH
$ aips tv=local:0
If you want to use old versions, please execute following script by using a source command (bash).
 31DEC17: /usr/local/aips-31DEC17/LOGIN.SH


2. CASA

Don't use CASA on disks that are NFS mounted (/lfs[01-16:)

We strongly recommend that you use CASA on the home or local disk areas (/wkm[01-20], wkh[01-12]) because if you use CASA on disks that are NFS mounted (/lfs[01-16]), all tasks could not be run normally with all versions of CASA.

How to start CASA

The default path of CASA is set to latest version basically. If you want to use old versions, please execute following lines.
 4.7.0-1: /usr/local/casa/casa-release-4.7.0-1-el7/bin/casa
 4.7.1: /usr/local/casa/casa-release-4.7.1-el7/bin/casa
 4.7.2: /usr/local/casa/casa-release-4.7.2-el7/bin/casa
 5.0.0: /usr/local/casa/casa-release-5.0.0-218.el7/bin/casa
 5.1.0: /usr/local/casa/casa-release-5.1.0-74.el7/bin/casa
 5.1.1: /usr/local/casa/casa-release-5.1.1-5.el7/bin/casa
 5.1.2: /usr/local/casa/casa-release-5.1.2-4.el7/bin/casa
 5.3.0: /usr/local/casa/casa-release-5.3.0-143.el7/bin/casa
 5.4.0: /usr/local/casa/casa-release-5.4.0-70.el7/bin/casa
 5.4.1: /usr/local/casa/casa-release-5.4.1-32.el7/bin/casa
 5.5.0: /usr/local/casa/casa-release-5.5.0-149.el7/bin/casa
 5.6.1(pipeline): /usr/local/casa/casa-pipeline-release-5.6.1-8.el7/bin/casa
 5.6.2(pipeline): /usr/local/casa/casa-pipeline-release-5.6.2-2.el7/bin/casa
 5.7.0: /usr/local/casa/casa-release-5.7.0-134.el7/bin/casa
 5.7.2: /usr/local/casa/casa-release-5.7.2-4.el7/bin/casa
 5.8.0: /usr/local/casa/casa-release-5.8.0-109.el7/bin/casa
 6.1.0: /usr/local/casa/casa-6.1.0-118/bin/casa
 6.1.1(pipeline): /usr/local/casa/casa-6.1.1-15-pipeline-2020.1.0.40/bin/casa
 6.1.2(pipeline): /usr/local/casa/casa-6.1.2-7-pipeline-2020.1.0.36/bin/casa
 6.2.0: /usr/local/casa/casa-6.2.0-124/bin/casa
 6.2.1: /usr/local/casa/casa-6.2.1-7-pipeline-2021.2.0.128/bin/casa
 6.3.0: /usr/local/casa/casa-6.3.0-48/bin/casa
 6.4.0(Python3.6): /usr/local/casa/casa-6.4.0-16-py3.6/bin/casa
 6.4.1(pipeline): /usr/local/casa/casa-6.4.1-12-pipeline-2022.2.0.64/bin/casa
 6.4.1(pipeline): /usr/local/casa/casa-6.4.1-12-pipeline-2022.2.0.68/bin/casa
 6.4.0(Python3.8): /usr/local/casa/casa-6.4.0-16-py3.8/bin/casa
 6.4.3(Python3.6): /usr/local/casa/casa-6.4.3-27-py3.6/bin/casa
 6.4.3(Python3.8): /usr/local/casa/casa-6.4.3-27-py3.8/bin/casa
 6.4.3(Python3.6): /usr/local/casa/casa-6.4.4-31-py3.6/bin/casa
 6.4.3(Python3.8): /usr/local/casa/casa-6.4.4-31-py3.8/bin/casa
 6.5.0(Python3.6): /usr/local/casa/casa-6.5.0-15-py3.6/bin/casa
 6.5.0(Python3.8): /usr/local/casa/casa-6.5.0-15-py3.8/bin/casa
 6.5.1(Python3.6): /usr/local/casa/casa-6.5.1-23-py3.6/bin/casa
 6.5.1(Python3.8): /usr/local/casa/casa-6.5.1-23-py3.8/bin/casa
 6.5.2(Python3.6): /usr/local/casa/casa-6.5.2-26-py3.6/bin/casa
 6.5.2(Python3.8): /usr/local/casa/casa-6.5.2-26-py3.8/bin/casa
 6.5.3(Python3.6): /usr/local/casa/casa-6.5.3-28-py3.6/bin/casa
 6.5.3(Python3.8): /usr/local/casa/casa-6.5.3-28-py3.8/bin/casa
 6.5.4(pipeline): /usr/local/casa/casa-6.5.4-9-pipeline-2023.1.0.124/bin/casa
 6.5.5(Python3.6): /usr/local/casa/casa-6.5.5-21-py3.6/bin/casa
 6.5.5(Python3.8): /usr/local/casa/casa-6.5.5-21-py3.8/bin/casa
 6.5.6(Python3.8): /usr/local/casa/casa-6.5.6-22-py3.8.el7/bin/casa
 6.6.0(Python3.8): /usr/local/casa/casa-6.6.0-20-py3.8.el7/bin/casa


3. CASA Analysis Utilities

How to use

CASA Analysis Utilities are installed in the following path: “/usr/local/src/casa/analysis_scripts/”. Edit your casapy initializing file “~/.casa/init.py” or create new file if it does not exist, and add the following.
import sys
aupath = '/usr/local/src/casa/analysis_scripts'
if aupath not in sys.path:
   sys.path.append(aupath)
import analysisUtils as aU

checked functions

Operation of function on the following web site was confirmed.
 Analysis Utilities in CASA Guide (https://casaguides.nrao.edu/index.php/Analysis_Utilities)
Note following points:

About Antenna Pad Information

Because antenna pad information is not installed, functions that require it can not work properly.

When you install into your home directory

You can install CASA Analysis Utilities also into your home directory. In that case, deploy the tools referring to the following site and change the path described in the init.py to the appropriate one.
 Analysis Utilities in CASA Guide (https://casaguides.nrao.edu/index.php/Analysis_Utilities)


4. GILDAS

How to start GILDAS

You need to input the following command before starting the GILDAS.
$ gilenv
After executing the command, you should be able to start the GILDAS only on the terminal emulator.


5. IDL

Can't start IDL (1)

After you kill IDL forcibly, you may have a trouble to restart IDL. The IDL configuration files may be damaged due to the forced termination. You may solve the problem with the following operation. However, the configuration file will be lost, and the IDL environment will be initialized.

Rename "~/IDLWorkspace8?"
Rename "~/.idl"

Can't start IDL (2)

If you change the shell after you log-in to the MDAS, you cannot start the IDL because IDL cannot read configuration files. Please use a following command if you want to change the shell.
$ modify_userinfo -s [Shell]


6. IRAF

How to start IRAF 2.14

The default path is IRAF 2.16. If you want to use IRAF 2.14, please append following lines into your configuration files.
[sh, bash]
Append following script to both "~/.bashrc" and "~/.bash_profile".
if [ -r /usr/local/iraf2141/iraf/unix/hlib/setup.sh ]; then
export IRAFARCH=redhat
export iraf=/usr/local/iraf2141/iraf/
. $iraf/unix/hlib/setup.sh
fi

[csh, tcsh]
Append following script to "~/.cshrc".
if ( -r /usr/local/iraf2141/iraf/unix/hlib/setup.csh ) then 
  setenv IRAFARCH redhat
  setenv iraf /usr/local/iraf2141/iraf/
  source $iraf/unix/hlib/setup.csh
endif

How to start IRAF 2.17

If you want to use IRAF 2.17, please execute the following command first.
[sh, bash]
source /usr/local/iraf217/iraf.sh

[csh, tcsh]
source /usr/local/iraf217/iraf.csh


7. Jupyter Notebook

When you launch the jupyter notebook with “-no-browser” option on the interactive data analysis servers and use the notebook from the user's PC on the NAOJ network, we strongly recommend to use the SSH port forwarding because the communication between the user's PC and the server is not encrypted.

If you use the MDAS vpn service, the SSH port forwarding is not required because the VPN encrypts the communication.

How to use the SSH port forwarding for Jupyter Notebook

  1. Launch the jupyter notebook on the interactive data analysis server with “-no-browser” option.
    $ jupyter notebook --no-browser
    
    --> URL to access the notebook is displayed.
    e.g.: http://localhost:8888/?token=...
    
  2. Execute SSH connection from the user's PC .
    $ ssh -L 8888:localhost:8888  your_account@server_name(executing jupyter)
    
    Note: If the port number in the URL differs from 8888,
          match the number in SSH option to the port number.
    
  3. Launch a web browser on user's PC, enter the URL in address bar, and access the URL.


8. MCSRED

How to start the MCSRED

When the mcsred is loaded from the IRAF, the MCSRED2 will be started by default. Those who want to use the MCSRED need to modify the following files.
<modification of the login.cl>
task $mcsred=/usr/local/subaru/MCSRED/mcsred.cl
set dir_mcsred="/usr/local/subaru/MCSRED/"
<modification of the sh/csh setting files>
[sh, bash]
Add the following line into the ~/.bashrc and ~/.bash_profile.
export MCSRED_DIR=/usr/local/subaru/MCSRED

[csh, tcsh]
Add the following line into ~/.cshrc.
setenv MCSRED_DIR /usr/local/subaru/MCSRED


9. Miriad

How to use Miriad

The following list is aliases of the Miriad environment setting scripts for each telescope. You need to call one of the following aliases before starting the Miriad.

[sh, bash]
alias mirenv="source /usr/local/miriad/miriad_start.sh" (for CARMA)
alias mirenv-sma="source /usr/local/miriad/miriad-sma/lib/miriad/automiriad.sh" 
(for SMA)
alias mirenv-ata="source /usr/local/miriad/miriad-ata/lib/miriad/automiriad.sh" 
(for ATA)
alias mirenv-bima="source /usr/local/miriad/miriad-bima/lib/miriad/automiriad.sh" 
(for BIMA)
alias mirenv-gmrt="source /usr/local/miriad/miriad-gmrt/lib/miriad/automiriad.sh" 
(for GMRT)
alias mirenv-wsrt="source /usr/local/miriad/miriad-wsrt/lib/miriad/automiriad.sh" 
(for WSRT)
alias mirenv-atnf="source /usr/local/miriad/miriad-atnf/miriad/MIRRC.sh" (for ATNF)
alias mirenv-atnf2="source /usr/local/miriad/miriad-atnf2/lib/miriad/automiriad.sh" 
(for ATNF, old version)
alias mirenv-fasr="source /usr/local/miriad/miriad-fasr/miriad_start.sh" (for FASR)
alias mirenv-lofar="source /usr/local/miriad/miriad-lofar/miriad_start.sh" (for LOFAR)
[Example: to start Miriad for SMA]
$ mirenv-sma
$ miriad


10. NEWSTAR

Can't start NEWSTAR

If empty temporary files such as “nsmmmlock”, “mmm*”, “pops*”, “AIPS*”, and “ttt*” exist in your home directory, then you can't open a login window or “AIPS can't start” would be displayed after you push a “ok” in the login window of the NEWSTAR. You can start NEWSTER normally after removing the temporary files.


11. pLaTeX

Compilation error

There is a case where EUC-JP LaTeX files can not be compiled using pLaTeX. The default character code of the LaTeX installed in the MDAS is UTF-8, so if you want to compile a EUC-JP LaTeX file, please use -kanji option.
$ platex -kanji=euc hoge.tex


12. SDFRED

How to start SDFRED

The default path of the SDFRED is a latest version. If you want to use SDFRED 1.4.1, please append following lines into your configuration files.
[sh, bash]
1) Append the following lines to both "~/.bashrc" and "~/.bash_profile".
  PATH=/usr/local/subaru/sdfred20100528/bin:$PATH export PATH
  export PATH
2) Execute "source /.bashrc"

[csh, tcsh]
1)Append the following line to "~/.cshrcf".
  set path=(/usr/local/subaru/sdfred20100528/bin $path)
2) Execute "source ~/.cshrc".
3) Execute "rehash".


13. xdvi

Text garbling

Files compiled with EUC-JP would be garbled by xdvi. Please use -kanji option if you compile EUC-JP files.
$ platex -kanji=euc hoge.tex


14. Karma

Environment setting

You need to execute the following command before starting Karma.
[sh, bash]
$ source /usr/local/karma/.karmarc

[csh, tcsh]
$ source /usr/local/karma/.login

(Notice)

The reference of the “convert” command will be changed from “/usr/bin/convert” to “/usr/local/karma/bin/convert” after executing the command above. Please check a full-path of the “convert” command if you use “/usr/bin/convert”.


15. CARTA

How to start CARTA

Please follow the steps below when you use CARTA 2.0 or later. It may not be started by the “carta” command alone.

(1) Start CARTA with “no browser” option.
    $ carta --no_browser &
(2) Start any browser on user's PC. 
(3) The following message is displayed in step (1).
     [info] CARTA is accessible at [http://...]
     Copy the URL and paste it into the browser.
     CARTA starts when you open the link.
The default path of CARTA is set to latest version basically. If you want to use old versions, please execute following lines.
 【1.1】/usr/local/carta/CARTA-v1.1-RedHat7.AppImage
 【1.2.1】/usr/local/carta/CARTA-v1.2.1.AppImage
 【1.3】/usr/local/carta/CARTA-v1.3.AppImage
 【1.4】/usr/local/carta/CARTA-v1.4.AppImage
 【2.0】/usr/local/carta/CARTA-v2.0-redhat.AppImage
 【3.0】/usr/local/carta/carta-3.0-x86_64.AppImage
 【4.0beta】/usr/local/carta/carta-v4.0.0-beta.1-x86_64.AppImage
 【4.0】/usr/local/carta/carta-4.0-x86_64.AppImage

ADC
2023-10-17