Software Problems That May Emulate Hard Disk and Solid State Drive Problems

Overview

In this article, we will be describing software problems that can exhibit symptoms similar to those associated with problematic hard disk drives (HDDs) and solid state drives (SSDs). The problems we will address may be operating system bugs, applications or processes that present problems to a system that may make the system act like it has a drive problem, or applications, processes, or drivers that may be incompatible with a system.

This page is one page in a series of five pages dealing with HDD and SSD problems and their associated symptoms. If you haven't read the main page of this article, we recommend clicking on the link to the left titled "Article Main Page" before proceeding. This article will focus solely on problems specific to software problems, and it will not directly address any of the problems that genuinely originate from a bad drive.

Symptoms of Software Problems

This article will address the list of symptoms that are defined in the main page of this article associated with software problems. Each of the following subsections will describe the symptom, its possible causes, and how to correct it if possible. For the sake of review and clarity, the symptoms we identified in the main page of this article were in the classification titled Operating system bugs or other software related problems and are as follows:

• Periodic delays when using the system.

• Running applications lock up for no apparent reason

• The drive is no longer recognized by the system

• A boot drive will no longer boot

• A drive ejects itself for no apparent reason or won't mount

Periodic delays when using the system

Software itself can cause problems by using high levels of CPU power, using large amounts of memory, or making excessive use of the hard drive. Some of these are addressed in the "User Problems" section associated with the link at the top of this page. Aside from actual user installed software, the following system applications may be responsible for problems:

• The mds (meta data server) process used primarily by Spotlight and Time Machine.
• The Icon Services Agent, which generates fairly large amounts of icon data.
• Safari Web Services and other browser plugins used to handle video content.
• Time Machine backups
• Automatic software updates and installations.
• Anti-virus software

The mds process was problematic primarily in Mountain Lion (MacOS 10.8) and earlier versions of the operating system. It can still be problematic on newer OS releases, but it seems to occur mostly in bursts. The mds process seems to have problems indexing certain types of files, and if a lot of them exist on a  system, it might cause the system to bottleneck as it can be extremely drive and CPU intensive. Additionally, if a user is using a system with multiple boot partitions with multiple versions of OS X on it, some the differing OS versions handle mds data differently and may force a re-index of all drives on the system subject to indexing. Indexing is used primarily by both Spotlight and TIme Machine and some other applications.

Resolution:

First, find out if mds is actually the problem. This can be done several ways:

• Use Activity Monitor (supplied with the OS) to monitor the system
• Download a copy of Spot-O-Meter from us and use it to see if there are periods of high indexing (a download may be obtained by clicking HERE)
• Monitor the system using Performance Probe which is included in the Scannerz package or may be obtained as a stand alone product. Performance Probe information may be obtained HERE.

Regardless of how you make the determination, if mds is found to be the culprit, the following techniques may be taken to minimize it:

Open up System Preferences, select the Spotlight option, and in the Privacy tab, add all the disks, volumes, or folders you don't want indexed to the list of excluded items. This will limit indexing for Spotlight but will not have any effect on Time Machine indexing if it's used. If the system is a multi-boot  system you will need to ensure the indexing limitations are consistent across all boot drives.

If you can do without Spotlight or Time Machine, ensure that Time Machine is disabled and then add all drives in the system to the excluded list for Spotlight via System Preferences as described above.

If the system is new, a fresh install, or it hasn't been used in a while, mds may initially start a full indexing session, which may take hours, and then settle down after a while. Once it's stabilized it may stop being problematic on its own. If a system is being used with only one drive or perhaps a drive an a backup drive, this should be worth a try.

If you're using a system that boots multiple partitions or frequently has external drives connected and disconnected, you may wish to try and control the indexing activity with SpotOff. Information on SpotOff may be obtained HERE.

The Icon Services Agent is a process that generates icons for every single user account on the system, even if they're redundant. When processing icon information, it can literally eat up gigabytes of data in a matter of minutes, and continue doing so until it's complete. When highly active, this process is CPU, memory, and drive intensive. The more accounts there are on a system, the more files it will generate. Icon Services Agent appeared in Mavericks (MacOS 10.9).

Resolution:

Generally this process will only be noticeably problematic during a new installation of the operating system and once in a rare while when using the system. Monitoring its activity may be done using Activity Monitor (provided with the operating system) or using Performance Probe (Performance Probe is included in the Scannerz package or may be obtained as a stand alone package. Information on Performance Probe may be obtained HERE). One negative side effect of this process is that the icon files can be several gigabytes in size and will grow with time. If the system is running low on drive space a user may need to start monitoring drive space more frequently to ensure a problem doesn't exist.

Safari Web Services and browser plugins may be extremely CPU and memory intensive. In some cases it may not really be the fault of the browser, but an abusively written set of web pages that can have the effect of "summoning up" several instances of these processes simultaneously. In most cases, the problems will stop when the browser is completely terminated.

Resolution:

This problem is typically web site specific and as stated is often the result of abusive sites. Monitoring system activity may be done using Activity Monitor (provided with the operating system) or using Performance Probe (Performance Probe is included in the Scannerz package or may be obtained as a stand alone package. Information on Performance Probe may be obtained HERE). Terminating web browsers completely should end the problem almost instantaneously

If a Time Machine backup is occurring unknown to the user, it can be responsible for a performance drop and delays. Versions of MacOS prior to Mavericks (10.9) had an icon that could be installed in the menu bar, and when a backup was occurring the icon would spin until the backup was complete, which would allow a user to know a backup was occurring. With Mavericks and later, the icon can still be placed in the menu bar but it no longer spins during a backup, and if the backup drive is out of sight or has no indicators to identify backup activity, a backup may be occurring without a users knowledge. 

Resolution:

Be aware of Time Machine and if delays are occurring, see if it's performing a backup. For systems where it may be difficult to identify this activity it may be necessary to start monitoring system activity using Activity Monitor (provided with the operating system) or using Performance Probe (Performance Probe is included in the Scannerz package or may be obtained as a stand alone package. Information on Performance Probe may be obtained HERE).

If the system has been configured to perform automatic downloads of software updates, it can appear to cause periodic, random delays. Typically during the download, network activity will go up as will disk activity, and when the installation starts, both drive and CPU activity can skyrocket. Fortunately automatic updates can usually be controlled by the user.

Resolution:

The user may either disable the features associated with automatic downloads and updates and initiate them manually. If needed, the system may be monitored for this activity using Activity Monitor (provided with the operating system) or using Performance Probe (Performance Probe is included in the Scannerz package or may be obtained as a stand alone package. Information on Performance Probe may be obtained HERE). In our opinion, this generally shouldn't be necessary because most automatic updates don't occur that frequently, but it might be worthwhile to monitor it just to ensure something else isn't wrong with the system.

Anti virus software can be notorious for causing not only delays, but sometimes lockups. Some anti-virus software needs to be "told" which applications on a system are allowed to gain access to resources. Most come preconfigured with many application and the operating system itself already allowed to run, but when a new, "foreign" application comes along that the anti-virus software doesn't recognize, it can delay it, subject it to extensive monitoring, or even block it completely until the user "tells" the anti-virus software that the application is allowed to run on the system.

Resolution:
Any time anti-virus software is being used, if "mysterious" lock ups start occurring, check the logs for the anti-virus software (if available) and see if it's blocking applications. It may be necessary to configure the anti-virus software to allow applications that appear to be intruders so they can function properly. As a quick check immediate disabling of the anti-virus software may restore the system to normal functioning. Viruses have typically not been a problem with OS X in the past, but that doesn't mean they won't be a problem in the future.

Running applications lock up for no apparent reason

If a running application locks up for no apparent reason and it's application specific it could be a bad sector on a hard drive or a bad block on an SSD. Assuming these have already been checked and no problems were found, the problem is likely with the application, a configuration setting that's changed with the application, or if the OS has just been updated, the application is no longer fully compatible with the operating system.

Resolution:

If the software is configurable, verify that none of the settings have become corrupt or set to values that would cause the application to lock up. Use Disk Utility to repair the permissions on the volumes to ensure that a permissions setting has not changed in such a manner that the application cannot read or write data as needed any longer. If an OS has been upgraded to a newer version it may be necessary to contact the vendor of the product to find out if an incompatibility exists, and what workarounds are available.

The drive is no longer recognized by the system or A boot drive will no longer boot

If a drive is no longer seen by the system or won't boot and the drive is in working order, it's likely a software problem either with the operating system or a third party driver or kernel extension. This type of problem typically occurs after either an operating system update or a driver or kernel extension update. Other possibilities include:

• A "cleanup" utility has deleted the a driver or kernel extensions as "junk" when it wasn't
• The file system permissions have been improperly modified
• Critical files have been accidentally deleted
• On MacOS 10.10 (Yosemite) and 10.11 (El Capitan) some kernel extensions may  be prohibited from loading
  

If a drive has suddenly become invisible and there were no operating system or driver updates, refer to the corresponding sections associated with the links titled Drive Problems and System Problems at the top of this page because it's very unlikely the problem is software related.

Resolution:

The first thing to do, if possible, is boot from an external drive or recovery partition and run Disk Utility to repair the permissions on the drive. If the system is using third party drivers or kernel extensions, check with the vendors website and see if they have information about possible incompatibilities and workarounds. If critical files have been deleted either accidentally or by a "cleaning" utility, the files will need to be restored.

A drive ejects itself for no apparent reason or won't mount

If the drive and system are known to be in good working order, drive ejection is most likely an operating system bug. The symptoms of this particular bug typically occur after the system goes to sleep and when it wakes up a dialog indicating the drive was improperly ejected appears. We've either seen first hand or had reports of this happening on MacOS 10.8, 10.9, and 10.10. Whether this is actually an operating system bug or hardware vendors failing to meet standards is debatable by some.

If the drive won't mount and the system and drive are known to be in good working order, it's quite possible some of the permissions on the drive have become corrupt and need to be repaired.

Resolution:

If the drive is ejecting after the system goes to sleep, in some cases the problem can be alleviated by opening System Preferences, selecting the Energy Saver option, and deselecting the Put hard disks to sleep when possible option. You may also wish to check with the drive manufacturer to see if they have a work around for the problem.

If the drive won't mount and it and the system are known to be in good working order it's most likely that a permissions setting has become corrupt. This can be corrected by booting from a recovery partition or another drive (such as an emergency boot drive, a clone, or another system using Target Mode) and using Disk Utility to correct the permissions on the drive.