02-11-2004
Executing mpirun commands
Basically, I would like to run an mpirun query on my web server to query your databases via yours when using the BLAST program, however the server seems not able to execute even basic mpirun programs such as cpi (to calculate pi). Are there any settings I should take note of?
I am running Perl CGI scripts via the Apache v1.3.28 server in a Unix environment, is there settings that should be taken care of when running command line in this particular case for mpirun (the script alias has already been set up - ScriptAliasMatch .../cgi-bin/... /usr/users/$1/public_html/cgi-bin/$2) :
The line in Perl script is :
`/usr/local/apps/mpich/bin/mpirun -machinefile /usr/users/utess/machines.ALPHA -np 2 /usr/local/apps/mpich/examples/cpi -o /usr/local/d.txt 2> /usr/local/err.txt`;
The relevant error is :
/usr/local/apps/mpich/bin/mpirun: pwd: read error in ..
/usr/local/apps/mpich/bin/mpirun: test: argument expected
Is there anything that should be taken care of when running scripts of this nature? Even when "nobody" user account has been set to a writable directory such that I could execute the command in "nobody"'s account I still could not execute the command via Perl script.
Is it a problem with the server configuration since "nobody"'s account can execute the command?
I really would appreciate any help.
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GZEXE(1) General Commands Manual GZEXE(1)
NAME
gzexe - compress executable files in place
SYNOPSIS
gzexe name ...
DESCRIPTION
The gzexe utility allows you to compress executables in place and have them automatically uncompress and execute when you run them (at a
penalty in performance). For example if you execute ``gzexe /usr/bin/gdb'' it will create the following two files:
-rwxr-xr-x 1 root root 1026675 Jun 7 13:53 /usr/bin/gdb
-rwxr-xr-x 1 root root 2304524 May 30 13:02 /usr/bin/gdb~
/usr/bin/gdb~ is the original file and /usr/bin/gdb is the self-uncompressing executable file. You can remove /usr/bin/gdb~ once you are
sure that /usr/bin/gdb works properly.
This utility is most useful on systems with very small disks.
OPTIONS
-d Decompress the given executables instead of compressing them.
SEE ALSO
gzip(1), znew(1), zmore(1), zcmp(1), zforce(1)
CAVEATS
The compressed executable is a shell script. This may create some security holes. In particular, the compressed executable relies on the
PATH environment variable to find gzip and some standard utilities (basename, chmod, ln, mkdir, mktemp, rm, sleep, and tail).
BUGS
gzexe attempts to retain the original file attributes on the compressed executable, but you may have to fix them manually in some cases,
using chmod or chown.
GZEXE(1)