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Summary of the available computing clusters and servers

The Department of Chemistry and Materials Science has the following computing resources for computational chemistry research and teaching:

  • wihuri.pub.chemistrylab.aalto.fi (96 CPU cores)
  • puhuri.pub.chemistrylab.aalto.fi (288 CPU cores)
  • suhari.pub.chemistrylab.aalto.fi (48 CPU cores)
  • mylly1.pub.chemistrylab.aalto.fi (128 CPU cores)
  • mylly2.pub.chemistrylab.aalto.fi (128 CPU cores)

The detailed configurations are as follows:

ServerYearNodes

CPU Cores/ node

CPU type

Memory/ node (GB)

Memory/ CPU core (GB)

Disk/ node (TB)

Other comments
Wihuri (stage1)2014412Xeon E5-2630 v2 (2.6 GHz)645.332Rocks Clusters 6.1 (Gigabit interconnect between nodes)
Wihuri (stage2)2015412Xeon E5-2620 v3 (2.4 GHz)645.332
Puhuri (stage1)2016436Xeon E5-2697 v4 (2.3 GHz)1283.562Rocks Clusters 7.1 (Gigabit interconnect between nodes)
Puhuri (stage2)2017436Xeon Gold 6140 (2.3 GHz)1925.332
Suhari2018148AMD EPYC 7451 (2.3/2.9 GHz)2565.334CentOS 7.9
Mylly120201128AMD EPYC 7702 (2.0/2.6 GHz)25623CentOS Stream 8.
GPU: PNY GeForce GTX 1080 Ti 11GB (Pascal)
Mylly220201128AMD EPYC 7702 (2.0/2.6 GHz)25623CentOS Stream 8.
GPU: PNY GeForce GTX 1080 Ti 11GB (Pascal)

General guidelines

  • Wihuri and Puhuri are computing clusters that consist of a frontend server and computing nodes. Users' home directories (/home/<userid>) are visible both on the frontend and on the computing nodes.
  • All jobs must be run on the computing nodes, using queuing system! Running them directly on the frontend is strictly forbidden. 
  • Only short pre- and post-processing tasks related to the jobs can be performed on the frontend (a rule of thumb for such tasks: max. 1 minute, 1 CPU, 1 GB memory). Interactive sessions should be used for tasks that consume more resources.
  • The home directories should not be considered as a very reliable location for long-term data storage (the home directories are backuped daily to a USB disk). Copy all important files regularly to your own workstation and keep personal backups.
  • Temporary directory on the frontend and all nodes is /chemtemp

Connecting to the computing servers

  • You can connect the servers using SSH
  • Each server can only be connected from Aalto network or by using Aalto VPN (first start VPN, then connect with SSH)

Connecting from a Windows computer

  • To use a computing server, you need an SSH client. For Windows, PuTTY is an excellent (and free) SSH client. Just download putty.exe to any folder and execute it. No installation is necessary. 
  • To transfer files between a cluster and your workstation, you can use SFTP. WinSCP is a reasonably good SFTP client.

Connecting from a Mac computer 

  • With Mac, you can either use the native terminal program or for example iTerm SSH client. 
  • To transfer files between a cluster and your workstation, you can use different options: 
    (1) using any SFTP client. For example, FileZilla
    (2) using the command line in iTerm. For example, to copy the file from puhuri to your computer: scp username@puhuri.pub.chemistrylab.aalto.fi:/home/path_to_the file/filename ./ 
    (3) using rsync utility

Working on the computing servers

  • You will need a basic knowledge of Linux to use the servers (good tutorials are available)
  • Any text files on the server can be edited over the SSH terminal connection by using a text editor. nano is an easy-to-use editor with a menu system. vi is a very convenient and fast editor with a bit steeper learning curve (a short vi reference might help). 
  • To edit a file, just execute nano myfile.txt or vi myfile.txt.

Computational chemistry software

All computing servers are equipped with the JCHEM sofware package, which includes a number of programs for computational chemistry research and teaching. The JCHEM package greatly simplifies the day-to-day life of the users by providing unified interfaces for the management and usage of the various program packages. Guidelines for using the software have been divided into the following sub-topics:

Note that the JCHEM software package is also installed on CSC Puhti supercluster. See the instructions to setup JCHEM at CSC.

SSH logins to compute nodes (Wihuri and Puhuri only)

Normally it is not necessary to login directly to the compute nodes. However, if a calculation crashes and leaves some important files to the temporary directory of the node (/chemtemp), it might be necessary to operate on the compute node via SSH. The file <job name.>batch-log in the job directory contains all the information on the job, including the full path of the temporary directory on the compute node.

Connecting works with the normal SSH approach (ssh <node>). For example, ssh compute-0-4. After moving to the temporary directory (cd /chemtemp/TM_4578) The important files in the directory can be copied normally to your cluster home directory, which is also available on the compute nodes (cp mydata.dat /home/antti/). Then you can exit the compute node and the files will available on the frontend.

Please note that it is forbidden to login directly to a compute node to perform any actual computational work. Use Interactive sessions for this, instead.

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