Executing mpirun commands


 
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Old 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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APPSCHEMA(5)							 LAM FILE FORMATS						      APPSCHEMA(5)

NAME
appschema - LAM application schema format SYNTAX
# # comments # [<where>] [-np #] [-s <where>] [-wd <dir>] [-x <env>] <program> [<args>] [<where>] [-np #] [-s <where>] [-wd <dir>] [-x <env>] <program> [<args>] ... DESCRIPTION
The application schema is an ASCII file containing a description of the programs which constitute an application. It is used by mpirun(1), MPI_Comm_spawn, and MPI_Comm_spawn_multiple to start an MPI application (the MPI_Info key "file" can be used to specify an app schema to MPI_Comm_spawn and MPI_Comm_spawn_multiple). All tokens after the program name will be passed as command line arguments to the new pro- cesses. Ordering of the other elements on the command line is not important. The meaning of the options is the same as in mpirun(1). See the mpirun(1) man page for a lengthy discussion of the nomenclature used for <where>. Note, however, that if -wd is used in the application schema file, it will override any -wd value specified on the command line. For each program line, processes will be created on LAM nodes according to the presence of <where> and the process count option (-np). only <where> One process is created on each node. only -np The specified number of processes are scheduled across all LAM nodes/CPUs. both The specified number of processes are scheduled across the specified nodes/CPUs. neither One process is created on the local node. Program Transfer By default, LAM searches for executable programs on the target node where a particular instantiation will run. If the file system is not shared, the target nodes are homogeneous, and the program is frequently recompiled, it can be convenient to have LAM transfer the program from a source node (usually the local node) to each target node. The -s option specifies this behaviour and identifies the single source node. EXAMPLE
# # Example application schema # Note that it may be necessary to specify the entire pathname for # "master" and "slave" if you get "File not found" errors from # mpirun(1). # # This schema starts a "master" process on CPU 0 with the argument # "42.0", and then 10 "slave" processes (that are all sent from the # local node) scheduled across all available CPUs. # c0 master 42.0 C -np 10 -s h slave SEE ALSO
mpirun(1), MPI_Comm_spawn(2), MPI_Comm_Spawn_multiple(2), MPIL_Spawn(2), introu(1) LAM 7.1.4 July, 2007 APPSCHEMA(5)