Changes between Version 5 and Version 6 of aurora


Ignore:
Timestamp:
01/10/19 08:27:45 (6 years ago)
Author:
Mathieu Morlighem
Comment:

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  • aurora

    v5 v6  
    88#!sh
    99Host aurora aurora.jpl.nasa.gov
    10    HostName aurora.jpl.nasa.gov
     10  HostName aurora.jpl.nasa.gov
    1111  User YOURUSERNAME
    1212  HostKeyAlias aurora.jpl.nasa.gov
    … …  
    2121ssh aurora
    2222}}}
    23 
    24 == Password-less ssh ==
    25 
    26 Once you have the account, you can setup a public key authentication in order to avoid having to input your password for each run.
    27 You need to have a SSH public/private key pair. If you do not, you can create a SSH public/private key pair by typing the following command and following the prompts (no passphrase necessary):
    28 {{{
    29 #!sh
    30 $your_localhost% ssh-keygen -t rsa
    31 Generating public/private rsa key pair.
    32 Enter file in which to save the key (/Users/username/.ssh/id_rsa):RETURN
    33 Enter passphrase (empty for no passphrase):RETURN
    34 Enter same passphrase again:RETURN
    35 Your identification has been saved in /Users/username/.ssh/id_rsa.
    36 Your public key has been saved in /Users/username/.ssh/id_rsa.pub.
    37 }}}
    38 
    39 Two files were created: your private key `/Users/username/.ssh/id_rsa`, and the public key `/Users/username/.ssh/id_rsa.pub`. The private key is read-only and only for you, it is used to decrypt all correspondence encrypted with the public key. The contents of the public key need to be copied to `~/.ssh/authorized_keys` on your aurora or halo account:
    40 
    41 {{{
    42 #!sh
    43 $your_localhost%scp ~/.ssh/id_rsa.pub username@your_remosthost:~
    44 }}}
    45 
    46 Now on '''aurora''', copy the content of id_rsa.pub:
    47 
    48 {{{
    49 #!sh
    50 $your_remosthost%cat ~/id_rsa.pub >> ~/.ssh/authorized_keys
    51 $your_remosthost%rm ~/id_rsa.pub
    52 }}}
     23(No password less ssh connection possible, sorry...)
    5324
    5425== Environment ==
    … …  
    6334module load apps/matlab-2016b
    6435
    65 export PATH="$PATH:~/bin:$ISSM_DIR/scripts"
    6636export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/intel/impi/4.1.3/intel64/lib/"
    6737}}}
    … …  
    7242
    7343aurora can be used to run the code or with MATLAB locally. You can check out ISSM and install the following packages:
    74  - autotools
    75  - PETSc (use the aurora script and ``follow`` the instructions, you will need to submit a job and compile PETSc manually, do not make test, it will not work on the cluster)
     44 - PETSc (use the aurora script and ''follow'' the instructions, you will need to submit a job and compile PETSc manually, do not make test, it will not work on the cluster)
    7645 - m1qn3
    7746
    … …  
    142111alias auroratunnel='ssh -L 1070:localhost:22 aurora'
    143112}}}
    144 That will open port number 1070 that you can then use in ISSM so that you don't need to enter your password.
    145 
     113That will open port number 1070 that you can then use in ISSM so that you don't need to enter your password. Make sure to use the same port number in md.cluster.
    146114
    147115Or, if you are launching from MATLAB on aurora/halo:
    … …  
    150118md.cluster=localaurora();
    151119}}}
    152 
    153 
    154 To submit a job on aurora, do:
    155 
    156  {{{
    157 #!m
    158 qsub job.queue
    159 }}}
    160 
    161 Now if you want to check the status of your job and the queue you are using, type in the bash with the aurora/halo session:
    162 
    163  {{{
    164 #!sh
    165 qstat -u USERNAME
    166 }}}
    167 
    168 You can delete your job manually by typing:
    169 
    170 {{{
    171 #!sh
    172 qdel JOBID
    173 }}}
    174 
    175 where JOBID is the ID of your job (indicated in the Matlab session). Matlab indicates too the directory of your job where you can find the files `JOBNAME.outlog` and `JOBNAME.errlog`. The outlog file contains the informations that would appear if you were running your job on your local machine and the errlog file contains the error information in case the job encounters an error.