Note: See To establish your own AVIDD account for more information on obtaining your own account.
Use the ssh command on a Unix based workstation/laptop or an SSH Client on Microsoft Windows to login to the AVIDD cluster.
$ ssh -x <your username>@avidd-b.iu.eduExample:
[agopu@peart agopu]$ ssh -x hpctrn01@avidd-b.iu.edu
The authenticity of host 'avidd-b.uits.indiana.edu (129.79.228.232)' can't be established.
RSA key fingerprint is 9c:63:4f:a0:90:95:5b:e3:76:c3:17:eb:96:9b:f3:87.
Are you sure you want to continue connecting (yes/no)? yes
hpctrn01@avidd-b.uits.indiana.edu's password:
[hpctrn01@bh2 hpctrn01]$
Set email address in ~/.forward file if you have not done that yet.
(Warning: You should use a valid email id!
Failing to do so will result in inability to check status of your jobs.)
[hpctrn01@bh2 hpctrn01]$ echo "myfavoriteemailid@hotmail.com" > ~/.forward
Note: Detailed information about SSHing onto AVIDD from
Microsoft Window/Unix machines is available in the
Login to AVIDD using SSH section of the
Working on AVIDD document.
Use of the -x flag to disable X11 forwarding from the AVIDD head-node is also
explained in that section. If you have not done so, we strongly recommend you go through
that document before proceeding forward in this workshop.
Copy example program files from HPC's account:
[agopu@bh2 agopu]$ cp -dr ~hpc/MPI_Tutorial ~/.
~/.soft fileSTOP! If you are using our training accounts [hpctrnXX]; you do not need to make any modifications.
When you use your own AVIDD account,
you will need to edit your ~/.soft file to include the lines shown in
bold (before the @avidd line):
[agopu@bh2 agopu]$ nano -w ~/.soft ## Set your environment for LAM GM (built with Intel compilers), Intel Trace tools and TotalView and remove default MPICH @remove +mpich-gm-intel +lam-gm-intel +ita-lam +totalview ## . . . @aviddNote: There is a file named
dot_soft available within the MPI_Tutorial
directory that you could use in place of (or to update) your ~/.soft file.
If you prefer MPICH over LAM, then you can use the file named dot_soft.mpich instead.
Also, do not remove the @avidd from your ~/.soft file
unless you know what you are doing.
More information about Softenv is available in the Login to AVIDD using SSH section of the Working on AVIDD document.
qsub -I[agopu@bh2 agopu]$ qsub -I -l nodes=2:ppn=2 -l walltime=6:00:00You can expect to see a message like this:
qsub: waiting for job 281988.aviss.avidd.iu.edu to start qsub: job 281988.aviss.avidd.iu.edu ready [agopu@bc56 agopu]$If you want to know what nodes have been allocated to your job, then you can find that information in a file pointed to, by $PBS_NODEFILE.
[agopu@bc81 agopu]$ cat $PBS_NODEFILE bc81 bc53 bc81 bc53
| Previous: Introduction | Up: Table of Contents | Next: HelloWorlds: My First MPI Program |
|---|
Last revised Tuesday, 07-Feb-2006 11:12:33 EST
http://www.indiana.edu/hpa/mpi_tutorial/s1_initial_setup.html
Comments and suggestions to rac@indiana.edu
Copyright 2004,
The Trustees of Indiana University
PRIVACY POLICY
| The activities of this group support and have been funded in part by the National Science Foundation [NSF] under Grant No. 0116050 and Grant CDA-9601632; Shared University Research Grants from International Business Machines Inc. [IBM]; and the Indiana Genomics Initiative [INGEN]. The Indiana Genomics Initiative of Indiana University is supported in part by Lilly Endowment Inc. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of NSF, IBM, or Lilly Endowment Inc. |
