5.3 How to use software

We introduce software which is required notice on the MDAS.

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

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 assign AIPS IDs to users who want to use AIPS. Users can only use assigned AIPS IDs but cannot use other AIPS IDs.

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

Data storage location

We set your AIPS data directory onto your home directory as we assign AIPS IDs. Since the home directory is the NFS, you can access same data from any data analysis servers.

If you do not have assigned AIPS IDs, your analysis data is stored into “/lfs01/aips/DATA/LOCALHOST_1”. Since /lfs01 is a target location of a scheduled data deletion, your analysis data may be deleted when the scheduled data deletion is carried out.

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 source command.

 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 versinos of CASA.

How to start CASA

The default path of CASA is a 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

 6.4.0(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

3. CASA Analysis Utilities

How to use

CASA Analysis Utilities are installed into 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:

• Functions of plotbandpass and plotweather are not confirmed because these functions are included in CASA. Use the CASA tasks of the same name.
• The following function was found not to work properly in some cases.
  • obslist: It does not work properly when antenna ID is set for parameter cofa.
  • plotWVRSolutions: Error when field is set by ID or name.
  • timeOnSource: Probably return incorrect results for mosaic observation data.

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 able to start the GILDAS only on the terminal.

5. IDL

Can't start IDL (1)

After you kill IDL, 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 following operation, but the operation can damage the configuration files.

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

Can't start IDL (2)

If you change shells after you login to the MDAS, you do not start IDL because IDL does not read configuration files. Please use a following command if you want to change shells.

$ modify_userinfo -s [Shells]

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

7. Jupyter Notebook

If you wish to execute jupyter notebook with “-no-browser” option on the MDAS interactive server, and use the notebook on a web browser on your local computer inside the network of NAOJ, we strongly recommend the use of SSH port forwarding, because the communication between your computer and the interactive server is not encrypted.

(If you use the VPN software and VPN servers of the MDAS, the software encrypts the communication between your computer and the VPN server of the MDAS, so that the use of SSH port forwarding is not required)

How to use SSH port forwarding for Jupyter Notebook

1. Execute jupyter notebook on the MDAS interactive 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 on your local computer (In case that the port number in URL is 8888).

   $ ssh -L 8888:localhost:8888  your_account@server_name(executing jupyter)
   
   Note: If the port number in URL differs from 8888,
         match the number in SSH option to the port number.
   

3. Execute web browser on your computer, input the URL in address bar, and access the URL.

8. MCSRED

How to start the MCSRED

When you load mscred on the IRAF, then the MCSRED2 will be started in default setting. If you would like to start the MCSRED, you need to modify the following files.

<login.cl>
task $mcsred=/usr/local/subaru/MCSRED/mcsred.cl
set dir_mcsred="/usr/local/subaru/MCSRED/"

<sh/csh setting files>
[sh, bash]
Plese add a following line into ~/.bashrc and ~/.bash_profile.
export MCSRED_DIR=/usr/local/subaru/MCSRED

[csh, tcsh]
Please add a following line into ~/.cshrc.
setenv MCSRED_DIR /usr/local/subaru/MCSRED

9. Miriad

How to use Miriad

You need to call any of the following aliases before starting the Miriad.

[e.g. 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)

[e.g. Starging Miriad for SMA]
$ mirenv-sma
$ miriad

• If you call an unsuitable alias, the Miriad would output incorrect results.
• We have prepared two ATNF aliases because a part of tasks did not work in the old version. If you would like to use old version, please call the “mirenv-atnf2”.

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. You can start NEWSTER normally after remove the temporary files.

11. pLaTeX

Compilation error

If you cannot compile LaTeX files with EUC-JP encoding, please use -kanji option because default character set of the pLaTeX on the MDAS is UTF-8.

$ platex -kanji=euc hoge.tex

12. SDFRED

How to start SDFRED

The default path of 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 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 a 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 encoding would be garbled on xdvi. Please use -kanji option if you compile files with EUC-JP encoding.

$ platex -kanji=euc hoge.tex

14. Karma

Environment setting

You need to execute a following command before starting Karma.

[If your shell is sh or bash]
$ source /usr/local/karma/.karmarc

[If your shell is csh or tcsh]
$ source /usr/local/karma/.login

(Notice)

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