Thanks for the suggestion cdarke. I think i didnt put it properly. I meant that the third party program writes to the current directory. for example, if i invoke the program as 
../../progs/<programname> <options> <parameters>

[download]
it writes to the current directory. I tried using chdir() and it partially solves the problem. There are two scripts written in Fortran, which i call in succession. The first one writes output to the required directory when i use chdir() and the other one does not. The third party one needs user intervention at runtime. I tried writing the required values to a file and giving that as an input during invocation as follows 
../../progs/<script> < <param input file>

[download]
where <param input file> contains different runtime parameters. This works like a charm when i use it on the command line and it does not work when i use it within backticks from the CGI script after issuing a chdir() to the required working directory.

In reply to Re^2: running process from CGI by kota_rocks
in thread running process from CGI by kota_rocks

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.