How to set up ATSAM3X8E microcontrollers for bare-metal programming in C

HOW TO SET UP ATSAM3X8E MICROCONTROLLERS FOR BARE-METAL PROGRAMMING IN C

05 OCTOBER 2024

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This article is a step-by-step guide for programming bare-metal ATSAM3X8E chips -found on Arduino Due boards. It also includes notes on the chip’s memory layout -relevant for writing linker scripts. The steps described in this article were -tested on an OpenBSD workstation.

- -

Toolchain

- -

To interact directly with a bare-metal ATSAM3X8E chips, we must bypass the -embedded bootloader. To do that, we need a hardware programmer capable of -communicating with the chip over the Serial Wire Debug (SWD) protocol. Since -the workstation we upload the program from presumably doesn’t speak SWD, the -hardware programmer acts as a SWD-USB adapter. The ST-LINK/V2 programmer fits this -bill.

- -

The OpenOCD on-chip debugger software supports -ATSAM3X8E chips. OpenOCD, on startup, runs a telnet server that we can connect to -to issue commands to the ATSAM3X8E chip. OpenOCD translates plain-text commands -into the binary sequences the chip understands, and sends them over the wire.

- -

Finally, we need the ARM GNU Compiler -Toolchain to compile C programs for the chip. The ARM GNU compiler -toolchain and OpenOCD, as a consequence of being free software, are available -on every conceivable platform, including OpenBSD.

- -

Electrical connections

- -

The following photos illustrate the electrical connections between the Arduino -Due, PC, and the ST-LINK/V2 programmer required to transfer a compiled program -from a PC to the MCU.

- - - - - - -

Wiring

Arduino Due

- -

Arduino Due exposes the ATSAM3X8E’s SWD interface via its DEBUG port. The -ST-LINK/v2 programmer connects to that to communicate with the chip.

- -

Uploading the program

- -

The source.tar.gz tarball at the end of this page contains a sample C program -(the classic LED blink program) with OpenOCD configuration and linker scripts. -First, use the following command to build it:

- -

$ arm-none-eabi-gcc -mcpu=cortex-m3 -mthumb -T script.ld \
-    -nostartfiles \
-    -nostdlib \
-    -o a.elf main.c
-

- -

Then, open a telnet session with OpenOCD and issue the following sequence of -commands to configure the chip and upload the compiled program to it:

- -

$ openocd -f openocd-due.cfg
-$ telnet localhost 4444
-  > halt
-  > at91sam3 gpnvm show
-  > at91sam3 gpnvm set 1
-  > at91sam3 gpnvm show
-$ openocd -f openocd-due.cfg -c "program a.elf verify reset exit"
-

- -

The first of the above commands starts OpenOCD. In the telnet session, the -first command halts the chip in preparation for receiving commands. Next, we -inspect the current GPNVM bit setting (more on this later). If the bit is unset -(the gpnvm show command returns 0), we set it to 1 and verify the update.

- -

The final command, issued from outside the telnet session, uploads the program -to the chip. Those are the bare minimum set of commands required to program the -chip. The AT91SAM3 flash driver section of the OpenOCD manual lists all -available commands for the ATSAM3X8E chip.

- -

GPNVM bits

- -

By design, ARM chips boot into address 0x00000. ATSAM3X8E’s memory consists of -a ROM and a dual-banked flash (flash0 and flash1), residing in different -locations of the chip’s address space. The GPNVM bits control which of them -maps to 0x00000. When GPNVM1 is cleared (the default), the chip boots from the ROM, -which contains Atmel’s SAM-BA bootloader.

- -

Conversely, when the GPNVM1 bit is 1 (and the GPNVM2 bit is 0), flash0 at -address 0x80000 maps to 0x00000. When both GPNVM bits are 0, flash1 maps to -0x00000. Since we place our program in flash0 in the linker script, we set the -GPNVM1 bit and leave the GPNVM2 bit unchanged to ensure the chip -executes our program instead of the embedded bootloader at startup.

- -

Linker script

- -

At a minimum, the linker script must place the vector table at the first -address of the flash. This is mandatory for ARM chips unless we relocate the -vector table using the VTOR register.

- -

The first entry of the vector table must be the stack pointer. The stack -pointer must be initializes to the highest memory location available to -accommodate the ATSAM3X8E’s descending stack.

- -

The second entry of the vector table must be the reset vector. In the reset -vector, we can perform tasks such as zeroing out memory and initializing -registers before passing control to the main program.

- -

Files: source.tar.gz

by W. D. Sadeep Madurange

HOW TO CONFIGURE ATMEGA328P MICROCONTROLLERS TO RUN AT 3.3V AND 5V

10 APRIL 2025

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This is a quick reference for wiring up ATmega328P ICs to run at 5V and 3.3V. -While the 5V configuration is common, the 3.3V configuration can be useful in -low-power applications and when interfacing with parts that themselves run at -3.3V. In this guide, the 5V setup is configured with a 16MHz crystal -oscillator, while the 3.3V configuration makes use of an 8MHz crystal -oscillator.

- -

The steps that follow refer to the following pinout.

- - - - - - -

Pinout

Breadboard

- -

5V-16MHz configuration

- -

Powering ATmega328P microcontrollers with 5V is the most common setup. This is -also how Arduino Uno boards are wired.

- -

In this configuration, the microcontroller’s pin 1 is connected to 5V via a -10kΩ resistor. Pins 9 and 10 are connected to a 16MHz crystal oscillator via -two 22pF capacitors connected to ground. The microcontroller is powered by -connecting pins 7, 20, and 21 to a 5V DC power supply. Lastly, pins 8 and 22 -are connected to ground. In addition to the these connections, which are -required, it’s a good idea to add 0.1μF decoupling capacitors between pins 7, -20, and 21 and ground.

- -

Here’s a sample Makefile for compiling C programs for ATmega328P -microcontrollers using avr-gcc/avrdude toolchain.

- -

3.3V-8MHz configuration

- -

Electrical connections for running an ATmega328P at 3.3V are identical to that -of the 5V circuit. The only differences are that all the 5V connections are -replaced with a 3.3V power source and a 8MHz crystal oscillator takes the place -of the 16MHz crystal.

- -

However, standard ATmega328P chips are preconfigured to run at 5V. To run one -at 3.3V, we must first modify its fuses that control characteristics like the -BOD level. If a bootloader that expects a 16MHz clock (e.g., Arduino -bootloader) is pre-installed on the ATmega328P, it must be swapped with one -that accepts an 8MHz clock. To accomplish that, we need an in-system programmer -(ISP).

- -

Fortunately, we can turn an ordinary Arduino Uno board into an ISP by uploading -the ‘ArduinoISP’ sketch found in the Arduino IDE. The ISP communicates with the -microcontroller using a Serial Peripheral Interface (SPI). So, connect the SPI -port of the ATmega328P to that of the Arduino Uno, and the Uno’s SS pin -to the ATmega328P’s RESET pin.

- -

Power up the the ATmega328P by connecting its V_CC to a 5V supply (we -can use Arduino Uno’s 5V pin). From the Arduino IDE, select ‘ATmega328P (3.3V, -8MHz)’ for processor from the tools menu. Also from the tools menu, select -‘Arduino as ISP’ as programmer. Finally, upload the new bootloader by selecting -‘Burn Bootloader’ from the tools menu.

- -

The ATmega328P is now ready to run at 8MHz with a 3.3V power supply. You can -upload programs to the ATmega328P as you normally would using avrdude. -Here’s a sample Makefile with adjusted parameters (e.g., baud -rate) for an 8MHz clock.

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Remarks

- -

In both configurations, if you intend to use the ATmega328P’s analog-to-digital -converter with the internal 1.1V or AV_cc voltage as reference, do -not connect AREF (pin 21) to V_cc. Refer to section 23.5.2 in the -datasheet for more information.

- -

by W. D. Sadeep Madurange

- -

MOSFETS AS ELECTRONIC SWITCHES

22 JUNE 2025

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Recently, I needed a low-power circuit for one of my battery-operated projects. -Much of the system’s power savings depended on its ability to electronically -switch off components, such as servos, that draw high levels of quiescent -currents. My search for a solution led me to MOSFETs, transistors capable of -controlling circuits operating at voltages far above their own.

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Acknowledgments

- -

This article is a summary of what I learnt about using MOSFETs as switches. -I’m not an electronics engineer, and this is not an authoritative guide. The -circuits in this post must be considered within the narrow context in which -I’ve used them. All credits for the schematics belong to Simon Fitch.

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Preamble

- -

For a typical MOSFET-based switch, we can connect a GPIO pin of a -microcontroller to the gate of a logic-level N-channel MOSFET placed on the low -side of the load and tie the gate and the drain pins of the MOSFET with a -pull-down resistor. This would work as long as the power supplies of the -microcontroller and the load don’t share a common ground. Things become more -complicated when they do (e.g., controlling power to a component driven by the -same microcontroller).

- -

In that scenario, the source potential visible to the load is the difference -between the gate and the threshold potentials of the MOSFET. For example, when -the gate and the threshold potentials are 3.3 V and 1.5 V, the potential the -load sees is 1.8 V. So, to use a low-side N-channel MOSFET, we need the gate -potential to be higher than the source potential, which may not always be -practical. The alternative would be a hide-side switch.

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P-channel high-side switch

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The following schematic shows how a high-side P-channel MOSFET (M1) could -switch power to a 6 V servo driven by a 3.3 V MCU.

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P-channel high-side switching circuit

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When the microcontroller outputs low, the M2 N-channel MOSFET stops conducting. -The R1 resistor pulls the gate of the M1 P-channel MOSFET up to +6 V, switching -the servo off. When the microcontroller outputs high on the GPIO pin, M2’s -source-drain connection starts conducting, causing M1’s gate potential to drop -to 0 V, which switches on power to the servo.

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N-channel high-side switch

- -

The P-channel high-side switch would be the typical architecture for our use -case. However, if we have access to a potential high enough to safely raise the -gate potential above the threshold such that their difference outputs the source -potential required to drive the load, we can switch on the high side using an -N-channel MOSFET:

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N-channel high-side switching circuit

- -

In the schematic, both M1 and M2 are N-channel MOSFETs. When the -microcontroller output is low, M2 stops conducting. This causes the M1’s gate -potential to rise above the threshold, turning the servo on. Conversely, a high -output on the GPIO line switches M2 on, which lowers M1’s gate potential. This -switches the servo off. The R2 pull-up resistor prevents the high impedance of -the output pins at power-up from switching the servo on.

- -

Both topologies require M2 to act as a level converter between circuits -containing the microcontroller and the servo, converting between 0 V and +6 V -or +9 V. M2 is a low-power signal converter carrying less than a milliamp of -current. The gate-source threshold voltage of M2 must be lower than the MCU’s -supply voltage. 2N7000, 2N7002, and BSS138 are popular choices for M2.

- -

The D1 flyback diodes used in the two topologies safeguard the MOSFET from -voltage spikes caused by inductive loads such as servos.

- -

A BJT alternative

- -

A Bipolar Junction Transistor (BJT) is a simpler, cheaper, and more widely -available type of transistor that can be used as a switch.

- -

BJT architecture

- -

In the schematic, when the MCU outputs high, Q2 starts conducting. Q2 amplifies -Q1’s base current. Unlike MOSFETs, which are voltage-driven, BJTs are driven by -base current. Resistors R3 and R4 must be chosen carefully to output the -desired base currents. “How to choose a -transistor as a switch” is an excellent guide on using BJTs as electronic -switches.

- -

Which topology to choose?

- -

The professional community appears to prefer MOSFETs over BJTs. MOSFETs are -more efficient when the switch is on. However, they are more challenging to -drive, especially with a 3.3 V MCU, due to the V_GS potentials -required to achieve specified R_DS(on) values (i.e., to turn them on -fully).

- -

N-channel MOSFETs have lower on-resistance values, making them more efficient -than P-channel ones. They are also cheaper. However, they are harder to drive -on the high side as their gate potential must be higher than the source -potential. This often requires extra circuitry such as MOSFET drivers.

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NEO4J A* SEARCH

14 SEPTEMBER 2025

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Back in 2018, we used Neo4J graph database to track the -movement of marine vessels. We were interested in the shortest path a ship -could take through a network of about 13,000 route points. Algorithms based on -graph theory, such as A* search, provide optimal solutions to such problems. -In other words, the set of route points lends itself well to a model based on -graphs.

- -

A graph is a finite set of vertices, and a subset of vertex pairs (edges). -Edges can have weights. In the case of vessel tracking, the route points form -the vertices of a graph; the routes between them, the edges; and the distances -between them are the weights. For different reasons, people are interested in -minimizing (or maximizing) the weight of a path through a set of vertices. For -instance, we may want to find the shortest path between two ports.

- -

Given such a graph, an algorithm like Dijkstra’s search could compute the -shortest path between two vertices. In fact, this was the algorithm Neo4J -shipped with at the time. One drawback of Dijkstra’s algorithm is that it -computes all the shortest paths from the source to all other vertices before -terminating at the destination vertex. The exhaustive nature of this search -limited our search to about 4,000 route points.

- -

The following enhancement to Dijkstra’s search, also known as the A* search, -employs a heuristic to steer the search in the direction of the destination -more quickly. In the case of our network of vessels, which are on the earth’s -surface, spherical distance is a good candidate for a heuristic:

- -

package org.neo4j.graphalgo.impl;
-
-import java.util.stream.Stream;
-import java.util.stream.StreamSupport;
-
-import org.neo4j.graphalgo.api.Graph;
-import org.neo4j.graphalgo.core.utils.ProgressLogger;
-import org.neo4j.graphalgo.core.utils.queue.IntPriorityQueue;
-import org.neo4j.graphalgo.core.utils.queue.SharedIntPriorityQueue;
-import org.neo4j.graphalgo.core.utils.traverse.SimpleBitSet;
-import org.neo4j.graphdb.Direction;
-import org.neo4j.graphdb.Node;
-import org.neo4j.kernel.internal.GraphDatabaseAPI;
-
-import com.carrotsearch.hppc.IntArrayDeque;
-import com.carrotsearch.hppc.IntDoubleMap;
-import com.carrotsearch.hppc.IntDoubleScatterMap;
-import com.carrotsearch.hppc.IntIntMap;
-import com.carrotsearch.hppc.IntIntScatterMap;
-
-public class ShortestPathAStar extends Algorithm<ShortestPathAStar> {
-    
-    private final GraphDatabaseAPI dbService;
-    private static final int PATH_END = -1;
-    
-    private Graph graph;
-    private final int nodeCount;
-    private IntDoubleMap gCosts;
-    private IntDoubleMap fCosts;
-    private double totalCost;
-    private IntPriorityQueue openNodes;
-    private IntIntMap path;
-    private IntArrayDeque shortestPath;
-    private SimpleBitSet closedNodes;
-    private final ProgressLogger progressLogger;
-    
-    public static final double NO_PATH_FOUND = -1.0;
-    
-    public ShortestPathAStar(
-        final Graph graph,
-        final GraphDatabaseAPI dbService) {
-
-        this.graph = graph;
-        this.dbService = dbService;
-
-        nodeCount = Math.toIntExact(graph.nodeCount());
-        gCosts = new IntDoubleScatterMap(nodeCount);
-        fCosts = new IntDoubleScatterMap(nodeCount);
-        openNodes = SharedIntPriorityQueue.min(
-            nodeCount,
-            fCosts,
-            Double.MAX_VALUE);
-        path = new IntIntScatterMap(nodeCount);
-        closedNodes = new SimpleBitSet(nodeCount);
-        shortestPath = new IntArrayDeque();
-        progressLogger = getProgressLogger();
-    }
-    
-    public ShortestPathAStar compute(
-        final long startNode,
-        final long goalNode,
-        final String propertyKeyLat,
-        final String propertyKeyLon,
-        final Direction direction) {
-
-        reset();
-
-        final int startNodeInternal = 
-            graph.toMappedNodeId(startNode);
-        final double startNodeLat =
-            getNodeCoordinate(startNodeInternal, propertyKeyLat);
-        final double startNodeLon = 
-            getNodeCoordinate(startNodeInternal, propertyKeyLon);
-
-        final int goalNodeInternal =
-            graph.toMappedNodeId(goalNode);
-        final double goalNodeLat = 
-            getNodeCoordinate(goalNodeInternal, propertyKeyLat);
-        final double goalNodeLon = 
-            getNodeCoordinate(goalNodeInternal, propertyKeyLon);
-
-        final double initialHeuristic = 
-            computeHeuristic(startNodeLat,
-                startNodeLon,
-                goalNodeLat,
-                goalNodeLon);
-
-        gCosts.put(startNodeInternal, 0.0);
-        fCosts.put(startNodeInternal, initialHeuristic);
-        openNodes.add(startNodeInternal, 0.0);
-
-        run(goalNodeInternal,
-            propertyKeyLat,
-            propertyKeyLon,
-            direction);
-
-        if (path.containsKey(goalNodeInternal)) {
-            totalCost = gCosts.get(goalNodeInternal);
-            int node = goalNodeInternal;
-            while (node != PATH_END) {
-                shortestPath.addFirst(node);
-                node = path.getOrDefault(node, PATH_END);
-            }
-        }
-        return this;
-    }
-    
-    private void run(
-        final int goalNodeId,
-        final String propertyKeyLat,
-        final String propertyKeyLon,
-        final Direction direction) {
-
-        final double goalLat = 
-            getNodeCoordinate(goalNodeId, propertyKeyLat);
-        final double goalLon =
-            getNodeCoordinate(goalNodeId, propertyKeyLon);
-
-        while (!openNodes.isEmpty() && running()) {
-            int currentNodeId = openNodes.pop();
-            if (currentNodeId == goalNodeId) {
-                return;
-            }
-
-            closedNodes.put(currentNodeId);
-
-            double currentNodeCost = 
-                this.gCosts.getOrDefault(
-                    currentNodeId, 
-                    Double.MAX_VALUE);
-
-            graph.forEachRelationship(
-                currentNodeId,
-                direction,
-                (source, target, relationshipId, weight) -> {
-                    double neighbourLat = 
-                        getNodeCoordinate(target, propertyKeyLat);
-                    double neighbourLon = 
-                        getNodeCoordinate(target, propertyKeyLon);
-                    double heuristic = 
-                        computeHeuristic(
-                            neighbourLat, 
-                            neighbourLon, 
-                            goalLat,
-                            goalLon);
-
-                    updateCosts(
-                        source,
-                        target,
-                        weight + currentNodeCost,
-                        heuristic);
-
-                    if (!closedNodes.contains(target)) {
-                        openNodes.add(target, 0);
-                    }
-                    return true;
-                });
-
-            progressLogger.logProgress(
-                (double) currentNodeId / (nodeCount - 1));
-        }
-    }
-    
-    private double computeHeuristic(
-        final double lat1,
-        final double lon1,
-        final double lat2,
-        final double lon2) {
-
-        final int earthRadius = 6371;
-        final double kmToNM = 0.539957;
-        final double latDistance = Math.toRadians(lat2 - lat1);
-        final double lonDistance = Math.toRadians(lon2 - lon1);
-        final double a = Math.sin(latDistance / 2)
-            * Math.sin(latDistance / 2)
-            + Math.cos(Math.toRadians(lat1))
-            * Math.cos(Math.toRadians(lat2))
-            * Math.sin(lonDistance / 2)
-            * Math.sin(lonDistance / 2);
-        final double c = 2
-            * Math.atan2(Math.sqrt(a), Math.sqrt(1 - a));
-        final double distance = earthRadius * c * kmToNM;
-        return distance;
-    }
-    
-    private double getNodeCoordinate(
-        final int nodeId,
-        final String coordinateType) {
-
-        final long neo4jId = graph.toOriginalNodeId(nodeId);
-        final Node node = dbService.getNodeById(neo4jId);
-        return (double) node.getProperty(coordinateType);
-    }
-    
-    private void updateCosts(
-        final int source, 
-        final int target, 
-        final double newCost,
-        final double heuristic) {
-
-        final double oldCost = 
-            gCosts.getOrDefault(target, Double.MAX_VALUE);
-
-        if (newCost < oldCost) {
-            gCosts.put(target, newCost);
-            fCosts.put(target, newCost + heuristic);
-            path.put(target, source);
-        }
-    }
-    
-    private void reset() {
-        closedNodes.clear();
-        openNodes.clear();
-        gCosts.clear();
-        fCosts.clear();
-        path.clear();
-        shortestPath.clear();
-        totalCost = NO_PATH_FOUND;
-    }
-    
-    public Stream<Result> resultStream() {
-        return StreamSupport.stream(
-            shortestPath.spliterator(), false)
-                .map(cursor -> new Result(
-                    graph.toOriginalNodeId(cursor.value),
-                    gCosts.get(cursor.value)));
-    }
-
-    public IntArrayDeque getFinalPath() {
-        return shortestPath;
-    }
-    
-    public double getTotalCost() {
-        return totalCost;
-    }
-
-    public int getPathLength() {
-        return shortestPath.size();
-    }
-    
-    @Override
-    public ShortestPathAStar me() {
-        return this;
-    }
-
-    @Override
-    public ShortestPathAStar release() {
-        graph = null;
-        gCosts = null;
-        fCosts = null;
-        openNodes = null;
-        path = null;
-        shortestPath = null;
-        closedNodes = null;
-        return this;
-    }
-    
-    public static class Result {
-
-        /**
-         * the neo4j node id
-         */
-        public final Long nodeId;
-
-        /**
-         * cost to reach the node from startNode
-         */
-        public final Double cost;
-
-        public Result(Long nodeId, Double cost) {
-            this.nodeId = nodeId;
-            this.cost = cost;
-        }
-    }
-}
-

- -

The heuristic function is domain-specific. If chosen wisely, it can -significantly speed up the search. In our case, we achieved a 300x speedup, -enabling us to expand our search from 4,000 to 13,000 route points. The v3.4.0 of the -Neo4J graph algorithms shipped with the A* search algorithm.

- -

by W. D. Sadeep Madurange

HOW I MANAGE SUCKLESS SOFTWARE PACKAGES

30 NOVEMBER 2025

-
-

Since suckless software requires users to modify the -source code and recompile to customize, I need a way to maintain patches over -the long term while retaining the ability to upgrade the software as new -versions are released.

- -

Initial setup

- -

When using a suckless program, I usually begin by cloning the project and -setting the remote URL to push a copy of the source code with my patches to my -own git repository:

- -

git clone git://git.suckless.org/dwm
-git reset --hard <tag>
-git remote set-url --push origin git@git.asciimx.com:/repos/dwm
-

- -

This way, I can pull updates from the upstream project whenever I want, while -committing my changes to my own git repository. The git reset command aligns my -branch head with a stable release before applying patches or installing the -software.

- -

If all I want to do is reconfigure the software (e.g., change key bindings), -which is what I need most of the time, the recommended approach is to modify -the config.h file. If the config.h isn’t yet in the project, the following -command generates it from the defaults and compiles the software using make -clean <target> here <target> is the name of the application (e.g., dwm) -found in the Makefile. I modify the resulting config.h file and run make clean -install to install the software before committing and pushing my changes to my -git repo.

- -

dwm and slstatus

- -

Since dwm and slstatus are always running, make install will likely fail for -them. The operating system will prevent the installer from replacing running -executables with new ones. Hence, we must first stop the running instances of -these programs (Mod + Shift + q). Then, switch to a tty (Ctrl + Alt + F1), -log in, and change the directory to where dwm/slstatus is. We can run make -install to install the software and switch back to the graphical session -(Ctrl + Alt + F5).

- -

The key combinations for switching to the tty and back may differ across -systems. The ones listed above are for OpenBSD.

- -

Subsequent upgrades

- -

When suckless releases a new version, I run git pull --rebase to fetch the -upstream changes and rebase my patches on top of them. Because I tend to use -stable versions, I perform another interactive rebase to drop the commits -between the latest stable version tag and my patch before installing the -software.

- -

Commit log before upgrading:

- -

dt236  My patch.
-3fkdf  Version 6.5.
-

- -

Commit log after pulling:

- -

w467d  My patch.
-gh25g  A commit.
-g525g  Another commit.
-3fkdf  Version 6.6.
-vd425  Old commit.
-q12vu  Another old commit.
-3fkdf  Version 6.5.
-

- -

Commit log after the interactive rebase:

- -

h57jh  My patch.
-3fkdf  Version 6.6.
-vd425  Old commit.
-q12vu  Another old commit.
-3fkdf  Version 6.5.
-

- -

And finally, commit and push all the changes to my own git repository.

- -

by W. D. Sadeep Madurange

- How I manage Suckless software packages -	- - 2025-11-30 - -
- Neo4J A* search -	- - 2025-09-14 - -
- MOSFETs as electronic switches -	- - 2025-06-22 - -
- How to configure ATmega328P microcontrollers to run at 3.3V and 5V -	- - 2025-04-10 - -
- How to set up ATSAM3X8E microcontrollers for bare-metal programming in C -	- - 2024-10-05 - -