How to Fix an Error When Running MongoDB on a Linux Server

As someone who’s worked with MongoDB on Linux servers, I’ve encountered my fair share of errors. One that stands out is the “cannot execute binary file: Exec format error”. If you’re running into this problem, you’re not alone. It can be frustrating, especially when the server fails to run a simple command like mongod --storageEngine wiredTiger --dbpath data --logpath logs/mongo.log. This issue usually arises when the binary you’re trying to run doesn’t match the architecture of your system. But don’t worry, I’m here to walk you through the process of understanding the error, troubleshooting its causes, and ultimately fixing it. Let’s dive in!

The Error: “Cannot Execute Binary File

The error message “cannot execute binary file: Exec format error” is typically an indication that the MongoDB binary you’re trying to execute is not compatible with the architecture of the machine. You may have downloaded the wrong version for your system, or there could be some other underlying issue. I’ll break this down into more detail to help you identify the root cause.

Explanation of the Error

Binary Mismatch:
- This is one of the most common causes. It happens when the mongod binary you’re trying to execute was compiled for a different platform or architecture. For example, you might be attempting to run a 64-bit version of MongoDB on a 32-bit system, or even worse, trying to run it on an ARM-based system when the binary is for x86-64.
Corruption:
- The binary itself might be corrupted. Maybe it didn’t download correctly, or some files got lost during the transfer. This can also lead to errors when trying to execute the binary.
Incorrect Permissions:
- Another possible culprit is that the binary file doesn’t have the proper execute permissions set. Without execute permissions, Linux will refuse to run the binary.

Steps to Troubleshoot the Error

Let’s break down the steps I took to fix this issue. Following this process should help you get MongoDB up and running again.

Check the Architecture of the Binary

One of the first things you should do is check the architecture of the mongod binary. This helps confirm whether it matches the architecture of your system.

To do this, run the following command:

file /path/to/mongod

This command will display the architecture of the binary. For example, you might see:

x86-64 for 64-bit systems
arm64 for ARM-based systems
i386 for 32-bit systems

Now, check your system’s architecture by running:

uname -m

If the binary doesn’t match your system’s architecture, you will need to download the correct version of MongoDB. You can get the appropriate version from the official MongoDB website or use the installation guide for your specific Linux distribution.

Re-download the MongoDB Binary

If you suspect the binary is corrupted, don’t hesitate to re-download it. Here’s a simple way to get the MongoDB package for Ubuntu (just an example; make sure to select the correct version for your distribution):

wget https://fastdl.mongodb.org/linux/mongodb-linux-x86_64-ubuntu2004-5.0.6.tgz
tar -zxvf mongodb-linux-x86_64-ubuntu2004-5.0.6.tgz

By re-downloading the binary, you can be sure that the file isn’t corrupted.

Check File Permissions

Another possible reason for the “Exec format error” is that the MongoDB binary doesn’t have the proper execute permissions. To fix this, simply run the following command:

chmod +x /path/to/mongod

This will grant execute permissions to the mongod binary, ensuring that your Linux system can run it.

Further Troubleshooting Dependencies and ELF Errors

While troubleshooting, I noticed some ELF-related errors when trying to inspect the binary using the readelf command:

readelf -d /path/to/mongod

These errors often indicate that the binary is either corrupt or mismatched in terms of architecture. Here are a couple of error messages you might encounter:

Warning: “The e_shentsize field in the ELF header is larger than the size of an ELF section header.”
Error: “Reading 0x9c00000 bytes extends past the end of the file for section headers.”

To resolve these errors, it’s crucial to ensure that your Linux distribution has all the necessary libraries for MongoDB. Some common libraries MongoDB depends on include:

libc (Standard C library)
libssl (SSL library)
libcurl (for network communications)

Make sure these libraries are installed and up to date. If your binary is still failing, the issue could very well be a mismatch of architectures, so make sure to download the appropriate MongoDB package for your system.

Adding Extra Practice Functionality to MongoDB

Once you’ve fixed the error and MongoDB is up and running, it’s time to dive deeper into MongoDB’s capabilities. Below are some advanced functionalities that you can experiment with to enhance your MongoDB experience on Linux.

Start MongoDB with Authentication

Enabling authentication adds an extra layer of security to your MongoDB instance. Here’s how you can do it:

Start MongoDB with the --auth flag to enable authentication:

mongod --auth --dbpath /data/db --logpath /var/log/mongodb/mongod.log

Next, create an admin user with the following commands:

mongo
use admin
db.createUser({ user: "admin", pwd: "password", roles: ["root"] })

Now, whenever you connect to MongoDB, you’ll need to authenticate:

mongo -u admin -p password --authenticationDatabase admin

Set Up MongoDB Replication

Replication ensures that your data is backed up across multiple nodes, providing high availability. Here’s a simple way to set up replication with MongoDB:

Start the primary node:

mongod --replSet rs0 --port 27017 --dbpath /data/db --bind_ip localhost

Initialize the replica set:

mongo
rs.initiate()

Add a secondary node:

mongod --replSet rs0 --port 27018 --dbpath /data/db2 --bind_ip localhost
mongo --port 27017
rs.add("localhost:27018")

You now have a basic replica set running with two nodes!

Back Up MongoDB Data

You should always back up your MongoDB data. Use the mongodump utility to create backups:

mongodump --db mydatabase --out /backup/directory

This will back up the mydatabase database to the specified directory.

Conclusion

In this blog post, I explained how to fix the “cannot execute binary file: Exec format error” that can occur when running MongoDB on a Linux server. I walked you through the steps to identify the cause of the error, troubleshoot it, and provided a solution. But that’s not all! After fixing the issue, I also shared a few MongoDB functionalities to enhance your server management skills, such as enabling authentication, setting up replication, and backing up your data.