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wiki:uso_sist_en [2022/07/01 12:35]
cnr-guest [Access procedure] 		wiki:uso_sist_en [2022/10/07 19:14] (current)
cnr-guest [Available file systems]
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 To access Ibisco from Windows systems a simple software is PuTTY, freely available at ''https://www.putty.org/''. From Windows 10 onwards it is also possible to use Openssh in a command window (CMD.exe o Powershell.exe). It is pre-installed (if it is not activated, it simply has to be activated in the Optional Features). To access Ibisco from Windows systems a simple software is PuTTY, freely available at ''https://www.putty.org/''. From Windows 10 onwards it is also possible to use Openssh in a command window (CMD.exe o Powershell.exe). It is pre-installed (if it is not activated, it simply has to be activated in the Optional Features).
  
-In a few months the access to the cluster will be exclusively via the "user-SSH Key" method.\\+In a few months the access to the cluster will be exclusively via the "user-SSH Key" method (other secure access methods are being studied).\\
 The current users are invited to generate their key pairs and upload the public key on the server in their home.\\ The current users are invited to generate their key pairs and upload the public key on the server in their home.\\
 The new users, when asking for an account, will follow a lightly different procedure: they will generate the keys pair but will not upload the public key to the server (they will not have yet access): they will send it to the Ibisco admin. The admin will copy it, with the right permissions, in the home of the new user. After that the user will have the ability to enter the system without digiting a server password (but still he/she will have to digit a passphrase, see ahead). \\ The new users, when asking for an account, will follow a lightly different procedure: they will generate the keys pair but will not upload the public key to the server (they will not have yet access): they will send it to the Ibisco admin. The admin will copy it, with the right permissions, in the home of the new user. After that the user will have the ability to enter the system without digiting a server password (but still he/she will have to digit a passphrase, see ahead). \\
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 ''$ ssh-keygen -t rsa''\\ ''$ ssh-keygen -t rsa''\\
 Press enter to first question (filename)\\ Press enter to first question (filename)\\
-In response to the prompt "Enter passphrase," enter a key passphrase to protect access to the private key. Using a passphrase enhances security, and a passphrase is recommended. +In response to the prompt "Enter passphrase", enter a key passphrase to protect access to the private key. Using a passphrase enhances security, and a passphrase is recommended.\\ 
-The key pair is generated. +The key pair is generated by the system. 
-   - If you still have access with password to the system (old users), you can execute the following command that copy yor public key to the server and append it to the file ./ssh/authorized_keys with the right permissions:+   * If you still have access with password to the system (old users), you can execute the following command that copy your public key to the server and append it to the file ./ssh/authorized_keys with the right permissions:
    ''$ ssh-copy-id -i ~/.ssh/id_rsa.pub <username>@ibiscohpc-wiki.scope.unina.it''    ''$ ssh-copy-id -i ~/.ssh/id_rsa.pub <username>@ibiscohpc-wiki.scope.unina.it''
-   - If you are a new user, simply send by mail the file ~/.ssh/id_rsa.pub to the Ibisco admins: they will provide for copying it in your .ssh directory on the cluster with the right permissions.+   * If you are a new user, simply send by mail the file ~/.ssh/id_rsa.pub to the Ibisco admins: they will provide for copying it in your .ssh directory on the cluster with the right permissions.
        
 **on a Windows system**\\ **on a Windows system**\\
  
-We suggest PuTTY, a package for Windows that simplifies the use of Windows as SSH client and the management of the connection to remote hosts\\+We suggest PuTTY, a package for Windows that simplifies the use of Windows as SSH client and the management of the connections to remote hosts\\
 To create the key pair (https://the.earth.li/~sgtatham/putty/0.77/htmldoc/) you can follow the following procedure. To create the key pair (https://the.earth.li/~sgtatham/putty/0.77/htmldoc/) you can follow the following procedure.
  
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    - when prompted for a passphrase, insert a good one and save it in a safe place    - when prompted for a passphrase, insert a good one and save it in a safe place
    - Save in some safe directory or external usb device the private key (remember the path, needed to run a session with PuTTY)    - Save in some safe directory or external usb device the private key (remember the path, needed to run a session with PuTTY)
-   - copy all the content of the box under "Public key for pasting ..." (copy-paste) in a file id_rsa.pub. It will have the right format to be accepted by the OpenSSH (the SSH package availlable on linux and therefore also on IBiSco)+   - copy all the content of the box under "Public key for pasting ..." (copy-paste) in a file id_rsa.pub. It will have the right format to be accepted by the OpenSSH (the SSH package available on linux and therefore also on IBiSco)
    - send by mail the public key to the admins: as written before, they will provide for copying it in your .ssh directory on the cluster with the right permissions.    - send by mail the public key to the admins: as written before, they will provide for copying it in your .ssh directory on the cluster with the right permissions.
  
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 In-depth documentation on Lustre is available online, at the link: '' https://www.lustre.org/ ''  In-depth documentation on Lustre is available online, at the link: '' https://www.lustre.org/ '' 
 +
 +''/ibiscostorage''
 +new scratch area shared among UI and computation nodes (available from 07/10/2022), **not** LUSTRE based
  
  
 ==== Job preparation ans submission ==== ==== Job preparation ans submission ====
 +
 +=== Premise: new job management rules active from 9/10/2022 ===
 +
 +To improve the use of resources, the job management rules have been changed.
 +
 + * New usage policies based on // fairshare // mechanisms have been implemented \\
 + * New queues for job submissions have been defined
 +    - ** sequential ** queue:
 +      * accepts only sequential jobs with a number of tasks not exceeding 1,
 +      * who do not use GP-GPUs,
 +      * for a total number of jobs running on it not exceeding 128
 +      * and maximum execution time limit of 1 week
 +    - ** parallel ** queue:
 +      * accepts only parallel jobs with task number greater than 1 and less than 1580,
 +      * that use no more 64 GP-GPUs
 +      * and maximum execution time limit of 1 week
 +     - ** gpus ** queue:
 +      * only accepts jobs that use no more than 64 GP-GPUs,
 +      * with task number less than 1580
 +      * and maximum execution time limit of 1 week
 +     - ** hparallel ** queue:
 +      * accepts only parallel jobs with task number greater than 1580 and less than 3160,
 +      * that make use of at least 64 GP-GPUs
 +      * and maximum execution time limit of 1 day
 +
 +From 9 October the current queue will be disabled and only those defined here will be active, to be explicitly selected. For example, to subdue a job in the ** parallel ** queue, execute \\
 +
 +  $ srun -p parallel <MORE OPTIONS> <COMMAND NAME>
 +
 +If the job does not comply with the rules of the queue used, it will be terminated.
 +
 +=== Use of resources ===
  
 In the system is installed the resource manager SLURM to manage the cluster resources. In the system is installed the resource manager SLURM to manage the cluster resources.
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 Example, submit an MPI interactive job with <N> tasks, from UI: Example, submit an MPI interactive job with <N> tasks, from UI:
     $ srun -n <N> <EXEFILE>     $ srun -n <N> <EXEFILE>
 +    
 +**Important command when using OpenMP**
 +
 +Add the following command in the script used to submit an OpenMP job:   
 +
 +    $ export OMP_NUM_THREADS = <nthreads>
 +
 +  * It specifies the number of threads to be used when running a code which uses OpenMP to execute parallel programming. The maximum value should be the number of processors available. For more information about OpenMP, please check [[https://www.openmp.org/spec-html/5.0/openmpse50.html|openMP]].
 +    
          
 ==== Tips for using the Intel OneAPI suite (suite compilers, libraries, etc provided by Intel) ==== ==== Tips for using the Intel OneAPI suite (suite compilers, libraries, etc provided by Intel) ====
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 <code>source /nfsexports/SOFTWARE/anaconda3.OK/setupconda.sh <code>source /nfsexports/SOFTWARE/anaconda3.OK/setupconda.sh
 conda activate bioconda conda activate bioconda
 +<commands execution> [Example: python example.py]
 +conda deactivate
 +conda deactivate</code>
 +
 +=== Pytorch ===
 +
 +To use Pytorch sub-environment, the following commands have to be executed.
 +
 +<code>source /nfsexports/SOFTWARE/anaconda3.OK/setupconda.sh
 +conda activate pytorchenv
 <commands execution> [Example: python example.py] <commands execution> [Example: python example.py]
 conda deactivate conda deactivate
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    * To use matlab command window, please use '' ssh ibiscohpc-ui.scope.unina.it -l [username] -Y '' when logging into the IBISCO cluster.    * To use matlab command window, please use '' ssh ibiscohpc-ui.scope.unina.it -l [username] -Y '' when logging into the IBISCO cluster.
    * Setup the matlab environment by using the command '' /nfsexports/SOFTWARE/MATLAB/R2020b/bin/matlab ''. This opens the mathworks command window where you will be able to add the settings file (see ahead).\\    * Setup the matlab environment by using the command '' /nfsexports/SOFTWARE/MATLAB/R2020b/bin/matlab ''. This opens the mathworks command window where you will be able to add the settings file (see ahead).\\
 +   * Matlab version R2022a can be accessed using the command '' /nfsexports/SOFTWARE/MATLAB/R2022a/bin/matlab ''. 
  
 == Configuration and execution == == Configuration and execution ==
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    - the ***Create and Manage Clusters*** window    - the ***Create and Manage Clusters*** window
    - the Matlab Profile commands such as saveProfile  (https://it.mathworks.com/help/parallel-computing/saveprofile.html)    - the Matlab Profile commands such as saveProfile  (https://it.mathworks.com/help/parallel-computing/saveprofile.html)
 +
 +=== Example of running a parallel matlab script ===
 +
 +This is an example of using **parfor** to parallelize the for loop (demonstrated at {{https://it.mathworks.com/help/parallel-computing/decide-when-to-use-parfor.html?s_eid=PSM_15028 | MathWorks}}).
 +This example calculates the spectral radius of a matrix and converts a for-loop into a parfor-loop. Open a file named as **test.m** with the following code
 +
 +<code>mypool=parpool('SlurmIBISCOHPC', 5) % 5 is the number of workers
 +n = 100;
 +A = 200;
 +a = zeros(n);
 +parfor i = 1:n
 +    a(i) = max(abs(eig(rand(A))));
 +end
 +delete(mypool); 
 +quit
 +</code>
 +
 +To run this code, the following command executed on the UI can be used:
 +<code>
 +/nfsexports/SOFTWARE/MATLAB/R2020b/bin/matlab -nodisplay -nosplash -nodesktop -r test
 +</code>
 +
 +
 +
 +
 +
  
  
wiki/uso_sist_en.1656678938.txt.gz · Last modified: 2022/07/01 12:35 by cnr-guest

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