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#printf("hi, this is perl pdf_extractor1.\n");

...
#printf("1, this is FILENAME $filename1.\n");

system("./xpdf-2.01/xpdf/pdftotext -raw $ARGV[0]");

yao@ubuntu:~/perl$ xpdf-2.01/xpdf/pdftotext 1.pdf
bash: xpdf-2.01/xpdf/pdftotext: Permission denied
...
yao@ubuntu:~/perl/xpdf-2.01$ cd xpdf
yao@ubuntu:~/perl/xpdf-2.01/xpdf$ pdftotext /home/yao/perl/1.pdf