Configuration file¶

nextPYP uses a single configuration file to provide all environmental information needed to run.

The file is written in TOML.

Placement¶

Complete Example¶

Here’s an example of a minimal configuration to run nextPYP on the command line:

[pyp]
container = '/storage/singularity-images/pyp.sif'
scratch = '/tmp/pyp-scratch/'
binds = ['/data']

[slurm]
user = 'pyp'
host = 'slurm-login-01.example.org'

Settings¶

PYP Section¶

[pyp]¶

Required:

yes

Occurs:

once

This section is for basic PYP configuration. PYP executes inside of a Singularity container, so much of this configuration is dedicated to configuring the container environment.

container¶

Type:

string

Required:

no in web mode, yes in CLI mode

Description:

Path to the PYP Singularity container on the SLURM cluster, ideally in a read-only location.

For web-enabled installations of nextPYP, this configuration option is not required. If this option is not explicitly specified, nextPYP will look for the pyp container at <web.sharedExecDir>/containers/pyp.sif, where <web.sharedExecDir> is the sharedExecDir configuration option in the [web] section, described below.

Examples:

container = '/storage/singularity-images/pyp.sif'

sources¶

Type:

string

Required:

no

Default:

none

Description:

Path to a local installation of PYP sources that will be bound over the PYP sources inside the Singularity container.

This is mostly only useful for developers of PYP looking for an easy way to edit and run PYP code. Most users will not need this option.

Examples:

sources = '/home/myuser/code/pyp'

scratch¶

Type:

string

Required:

yes

Description:

Directory for large (multi-GiB) temporary files on the compute nodes. This location should have fast read/write speeds, ideally in local storage.

Examples:

scratch = '/tmp/pyp-scratch'

binds¶

Type:

array of strings

Required:

no

Default:

empty list

Description:

List of filesystem paths to bind into the Singularity container.

Since the PYP runs inside of a Singularity container, by default, no files from outside of the container will be visibile to PYP. To make files visible to PYP, bind the directories containing those files into the container.

The following directories are not allowed to be bound because they will interfere with the PYP code inside the container:

• /

• /bin/**

• /dev/**

• /environment/**

• /etc/**

• /lib/**

• /lib64/**

• /opt/**

• /proc/**

• /root/**

• /run/**

• /sbin/**

• /scif/**

• /singularity/**

• /apptainer/**

• /srv/**

• /sys/**

• /usr/**

• /var/**

The ** means any subdirectory under the listed directory is also not allowed to be bound.

Examples:

binds = ['/data']

binds = ['/storage1/cryoem-data', '/storage2/cryoem-data']

containerExec¶

Type:

string or table

Required:

no

Default:

singularity

Description:

The name or path of the container executable. To load a module, use a table with the key module instead. In module mode, the executable name will be the same as the module name by default. Override the default behavior by adding an exec key to the table with the name or path of the executable.

Examples:

containerExec = '/bin/singularity

containerExec = 'apptainer'

containerExec = { module = 'singularity' }

containerExec = { module = 'singularity', exec = 'apptainer' }

cudaLibs¶

Type:

array of strings

Required:

no

Default:

empty array

Description:

Path to a folder containing CUDA runtime libraries. When pyp is launched, these folder paths will be added to LD_LIBRARY_PATH.

Examples:

cudaLibs = ['/usr/bin/cuda']

SLURM Section¶

[slurm]¶

Required:

no

Occurs:

once

This section is used to configure properties of the SLURM cluster.

user¶

Type:

string

Required:

no

Default:

The username of the website process

Description:

The user name PYP will use to SSH into the SLURM login node.

Examples:

user = 'pyp'

host¶

Type:

string

Required:

no

Description:

Hostname of a login node for the SLURM cluster.

If no hostname is given, nextPYP will instead submit jobs by calling SLURM commands locally on the web server machine. This option requires that SLURM be installed and configured on the web server machine.

If SLURM commands are not directly available on the web server machine, then you’ll need to provide a hostname for the SLURM login node.

Examples:

host = 'slurm-login-01.example.org'

key¶

Type:

string

Required:

no

Default:

~/.ssh/id_rsa

Description:

Path to SSH private key to log into the SLURM login node.

Examples:

key = '/path/to/ssh/mykey'

port¶

Type:

int

Required:

no

Default:

22

Description:

Network port to use to connect to the SSH daemon on the SLURM login node.

Examples:

port = 2204

maxConnections¶

Type:

int

Required:

no

Default:

8

Description:

The maximum number of simuntaneous connections to use to SSH into the SLURM login node. Many SSH daemons allow up to 10 connetions by default. Using more connections that that may require special configuration of the SSH daemon.

Examples:

maxConnections = 10

timeoutSeconds¶

Type:

int

Required:

no

Default:

300

Description:

The number of seconds to wait before closing an idle SSH connection.

Examples:

timeoutSeconds = 500

path¶

Type:

string

Required:

no

Default:

/usr/bin

Description:

Path to the slurm binaries on the cluster nodes.

Examples:

path = '/opt/slurm/bin'

templatesDir¶

Type:

string

Required:

yes

Description:

Path to the folder containing SLURM template files.

See also

(TODO: add a link to the templates documentation here)

Standalone Section¶

[standalone]¶

Required:

no

Occurs:

once

This section is used to configure properties of the job launcher in non-cluster (aka standalone) mode.

availableCpus¶

Type:

int

Required:

no

Default:

One less than the number of processors in the system

Description:

The number of CPUs the standalone job launcher will use for jobs. You may want to set this to something less than the maximum your system supports, so there are always some CPU resources reserved to run the website, reverse proxy, database processes, and anything else your system needs to run.

Examples:

availableCpus = 4

availabileMemoryGiB¶

Type:

int

Required:

no

Default:

80% of the available total memory

Description:

The amount of memory, in GiB, the standalone job launcher will use for jobs. You may want to set this to something less than the maximum your system supports, so there is always some leftover memory to run the website, reverse proxy, database processes, and anything else your system needs to run.

Examples:

availabileMemoryGiB = 4

availableGpus¶

Type:

int

Required:

no

Default:

The total number of NVidia GPUs in your system

Description:

The number of NVidia GPUs the standalone job launcher will use for jobs. AMD, Intel, and other GPU types aren’t supported yet, unless they somehow are visible to and usable by the NVidia Cuda runtime.

Examples:

availableGpus = 4

Web Section¶

This section is used to configure the web interface to PYP. It is not required at all for the command line interface.

Throughout the web interface configuration, we will assume that the server running the web interface (the web server) can see the same filesystem as the SLURM nodes. Meaning, that if a file /data/project/file.dat is visible on a SLURM node, that same file will also be visible at /data/project/file.dat on the web server.

If this is not generally true, e.g. due to networked filesystems being mounted in different directories on different servers, there are two ways to fix it:

• Reconfigure the web server so the networked filesystems are mounted in the same locations as on the SLURM nodes.

• Add symbolic links to the web server filesystem so the networked filesystems appear to be mounted in the same locations as on the SLURM nodes.

[web]¶

Required:

for command line interface: no

for web interface: yes

Occurs:

once

host¶

Type:

string

Required:

no

Default:

127.0.0.1

Description:

The network interface to which the application HTTP server (not the reverse proxy HTTP server) should bind.

By default, the application HTTP server binds only to the loopback network interface, i.e. localhost, so the application HTTP server will only be reachable from the local computer.

To make the application HTTP server reachable from an external private network, set host to 0.0.0.0 to bind to all available network interfaces.

Warning

The application HTTP server is not designed to securely handle traffic from the public internet. Exposing the application HTTP server directly to the public internet increases your risk of a security compromise.

Only set host to 0.0.0.0 if the application HTTP server is isolated from the public internet by a firewall or a private network.

To make the website securely accessible from the public internet, install the reverse proxy HTTP server that is bundled with nextPYP, which is designed to operate securely in that environment.

Examples:

host = '10.0.3.4'

host = '0.0.0.0'

port¶

Type:

int

Required:

no

Default:

8080

Description:

The network port to which the application HTTP server (not the reverse proxy HTTP server) should bind.

By default, the application HTTP server binds to the port 8080, which is an unofficial secondary port for HTTP traffic. Since port 8080 is not a privileged port, the application HTTP server can run without root privileges.

Since port 8080 is a common port for locally-running HTTP applications, you may already have another service installed that uses that port. To avoid a port conflict, you can configure the application HTTP server to use a different port, but be sure to use a non-privileged port at or above 1024.

Warning

Using a privileged port (below 1024) like 80 or 443 for the application server requires root privileges, but the application HTTP server was not designed to run with root privileges. Doing so would be insecure, and any security compromise that had access to elevated permissions would be much more severe. If you wish to run the website on a canonical HTTP port like 80 or 443, you should use the reverse proxy HTTP server bundled with nextPYP, which is designed to operate securely when exposed to the public internet.

Examples:

port = 8082

localDir¶

Type:

string

Required:

yes

Description:

Directory for the database and web server assets.

This location should have fast read/write speeds, ideally in local storage on the web server.

This location does not need to be shared with the SLURM nodes.

Note

This setting is initially set by the installation script using the PYP_LOCAL environment variable.

Examples:

localDir = '/home/streamPYP/web'

sharedDir¶

Type:

string

Required:

yes

Description:

Directory for intermediate files and metadata for each user of the web interface.

Since this location holds the bulk of the intermediate Cryo-EM and Cryo-ET metadata for each user of the website, it should have a large amount of available space. This folder must also be available to both the website and the SLURM nodes at the same location in the filesystem.

This folder should also be writable by the service account running the website process.

Note

This setting is initially set by the installation script using the PYP_SHARED_DATA environment variable.

Examples:

sharedDir = '/network/streamPYP/sharedData'

sharedExecDir¶

Type:

string

Required:

yes

Description:

Directory for executables needed by both the web server and the SLURM nodes.

This location should have a enough space to host the executable files (mostly Apptainer containers, ~10s of GiB). This folder must also be available to both the website and the SLURM nodes at the same location in the filesystem.

Warning

Since this folder hosts executable files, for security reasons, it should not be writable by the service account running the website process.

Note

This setting is initially set by the installation script using the PYP_SHARED_EXEC environment variable.

Examples:

sharedExecDir = '/network/streamPYP/sharedExec'

auth¶

Type:

string

Required:

no

Default:

none

Description:

Which type of user authentication is used for the web interface:

• login: Users log into the web interface with a username and password.

  Users are then assigned fine-grained permissions to website features by privileged administrator accounts.

  This option is suitable for most users of nextPYP.

• none: No user authentication is performed by the web interface.

  All visitors to the website are associated with the administrator account and are granted full permissions to all website features.

  This option is suitable for single-user instances of nextPYP or developers.

• reverse-proxy: Users are authenticated by a reverse-proxy server (perhaps implementing SSO for an organization) before reaching nextPYP.

  nextPYP will use the X-userid HTTP header to identify users, which must be securely provided by the reverse proxy server.

  Warning

  To provide the X-userid HTTP header securely, the reverse proxy server must block any submission of this HTTP header from the HTTP client (eg, the user’s web browser).

  Users are then assigned fine-grained permissions to website features by privileged administrator accounts.

Examples:

auth = 'login'

webhost¶

Type:

string

Required:

no

Default:

http://$host:$port, where $host and $port are the values of the web.host and web.port configuration values respectively.

Description:

The URL of the webserver as visible from the pyp process.

This value should include the full URL prefix for the web server, including the protocol (HTTP or HTTPs) and the port number (if non-standard). Do not include a trailing slash.

When running in standalone mode, the pyp process will run on the same machine as the web server. In this environment, the default value will be correct, and there should be no need to choose a different value.

When the pyp process runs on an external compute node (in, say, a SLURM cluster), this value must be the URL of the website from the point of view of the compute node. The default value will not be correct in this case, so be sure to set webhost to the correct value for your environment.

If the compute node is on a private network that is shared with the web server, then the correct value of webhost will be http://$hostname:$port where $port is the web.port configuration value and $hostname is the host name of the server from the point of view of the compute node. Note this configuration uses unencrypted HTTP rather than encrypted HTTPs.

Warning

In this private network configuration, if the web server has any public network interfaces, be sure to configure the firewall to only allow connections to the port defined by web.port over the private network interface. Connections over the public network interface should be blocked by the firewall.

If the compute node is not on a shared private network with the web server, then the correct value will be https://$domain where $domain is the domain name of the web server as configured in the DNS registry. This configuration requires using the reverse proxy HTTP server bundled with nextPYP to enable encrypted HTTPs connections, since the connection may travel over an untrusted network, like the public internet.

Examples:

webhost = 'https://streampyp.example.org'

webhost = 'http://dev.streampyp.example.org:8080'

debug¶

Type:

boolean

Required:

no

Default:

false

Description:

If true, enables extra features for PYP developers.

Most users will not need this option.

heapMiB¶

Type:

integer

Required:

no

Default:

2048

Description:

Number of MiB to use for the JVM heap for the website process.

If you find the website becoming slow and less responsive, try allowing the website to use more memory by increasing the maximum heap size.

databaseGB¶

Type:

float

Required:

no

Default:

1.0

Description:

Number of GB to use for the database cache in the web server memory (RAM).

jmx¶

Type:

boolean

Required:

no

Default:

false

Description:

True to enable remote monitoring for the JVM via JMX.

Most users will not need this option.

oomdump¶

Type:

boolean

Required:

no

Default:

false

Description:

True to enable heap dumps when the JVM runs out of memory. Heap dumps are useful to help diagnose memory issues, but are not needed for normal operation.

Most users will not need this option.

workflowDirs¶

Type:

array of strings

Required:

no

Default:

empty list

Description:

List of folder paths containing workflow files.

Any files found in these folders will be loaded as workflows when the web server starts. Any errors with reading the workflow files will be printed to the error log

Examples:

workflowDirs = ['/storage/workflows']

minPasswordLength¶

Type:

integer

Required:

no

Default:

12

Description:

The minimum length accepted for new passwords. This setting only applies when web.auth is login.