Using the geo-hpcc cluster

User accounts

Accounts have been created for you on geo-hpcc and sculpin, the gateway machine you need to connect through if you are trying to access the cluster from outside the Institute of Seismology. Some basic information about the machines, including how to change your password, can be found below.

sculpin

• Host: sculpin.seismo.helsinki.fi

• To change your password you can log in to sculpin and type passwd.

geo-hpcc

• Host: geo-hpfe.seismo.helsinki.fi (geo-hpfe is a frontend virtual machine)

• To change your password you can log in to geo-hpfe and type passwd.

Connecting from Windows

Command line access

1. Open PuTTY

2. Host name: sculpin.seismo.helsinki.fi

3. Click Open

4. Type in your username and password

5. Type the command ssh USERNAME@geo-hpfe.seismo.helsinki.fi, where USERNAME is your username

File transfers/access

1. Open WinSCP

2. Click New Site, fill in Host name: geo-hpfe.seismo.helsinki.fi, User name and Password.

3. Click Advanced…

4. Choose Connection, Tunnel, and check Connect through SSH tunnel

5. Fill in values: Host name: sculpin.seismo.helsinki.fi, User name and Password

6. Click OK

7. Click Save

8. Click Login

The WinSCP session will be saved, so that next time you can just double-click the hostname on the left, and the connection will be opened.

Connecting from Mac/Linux

Command line access

1. ssh USERNAME@sculpin.seismo.helsinki.fi

2. ssh USERNAME@geo-hpfe.seismo.helsinki.fi

Note, USERNAME should be replaced with your username.

File transfers/access

There are three options for copying the model files:

1. To copy the .pvtu and .vut files one by one you can use the following two commands:

   • scp -O -oProxyCommand="ssh -W %h:%p USERNAME@sculpin.seismo.helsinki.fi" USERNAME@geo-hpfe.seismo.helsinki.fi:/data/home/USERNAME/output-continental_extension/solution/\*.pvtu .

   • scp -O -oProxyCommand="ssh -W %h:%p USERNAME@sculpin.seismo.helsinki.fi" USERNAME@geo-hpfe.seismo.helsinki.fi:/data/home/USERNAME/output-continental_extension/solution/\*.vtu .

2. Alternatively, you can copy the whole solution directory by typing

   • scp -r -O -oProxyCommand="ssh -W %h:%p USERNAME@sculpin.seismo.helsinki.fi" USERNAME@geo-hpfe.seismo.helsinki.fi:/data/home/USERNAME/output-continental_extension/solution/ .

3. If you have created a tar file (e.g., modelname.tar.gz) you can use the following:

   • scp -O -oProxyCommand="ssh -W %h:%p USERNAME@sculpin.seismo.helsinki.fi" USERNAME@geo-hpfe.seismo.helsinki.fi:/data/home/USERNAME/output-continental_extension/solution/modelname.tar.gz .

Navigating the filesystem

• less FILENAME: Show the contents of a text file

  • Scroll up and down in file with arrow keys or page-up, page-down

  • Exit by pressing q

• ls DIRECTORY: List the contents of a directory

• cd DIRECTORY: Change into directory DIRECTORY

  • Note: Typing cd with no directory name given will change to your home directory

• cp FILENAME DESTINATION: Copy a file from FILENAME to DESTINATION

  • Note: To copy a directory you must include the -r flag. For example, cp -r DIRECTORY DESTINATION

Running ASPECT models

1. Load ASPECT and its dependencies using spack

   spack load aspect

2. Copy the cookbooks (=input files) to your home directory

   cp -r /globalscratch/public/aspect/cookbooks/ ~/

3. Copy the ASPECT run scheduler file to your home directory

   cp /globalscratch/public/aspect.batch ~/

4. Now you should be cleared to submit the first ASPECT model by executing

   sbatch aspect.batch

5. Monitor the job status: squeue

   • Note that the directory name of the output is formed from the model name (output-continental_extension/solution)

6. Copy VTU files to your local machine (see instructions above) to be opened in ParaView

   • You can cancel your job with scancel jobid where jobid is the numerical ID of the job, and can be found using squeue

7. To modify your model, open the input file

   vim ~/cookbooks/continental_extension/continental_extension.prm

   …to change the parameters you want.

Monitoring job status/cancelling a job

• squeue: Show a list of models running on the geo-hpcc cluster

• scancel JOB_ID: Cancel a job running on the cluster