Host CL Scripting not working

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Host CL Scripting not working

iaa

01/21/2014 01:10PM (Read 4449 times)

Newbie

Status: offline

Registered: 02/14/2011
Posts: 11

I have read all the forum posts on host CL scripting, as well as the web page at http://iraf.noao.edu/iraf/web/new_stuff/cl_host.html, but still cannot get it to work on my machine. I think that I have defined the correct environment variables and used the executable that I should. After two days trying to find a solution I am absolutely clueless as to how to proceed. Hopefully somebody will be able to point me in the right direction? Any help would be much appreciated.

The script:

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images                                                                                                                                 

util                                                                                                                                   

real mean                                                                                                                              

string path                                                                                                                            

string area                                                                                                                            

string output                                                                                                                          

mkdir112_o                                                                                                                            
printf("mkdir: created directory `112_o'\n")
printf("\n")

path ="/data/120104/NGC2264_0001.fits"

area ="[2069:2166,2:2047]"

output ="112_o/NGC2264_0001_o.fits"

imstat (path // area, fields='mean', format=no) | scan(mean)                                                                           

imarith (path,"-", mean, output)
printf("%s - %.5f = %s\n", path, mean, output)

Run from within IRAF, it works as expected:

PHP Formatted Code
iaa@csic:~/util$ cl

Warning: no login.cl found in login directory

      dataio      gemini      lists       plot        stsdas      xdimsum

      dbms        gmisc       mscred      proto       system

      fitsutil    images      noao        rvsao       tables      

      fuzzy       language    obsolete    softools    utilities   

ecl> cl < script.cl
mkdir: created directory `112_o'

/data/120104/NGC2264_0001.fits - 84.18766 = 112_o/NGC2264_0001_o.fits

ecl>

However:

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iaa@csic:~/util$ export iraf=/iraf/iraf/

iaa@csic:~/util$ export arch=.linux

iaa@csic:~/util$ export IRAFARCH=linux

iaa@csic:~/util$ export IRAFBIN=/iraf/iraf/bin.linux/

iaa@csic:~/util$ export mach=linux

Warning: no login.cl found in login directory

      dataio      gemini      lists       plot        stsdas      xdimsum

      dbms        gmisc       mscred      proto       system

      fitsutil    images      noao        rvsao       tables      

      fuzzy       language    obsolete    softools    utilities   

ecl>       chpixtype     imdelete      imheader      imslice       listpixels

      hedit         imdivide      imhistogram   imstack       minmax

      hselect       imexpr        imjoin        imstatistics  nhedit

      imarith       imfunction    imrename      imsum         sections

      imcopy        imgets        imreplace     imtile        

imutil>       curfit    entab     polyfit   surfit    ucase     

      detab     lcase     split     translit  urand     

utilities> utilities> utilities> utilities> utilities> utilities> utilities> ERROR: Cannot make directory (112_o)^G

utilities>mkdir: created directory `112_o'

utilities> 

utilities> utilities> utilities> utilities> utilities> 

PANIC in `/iraf/iraf/bin.linux/x_images.e': Memory has been corrupted

utilities> mean: ERROR: Parameter value is out of range; try again

mean: ERROR: Parameter value is out of range; try again

mean: ERROR: Parameter value is out of range; try again

mean: ERROR: Parameter value is out of range; try again

mean: ERROR: Parameter value is out of range; try again

mean: ERROR: Parameter value is out of range; try again

mean: ERROR: Parameter value is out of range; try again

If I follow this advice and add "ulimit -s unlimited" to my Bash environment, the script runs successfully, but the output is full of error messages. I am afraid this is symptomatic that there is something I am not doing correctly.

PHP Formatted Code
iaa@csic:~/util$ /iraf/iraf/bin.linux/ecl.e < script.cl 

Warning: no login.cl found in login directory

      dataio      gemini      lists       plot        stsdas      xdimsum

      dbms        gmisc       mscred      proto       system

      fitsutil    images      noao        rvsao       tables      

      fuzzy       language    obsolete    softools    utilities   

ecl>       chpixtype     imdelete      imheader      imslice       listpixels

      hedit         imdivide      imhistogram   imstack       minmax

      hselect       imexpr        imjoin        imstatistics  nhedit

      imarith       imfunction    imrename      imsum         sections

      imcopy        imgets        imreplace     imtile        

imutil>       curfit    entab     polyfit   surfit    ucase     

      detab     lcase     split     translit  urand     

utilities> utilities> utilities> utilities> utilities> utilities> utilities> utilities>mkdir: created directory `112_o'

utilities> 

utilities> utilities> utilities> utilities> utilities> utilities> utilities> /data/120104/NGC2264_0001.fits - 84.18766 = 112_o/NGC2264_0001_o.fits

utilities>       chpixtype     imdelete      imheader      imslice       listpixels

      hedit         imdivide      imhistogram   imstack       minmax

      hselect       imexpr        imjoin        imstatistics  nhedit

      imarith       imfunction    imrename      imsum         sections

      imcopy        imgets        imreplace     imtile        

imutil>       dataio      gemini      lists       plot        stsdas      xdimsum

      dbms        gmisc       mscred      proto       system      

      fitsutil    images      noao        rvsao       tables      

      fuzzy       language    obsolete    softools    utilities   

ecl> ERROR: use `logout' to log out of the CL

ecl> ERROR:use `logout' to log out of the CL

ecl> ERROR: use `logout' to log out of the CL

ecl> ERROR:use `logout' to log out of the CL

ecl> ERROR: use `logout' to log out of the CL

ecl> ERROR:use `logout' to log out of the CL

ecl> ERROR: use `logout' to log out of the CL

ecl> ERROR:use `logout' to log out of the CL

Does anybody know what I am doing wrong? Would it be possible to get the script to run cleanly?

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fitz

01/22/2014 09:33PM

Admin

Status: offline

Registered: 09/30/2005
Posts: 4040

The quick answer to your question is that you should put the following as the first line of the script and them make it executable:

#!/iraf/iraf/bin.linux/ecl.e -f

and then execute as

% ./script.cl

rather than with the redirection. Note the '-f' flag is required to suppress the need for a login.cl file.

The reason that you see the prompts and other output is because of the redirection, i.e. the CL output is as if you had typed each command at the prompt. The reason you might be seeing the "use 'logout' to log out" messages is sometimes in cases where the script file isn't properly terminated with a newline or EOF (as can sometimes happen with emacs or certain editors), however in this case I think it is simply because you don't have an explicit 'logout' command in the script. The ulimit command is in the 'cl' startup command script but again you aren't using this and so should be in your normal shell environment as you've done.

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iaa

01/28/2014 06:19PM

Newbie

Status: offline

Registered: 02/14/2011
Posts: 11

Thanks so much, fitz. My IRAF scripts are working now.

Just to confirm — are all of the following environment variables needed for host CL scripts to work? They seem to do the trick on the two machines on which I have tested the scripts to far, but I would like to make sure they are completely portable (provided they are run on systems with the same architecture and IRAF installation path).

export iraf=/iraf/iraf/
export arch=.linux64
export IRAFARCH=linux64
export IRAFBIN=/iraf/iraf/bin.linux64/
export MACH=linux64

Am I missing anything / any unnecessary variable?

Thanks again for such superb support.

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fitz

01/28/2014 06:25PM

Admin

Status: offline

Registered: 09/30/2005
Posts: 4040

The "normal" development environment requires only something like

setenv iraf /iraf/iraf/ <--- remember the trailing '/'
setenv IRAFARCH linux
source $iraf/unix/hlib/irafuser.csh

or the equivalent for a Bash shell, the 'irafuser.[c]sh' script defines all additional variables. In your example you probably don't explicityly need IRAFBIN or MACH, however the 'arch' should be set for host CL scripts since this is normally defined in the CL startup command (as ".$IRAFARCH"

, likewise for the ulimit command.

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iaa

01/29/2014 09:30AM

Newbie

Status: offline

Registered: 02/14/2011
Posts: 11

Thanks so much.

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