Network for Advanced NMR - User contributions [en]

Alma Linux 9.6 - Creating systemctl capability

2025-06-27T16:07:32Z

Lmorris:

For Alma Linux 9.6, the standard

<pre>
service data-transport-daemon status
</pre>

command doesn't work.

Let's make the daemon work with systemctl.

=== Step 1. Create the service file. ===

<pre>
sudo vi /etc/systemd/system/data-transport-daemon.service
</pre>

Enter the following lines in the file:
<pre>
[Unit]
Description=Data Transport Daemon
After=network.target

[Service]
Type=forking
ExecStart=/opt/nan-dtdaemon/data-transport-daemon
TimeoutStopSec=10
KillSignal=SIGINT
Restart=on-failure
User=root

[Install]
WantedBy=multi-user.target
</pre>

=== Step 2. Get the daemon started ===

<pre>
sudo systemctl daemon-reload

sudo systemctl restart data-transport-daemon
</pre>

=== Helpful Commands ===

<pre>
systemctl start data-transport-daemon

systemctl stop data-transport-daemon

systemctl restart data-transport-daemon

systemctl status data-transport-daemon

# investigating problems
journalctl -xeu data-transport-daemon
</pre>

=== Bonus Material (very optional) ===

I like to get the status of a few things when I log onto one of the NMR spectrometer workstations remotely.

In my .bash_profile, I added:

<pre>
# Check if the shell is interactive
if [[ $- == *i* ]]; then
/home/lmorris/scripts/checkNDTS.sh
fi
</pre>

Edit the path and filename as appropriate.

My version of checkNDTS.sh is:

<pre>
#!/usr/bin/bash

# v 1.10 (2025.06jun.19)

# 1. see who's on the system
echo -e "\n\n================================================\n"

# for Alma Linux 9 use
user=$(who | awk '$2 == "seat0" { print $1 }')
# for Centos 7 use
# user=$(who | awk '$2 == ":0" { print $1 }')

if [ -n "$user" ]; then
echo "User: $user"
else
echo "No user logged into graphical session."
fi

echo ""

# 2. make sure the daemon is running

NDTS=$(systemctl status data-transport-daemon |grep Active)
CK_NDTS="active"

# Define ANSI color codes
RED="\033[0;31m"
# YELLOW="\033[0;33m" # for reference (not used)
GREEN="\033[0;32m"
# CYAN="\033[0;36m" # for reference (not used)
RESET="\033[0m" # Reset color back to default

# ndts daemon status
if [[ "$NDTS" == *"$CK_NDTS"* ]]; then
echo -e "${GREEN}NDTS daemon${RESET} status: ${GREEN}running${RESET}"
else
echo -e "${RED}NDTS daemon${RESET} status: ${RED}INACTIVE${RESET}"
fi

echo ""

# 3. check the port on gateway computer

HOST="128.192.9.245" # edit for the IP address of your gateway computer
PORT=60195 # port used by ndts to communicate to the gateway computer

if nc -z -w3 $HOST $PORT; then
echo "✅ Port $PORT is open on $HOST"
else
echo "❌ Port $PORT is NOT reachable on $HOST"
fi

echo -e "\n================================================\n"
</pre>

Alma Linux 9.6 - Creating systemctl capability

2025-06-20T20:39:42Z

Lmorris: Created page with "For Alma Linux 9.6, the standard <pre> service data-transport-daemon status </pre> command doesn't work. Let's make the daemon work with systemctl. === Step 1. Create the service file. === <pre> sudo vi /etc/systemd/system/data-transport-daemon.service </pre> Enter the following lines in the file: <pre> [Unit] Description=Data Transport Daemon After=network.target [Service] Type=forking ExecStart=/opt/nan-dtdaemon/data-transport-daemon TimeoutStopSec=10 KillSign..."

For Alma Linux 9.6, the standard

<pre>
service data-transport-daemon status
</pre>

command doesn't work.

Let's make the daemon work with systemctl.

=== Step 1. Create the service file. ===

<pre>
sudo vi /etc/systemd/system/data-transport-daemon.service
</pre>

Enter the following lines in the file:
<pre>
[Unit]
Description=Data Transport Daemon
After=network.target

[Service]
Type=forking
ExecStart=/opt/nan-dtdaemon/data-transport-daemon
TimeoutStopSec=10
KillSignal=SIGINT
Restart=on-failure
User=nandt-gateway

[Install]
WantedBy=multi-user.target
</pre>

=== Step 2. Create the nandt-gateway user ===

<pre>
sudo useradd --system --no-create-home --shell /sbin/nologin nandt-gateway
</pre>

Make sure the binary is executable by the user nandt-gateway:

<pre>
sudo chown root:nandt-gateway /opt/nan-dtdaemon/data-transport-daemon

sudo chmod 750 /opt/nan-dtdaemon/data-transport-daemon
</pre>

=== Step 3. Get the daemon started ===

<pre>
sudo systemctl daemon-reload

sudo systemctl restart data-transport-daemon
</pre>

=== Helpful Commands ===

<pre>
systemctl start data-transport-daemon

systemctl stop data-transport-daemon

systemctl restart data-transport-daemon

systemctl status data-transport-daemon

# investigating problems
journalctl -xeu data-transport-daemon
</pre>

=== Bonus Material (very optional) ===

I like to get the status of a few things when I log onto one of the NMR spectrometer workstations remotely.

In my .bash_profile, I added:

<pre>
# Check if the shell is interactive
if [[ $- == *i* ]]; then
/home/lmorris/scripts/checkNDTS.sh
fi
</pre>

Edit the path and filename as appropriate.

My version of checkNDTS.sh is:

<pre>
#!/usr/bin/bash

# v 1.10 (2025.06jun.19)

# 1. see who's on the system
echo -e "\n\n================================================\n"

# for Alma Linux 9 use
user=$(who | awk '$2 == "seat0" { print $1 }')
# for Centos 7 use
# user=$(who | awk '$2 == ":0" { print $1 }')

if [ -n "$user" ]; then
echo "User: $user"
else
echo "No user logged into graphical session."
fi

echo ""

# 2. make sure the daemon is running

NDTS=$(systemctl status data-transport-daemon |grep Active)
CK_NDTS="active"

# Define ANSI color codes
RED="\033[0;31m"
# YELLOW="\033[0;33m" # for reference (not used)
GREEN="\033[0;32m"
# CYAN="\033[0;36m" # for reference (not used)
RESET="\033[0m" # Reset color back to default

# ndts daemon status
if [[ "$NDTS" == *"$CK_NDTS"* ]]; then
echo -e "${GREEN}NDTS daemon${RESET} status: ${GREEN}running${RESET}"
else
echo -e "${RED}NDTS daemon${RESET} status: ${RED}INACTIVE${RESET}"
fi

echo ""

# 3. check the port on gateway computer

HOST="128.192.9.245" # edit for the IP address of your gateway computer
PORT=60195 # port used by ndts to communicate to the gateway computer

if nc -z -w3 $HOST $PORT; then
echo "✅ Port $PORT is open on $HOST"
else
echo "❌ Port $PORT is NOT reachable on $HOST"
fi

echo -e "\n================================================\n"
</pre>

NDTS Daemon Installation

2025-06-20T19:50:45Z

Lmorris:

{{NDTS_Navbox}}

== NDTS Daemon & GUI Installation (Spectrometer Workstation) ==
The NDTS Daemon and GUI must be installed separately on each NAN connected spectrometer

=== Prerequisites ===
# '''Gateway IP address'''
#* The spectrometer workstation must be able to connect to the Gateway IP address on TCP port 60195
# Exact '''Instrument Name''' (set in the Facility Dashboard – no spaces)
# '''Workstation UUID''' (generated when the spectrometer was added)
<mark>WARNING: If you are installing on Alma Linux make sure that the <code>'''chkconfig'''</code> package is installed before proceeding. Without this service package, the NDTS Workstation will not properly install or run on Alma.</mark>

===== [[Alma Linux 9.6 - Creating systemctl capability]] =====

=== Installation Steps ===
<pre>
# 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
</pre>

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

=== Uninstalling the Daemon ===
<pre>
# Download the latest installation package and execute uninstall.sh
sudo ./uninstall.sh
</pre>

=== Rolling Back the Daemon ===
<pre>
# 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
</pre>

=== Installation and Update Examples ===

===== [[NDTS Daemon and GUI Install Example]] =====

===== [[NDTS Daemon and GUI Update Example]] =====
== Configuring the Daemon ==
The NDTS daemon reads its settings from a simple key/value dat file

=== Location ===
<pre>/opt/nan-dtdaemon/data/ndtd_configuration.dat</pre>

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

<pre>sudo nano /opt/nan-dtdaemon/data/ndtd_configuration.dat</pre>

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

=== Configuration Parameters ===
{| class="wikitable"
! 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: <code>use_accounting=true</code> 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
{| class="wikitable"
|+
!log level
!verbosity
!default
|-
|fatal
|minimal
|
|-
|error
|low
|
|-
|warning
|medium
|
|-
|'''info'''
|'''high'''
|'''yes'''
|-
|debug
|very high
|
|-
|trace
|extreme
|
|}

=== Example File ===
<pre>
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)
</pre>

=== 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|NDTS Daemon Operation guide]] for more information on running and monitoring the Daemon<pre>
sudo /sbin/service data-transport-daemon start
sudo /sbin/service data-transport-daemon status
</pre>
If the Daemon configuration file is adjusted the daemon service should be restarted with <pre>sudo /sbin/service data-transport-daemon status</pre>

== Installed NDTS Files and Directory Structure ==
All daemon-related files reside under <code>/opt/nan-dtdaemon</code> (except the SysV service script).
Knowing where each file lives helps with troubleshooting, backups, and upgrades.

=== Top-Level Executable and Service Script ===
{| class="wikitable"
! Path !! Purpose
|-
| <code>/opt/nan-dtdaemon/data-transport-daemon</code> || Main daemon executable. Forks, then exits; detects if another instance is running.
|-
| <code>/etc/init.d/data-transport-daemon</code> || SysV script used by <code>/sbin/service</code> for start/stop/status and boot-time launch.
|}

=== User-Interface Scripts ===
{| class="wikitable"
! File(s) !! Role
|-
| <code>nan_gui</code>  /  <code>nan_gui.tcl</code> || Launch shell + Tcl code for the NDTS Workstation UI.
|-
| <code>topspin_finder.sh</code>  /  <code>vnmrj_finder.sh</code> || Locate spectrometer software and pull metadata.
|-
| <code>tcllib/</code> || Supporting Tcl libraries for the UI.
|}

=== Version Marker ===
<pre>/opt/nan-dtdaemon/running_workstation_version-X.Y.Z</pre>
Filename contains the current daemon version; file body is the daemon start timestamp.

=== Logs ===
<pre>/opt/nan-dtdaemon/logs/</pre>
* <code>nan-dtdaemon.log</code> – main runtime log
* <code>ndtd_audit.txt</code> – one line per processed experiment

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

=== Spool Directory ===
<pre>/opt/nan-dtdaemon/spool/</pre>
Temporary copy of any acquisition that failed to reach the Gateway.
Daemon retries each spooled item at every heartbeat until sent.

=== Summary Diagram ===
<pre>
/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/
</pre>