NDTS Daemon Installation

Navigation of NDTS Documentation

• NAN Data Transport System
  • NDTS Overview
  • NDTS Installation
    • Installation Overview
    • Installing and Configuring the Gateway Software
    • Installing and Configuring the Daemon Software
  • TopSpin 3.x Requirement
    • Enable TopSpin accounting
      • How NDTS monitors accounting file
  • Managing, Monitoring, and Logging
    • Managing, Monitoring, and Logging the Daemon
  • NDTS Usage Guides
    • NDTS Graphical User Interface (NDTS-GUI)
    • Understanding Experiment Harvesting

NDTS Daemon & GUI Installation (Spectrometer Workstation)

The NDTS Daemon and GUI must be installed separately on each NAN connected spectrometer

Prerequisites

1. Gateway IP address
   • The spectrometer workstation must be able to connect to the Gateway IP address on TCP port 60195
2. Exact Instrument Name (set in the Facility Dashboard – no spaces)
3. Workstation UUID (generated when the spectrometer was added)

WARNING: If you are installing on Alma Linux make sure that the chkconfig package is installed before proceeding. Without this service package, the NDTS Workstation will not properly install or run on Alma.

Installation Steps

# Copy the .gz file to the workstation
tar xf data-transport-daemon.<distro>-<version>.tar.gz
cd dtdaemon-installer
sudo ./install.sh
# → Prompts:
#   • Gateway IP address
#   • Instrument name  (e.g., nmr600)
#   • Workstation UUID

Updating the Daemon

# Best practice: ensure no acquisition is running and the UI is closed
cd dtdaemon-installer
sudo ./install.sh              # updates binaries and restarts the daemon

Uninstalling the Daemon

# Download the latest installation package and execute uninstall.sh
sudo ./uninstall.sh

Rolling Back the Daemon

# The system is designed to allow roll-back to any previous version
# However, best practice would be to only roll-back one version in the event that a new version was causing issues.
# Download previous version and install
tar xf data-transport-daemon.<distro>-<old-version>.tar.gz
cd dtdaemon-installer
sudo ./install.sh

Configuring the Daemon

The NDTS daemon reads its settings from a simple key/value dat file

Location

/opt/nan-dtdaemon/data/ndtd_configuration.dat

The file may list parameters in any order. Edit with nano or your favorite editor

sudo nano /opt/nan-dtdaemon/data/ndtd_configuration.dat

Changes take effect only after the daemon restarts (see below).

Configuration Parameters

Parameter	Default	Notes	Required
gateway_ip_address	-	IP address of the on-site NDTS Gateway	Yes
gateway_port	-	TCP port used by the Gateway (usually 60195)	Yes
instrument_name	-	Spectrometer name exactly as entered in the Facility Dashboard	Yes
instrument_workstation_uuid	-	UUID generated for this workstation in the Facility Dashboard	Yes
log_level	info	Six log levels exist with different levels of information: fatal < error < warning < info < debug < trace (trace is extremely verbose and should only be used when debugging issues as it will fill the disk if left on too long)	No
use_accounting	false	TopSpin only – set true for TopSpin versions < 4.x	No
highest_job_number	8999	Experiments with a higher job number are ignored	No

NOTE: use_accounting=true must be set for versions of TopSpin prior to 4.x

Log levels

Values range from low to extremely high. Note that trace is used for troubleshooting and creates huge log files that will fill the disk if left in trace mode

log level	verbosity	default
fatal	minimal
error	low
warning	medium
info	high	yes
debug	very high
trace	extreme

Example File

gateway_ip_address=155.37.253.192
gateway_port=60195
instrument_name=nmr600
instrument_workstation_uuid=7b20d851-546c-497d-8fad-ef9223b09eab
log_level=info
# use_accounting=true      # (uncomment if needed)
# highest_job_number=9999  # (override default)

Starting the service

The daemon uses SysV service scripts for maximum compatibility and the system is designed to be running at all times. See the NDTS Daemon Operation guide for more information on running and monitoring the Daemon

sudo /sbin/service data-transport-daemon start
sudo /sbin/service data-transport-daemon status

If the Daemon configuration file is adjusted the daemon service should be restarted with

sudo /sbin/service data-transport-daemon status

Starting the Service

The daemon uses SysV service scripts for maximum compatibility, though most modern systems now use systemd. The system is designed to run at all times. See the NDTS Daemon Operation guide for more information on running and monitoring the Daemon.

If your system uses traditional init scripts:

sudo /sbin/service data-transport-daemon start
sudo /sbin/service data-transport-daemon status
sudo /sbin/service data-transport-daemon restart

If your system uses systemd:

sudo systemctl start data-transport-daemon
sudo systemctl status data-transport-daemon
sudo systemctl restart data-transport-daemon

Determining Which Command to Use

To check which command is available on your system, you can run:

command -v systemctl && echo "Use systemctl" || echo "Use service"

Init System by OS Version

Distribution	OS Version(s)	Init System	Command to Use
Red Hat Enterprise Linux	RHEL 5, RHEL 6	SysV Init	service
Red Hat Enterprise Linux	RHEL 7 and later	systemd	systemctl
CentOS	CentOS 5, CentOS 6	SysV Init	service
CentOS	CentOS 7, CentOS 8	systemd	systemctl
Ubuntu	≤ 14.10	Upstart/SysV Init	service
Ubuntu	15.04 and later	systemd	systemctl
AlmaLinux	AlmaLinux 8 and later	systemd	systemctl

Installed NDTS Files and Directory Structure

All daemon-related files reside under /opt/nan-dtdaemon (except the SysV service script). Knowing where each file lives helps with troubleshooting, backups, and upgrades.

Top-Level Executable and Service Script

Path	Purpose
/opt/nan-dtdaemon/data-transport-daemon	Main daemon executable. Forks, then exits; detects if another instance is running.
/etc/init.d/data-transport-daemon	SysV script used by /sbin/service for start/stop/status and boot-time launch.

User-Interface Scripts

File(s)	Role
nan_gui  /  nan_gui.tcl	Launch shell + Tcl code for the NDTS Workstation UI.
topspin_finder.sh  /  vnmrj_finder.sh	Locate spectrometer software and pull metadata.
tcllib/	Supporting Tcl libraries for the UI.

Version Marker

/opt/nan-dtdaemon/running_workstation_version-X.Y.Z

Filename contains the current daemon version; file body is the daemon start timestamp.

Logs

/opt/nan-dtdaemon/logs/

• nan-dtdaemon.log – main runtime log
• ndtd_audit.txt – one line per processed experiment

Data Directory

/opt/nan-dtdaemon/data/

File / Sub-dir	Purpose
experiment_addenda.dat	Selected user, plus placeholders for sample & project (auto-filled by UI).
ndtd_configuration.dat	Key / value daemon configuration file (gateway IP, log_level, etc.).
processing_history.dat	Unix timestamps of all acquisitions already handled (read at daemon start).
users_checksum.dat	MD5 of last user list; delete to force refresh.
users.dat	Current NMRhub user list sent by the Gateway (never edit manually).
user-configuration.dat	Per-user defaults: harvesting on/off, change-user permission.
samples/	Cached sample metadata.
projects/	Cached project metadata.
studies/	Cached study metadata.

Spool Directory

/opt/nan-dtdaemon/spool/

Temporary copy of any acquisition that failed to reach the Gateway. Daemon retries each spooled item at every heartbeat until sent.

Summary Diagram

/opt/nan-dtdaemon
├─ data-transport-daemon
├─ nan_gui   ─┐
├─ nan_gui.tcl│ UI layer
├─ topspin_finder.sh│
├─ vnmrj_finder.sh ┘
├─ tcllib/
├─ running_workstation_version-X.Y.Z
├─ logs/
│  ├─ nan-dtdaemon.log
│  └─ ndtd_audit.txt
├─ data/
│  ├─ ndtd_configuration.dat
│  ├─ experiment_addenda.dat
│  ├─ processing_history.dat
│  ├─ users*.dat …
│  ├─ samples/ projects/ studies/
└─ spool/