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calcoloscientifico:guidautente_slurm_en [24/04/2018 12:44] – [Serial jobs, compiler GNU] paolo.oggianocalcoloscientifico:guidautente_slurm_en [27/04/2018 10:01] (versione attuale) – [Batch job ===== ====SLURM FATTO] roberto.alfieri
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 ===== Access / Login ===== ===== Access / Login =====
  
-In order to access the resources, you must be included in the database LDAP of HPC service.+In order to access the resources, you must be included in the LDAP database  of the HPC management server.
 Requests for access or general assistance must be sent to: es_calcolo@unipr.it. Requests for access or general assistance must be sent to: es_calcolo@unipr.it.
  
-Once enabled, the login is done throughput SSH on host login:+Once enabled, the login is done through SSH on the login host:
  
   ssh <name.surname>@login.hpc.unipr.it    ssh <name.surname>@login.hpc.unipr.it 
  
-Password access is allowed only within the University network (160.78.0.0/16). Outside this context it is necessary to use the [[http://noc.unipr.it/public/vpn/home|VPN]] of University or access with a public key.  +Password access is allowed only within the University network (160.78.0.0/16). Outside this context it is necessary to use the University [[http://noc.unipr.it/public/vpn/home|VPN]]  or access with public key authentication.  
  
 ==== Access password-less between nodes ==== ==== Access password-less between nodes ====
  
-** To use the cluster it is necessary to eliminate the need to use the password between the nodes**, using public key authentication. It is necessary to generate on login.hpc.unipr.it the pair of keys, without passphrase,  and add the public key in the authorization file (authorized_keys):+** In order to use the cluster it is necessary to eliminate the need to use the password between nodes**, using public key authentication. It is necessary to generate on login.hpc.unipr.it the pair of keys, without passphrase,  and add the public key in the authorization file (authorized_keys):
  
-Key generation. Accept the defaults by pressing enter. +Key generation. Accept the defaults by pressing enter:
   ssh-keygen -t rsa   ssh-keygen -t rsa
  
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   cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys   cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
  
-==== Access from the outside with a public key ====+==== External Access  with  public key Authentication ====
  
-The key pair must be generated with the client SSH. The private key should be protected by an appropriate passphrase (it is not obligatory but recommended). The public key must +The key pair must be generated with the SSH client. The private key should be protected by an appropriate passphrase (it is not mandarory but recommended). 
-be inserted in your authorized keys (.ssh/authorized_keys) on the login host.+ The public key must be included in your authorized_keys file on the login host.
  
-If you use the SSH client for Windows **PuTTY** (http://www.putty.org), you need to generate the public and private key pair with PuTTYgen and save them to a file. +If you use the SSH client for Windows **PuTTY** (http://www.putty.org), you need to generate the public and private key pair with PuTTYgen and save them into a file. 
-The private key must be entered in the Putty configuration (or WinSCP): +The private key must be included in the Putty  (or WinSCP) configuration panel: 
   Configuration -> Connection -> SSH -> Auth -> Private key file for authentication   Configuration -> Connection -> SSH -> Auth -> Private key file for authentication
-The public key must be inserted in the file .ssh/authorized_keys of login.hpc.unipr.it+The public key must be included in the  .ssh/authorized_keys file on login.hpc.unipr.it
  
 Useful links for SSH clients configuration: [[ https://kb.iu.edu/d/aews | Linux, MacOS X, PuTTY ]],  Useful links for SSH clients configuration: [[ https://kb.iu.edu/d/aews | Linux, MacOS X, PuTTY ]], 
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 SSH is the only protocol for external communication and can also be used for file transfer.  SSH is the only protocol for external communication and can also be used for file transfer. 
  
-In a Unix-like environment (Linux, MacOS X) you can use the commands scp or sftp.+If you use  a Unix-like client (Linux, MacOS X) you can use the command scp or sftp.
  
-In Windows, the most used program is WinSCP (https://winscp.net/eng/docs/introduction). During the installation of WinSCP it is possible to import Putty profiles.+On Windows systems, the most used tool is WinSCP (https://winscp.net/eng/docs/introduction). During the installation of WinSCP it is possible to import Putty profiles.
  
-SSH can also be used to mount a remote file-system using SshFS (see http://www.fis.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:guidautente#sshfs)+SSH can also be used to mount a remote file-system using SshFS (see http://www.fis.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:guidautente_slurm_en#sshfs)
  
 ===== Hardware ===== ===== Hardware =====
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 Nodes details: Nodes details:
  
-[[ http://www.fis.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:nodicalcolo | Elenco ita  ]]+[[ calcoloscientifico:nodicalcolo | Node list  ]]
 - -
-[[  http://cm01.hpc.unipr.it/ganglia/ |  Utilizzo ita  ]]  (intranet)+[[  http://cm01.hpc.unipr.it/ganglia/ |  Usage  ]]  (intranet only)
  
 Peak performance (double precision): Peak performance (double precision):
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 Environment Software (libraries, compilers e tools):  Environment Software (libraries, compilers e tools): 
-[[ http://www.hpc.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:softwareapplicativo | List (ita) ]]+[[ http://www.hpc.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:softwareapplicativo | List ]]
  
 Some software components must be loaded in order to be used. Some software components must be loaded in order to be used.
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 </note> </note>
  
-[[ http://www.fis.unipr.it/dokuwiki/doku.php?id=calcoloscientifico:priv:cluster:storage | Private Area ]]+[[ calcoloscientifico:priv:cluster:storage | Private Area ]]
  
  
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 Specifies the account to be charged for using resources. (Mandatory ??)  Specifies the account to be charged for using resources. (Mandatory ??) 
  
-Default group equal to account ??? 
  
 See [[ calcoloscientifico:guidautente_slurm_en#teamwork | Teamwork paragraph ]] See [[ calcoloscientifico:guidautente_slurm_en#teamwork | Teamwork paragraph ]]
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-===== Batch job ===== ====SLURM FATTO =====+===== Batch job ===== 
  
 A shell script must be created that includes the SLURM options and the commands that must be executed on the nodes. A shell script must be created that includes the SLURM options and the commands that must be executed on the nodes.
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 #SBATCH -p bdw -N1 -n32 #SBATCH -p bdw -N1 -n32
  
-#< Its declares that the job will last at most 30 minutes (days-hours:minutes:s$+#< Its declares that the job will last at most 30 minutes (days-hours:minutes:seconds)
 #SBATCH --time 0-00:30:00 #SBATCH --time 0-00:30:00
  
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 cat  $SLURM_JOB_NODELIST cat  $SLURM_JOB_NODELIST
  
-# Enter the directory that contains the script+#< Enter the directory that contains the script
 cd "$SLURM_SUBMIT_DIR" cd "$SLURM_SUBMIT_DIR"
  
-# Executes the program+#< Executes the program
 ./mm ./mm
  
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   scancel <Job id>   scancel <Job id>
  
-==== Serial jobs, compiler Intel ==== ==== FATTO SLURM ====+==== Serial jobs, compiler Intel ====
  
 Compiling the cpi_mc.c example for the calculation of Pi: Compiling the cpi_mc.c example for the calculation of Pi:
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 #!/bin/bash #!/bin/bash
  
-# Print the node name assigned+#< Print the node name assigned
 cat $SLURM_JOB_NODELIST cat $SLURM_JOB_NODELIST
  
-# Load the compiler module Intel+#< Charge resources to own account 
 +#SBATCH $SBATCH_ACCOUNT 
 + 
 +#< Load the compiler module Intel
 module load intel module load intel
  
-# Enter the directory that contains the script+#< Enter the directory that contains the script
 cd "$SLURM_SUBMIT_DIR" cd "$SLURM_SUBMIT_DIR"
  
-# Executes the program+#< Executes the program
  
 N=10000000 N=10000000
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 Submission: Submission:
  
-  sbatch -A <name account> cpi_mc.bash+  sbatch cpi_mc.bash
  
-==== Serial job, compiler PGI ==== ==== SLURM FATTO ====+==== Serial job, compiler PGI ==== 
  
 Compiling the cpi_sqrt.c example for the computing of Pi: Compiling the cpi_sqrt.c example for the computing of Pi:
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 #!/bin/bash #!/bin/bash
  
-# Options SLURM default. They can be omitted +#< Options SLURM default. They can be omitted 
-#SBATCH -p bdw_debug -N1 -n32+#SBATCH -p bdw -N1 -n32
 #SBATCH --time 0-00:30:00 #SBATCH --time 0-00:30:00
  
-# Print name node assigned+#< Charge resources to own account 
 +#SBATCH $SBATCH_ACCOUNT 
 + 
 +#< Print name node assigned
 cat $SLURM_JOB_NODELIST cat $SLURM_JOB_NODELIST
  
 module load pgi module load pgi
-# Enter the directory that contains the script+#< Enter the directory that contains the script
 cd "$SLURM_SUBMIT_DIR" cd "$SLURM_SUBMIT_DIR"
  
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 </code> </code>
  
-  sbatch -A <name account> cpi_sqrt_pgi.bash+  sbatch cpi_sqrt_pgi.bash
  
-==== Job OpenMP with GNU 4.8 ==== ==== SLURM FATTO ====+==== Job OpenMP with GNU 4.8 ====
  
   cp /hpc/share/samples/omp/omp_hello.c .   cp /hpc/share/samples/omp/omp_hello.c .
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 #!/bin/bash #!/bin/bash
  
-#SBATCH -p bdw_debug -N1 -n32+#SBATCH -p bdw -N1 -n32
 #SBATCH --exclusive #SBATCH --exclusive
 #SBATCH -t 0-00:30:00 #SBATCH -t 0-00:30:00
 +#SBATCH $SBATCH_ACCOUNT
  
-#Merge strerr with stdout+#< Merge strerr with stdout
 #SBATCH -oe #SBATCH -oe
  
calcoloscientifico/guidautente_slurm_en.1524566651.txt.gz · Ultima modifica: 24/04/2018 12:44 da paolo.oggiano
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