Computing Environment

Table of Contents

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Connecting to SSRL computers using NoMachine (NX)

As most experiments are conducted remotely, the way to access the beamline control software, blu-ice, is by establishing a remote desktop session to SSRL. For this purpose, we run two servers with the NoMachine Terminal Server software.

  • smbnxs1.slac.stanford.edu
  • smbnxs2.slac.stanford.edu

Detailed information on how to setup and configure the client software on your computer is available here; Remote Unix Desktop

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Computers at the beam lines

The naming convention of computers described below are for BL9-2. The pattern is the same for all crystallography beam lines. Replace '92' with '71', '121', '122' and '141' for beam lines 7-1, 12-1, 12-2 and 14-1 respectively. All computers are on the domain slac.stanford.edu i.e. the full name of the hosts below are node.slac.stanford.edu.

Data collection:

  • bl92[a]: data collection, backup and graphics (Linux Workstation)
  • bl92[b]: data collection, backup and graphics (Windows Workstation, Access to our servers via NXClient)
  • bl92hutch: A terminal located inside the hutch for running the beamline control software.

Data processing:

  • pxproc[01-12]: 2xIntel Xeon Gold 6140 with 36 cores/72 threads total, 188GiB of memory, Debian 10 (buster).
  • pxproc[13-24]: 2xIntel Xeon E5-2670 v3 with 24 cores/48 threads total, 125 GiB of memory, Debian 10 (buster).

File transfer:

  • smbcopy: dedicated host for file transfers. Use this host to avoid having file transfers interfere with data processing.

Remote access servers:

  • smbnxs[1,2]: These are the gateway machines for remote access using the NX client software. Please don't run data processing or data transfer directly on these nodes. Use the ones mentioned above.

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Accounts

A personal Unix account is required to log in to the beamline computers, data processing computers and web applications. Follow the instructions to request and maintain a computer account. Contact PX_Accounts@SLAC.STANFORD.EDU for additional questions about accounts.

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Disk management and directories

/home file system

Home directories are mounted as /home/accountname.

This is a small, relatively fast file system. It does not have the capacity to store diffraction images or the endless amount of output from automatic build processes.

Note that diffraction images must not be stored in the /home disk. They may be deleted without notice!

/data file system

Diffraction images and data processing should be stored in the directory /data/accountname.

This is a large, relatively slow file system. It is not backed up. We make every effort to keep data as longs as possible, but if the file system is filling up, we will start to purge older data.

Your are responsible for backing up your data. We do not keep any backups.

At login the following directories are created unless they already exist:

/home/accountname/www
/data/accountname
/data/accountname/templates

The 'www' subdirectory can be used to make information available through HTTP (web browser). It can be accessed via the URL:

http://smb.slac.stanford.edu/~accountname/

Copies of the default data processing template files are stored in the 'templates' subdirectory.

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File Permissions

The default file permissions restricts anyone but the owner to access directories and files.
Files located in your 'www' directory are readable by everyone.

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Command Line Login

SSH connections from offsite are allowed only to the smbcopy.slac.stanford.edu computer.

There are no restrictions on outgoing connections.

See the Remote File Transfer section in the backup documentation for further information.

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Connecting a laptop to the local network

The SLAC visitor network is available at all SSRL macromolecular crystallography beamlines. The SLAC visitor network is a SLAC owned network which is outside the SLAC network firewall. Access to SSRL computers through the SLAC visitor network are treated as external connections.

Access to the SLAC visitor network at the beamlines is available via a wireless LAN and a standard wired network. Red network cables at the beamlines indicate that they are configured for the visitor network. Both wireless and cable connections require configuring the network interface on laptop computers to use DHCP (Dynamic Host Configuration Protocol) to obtain a valid network address. DHCP is the only way that laptops and computers can connect to the visitor network. Users are responsible for all network configuration and other equipment required for access (i.e. network card or wireless network card). SLAC's website provides information about how to configure your laptop for DHCP and wireless networking and the wireless PC card.

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