My 13" Mac Pro behaves like everything is in slow motion. Takes forever to do anything, on or offline. Would this be a software conflict or a hardware problem?

My 13" Mac Pro behaves like everything is in slow motion. Takes forever to do anything. Wondering if this is a software issue or a hard drive problem?

Maybe some maintenance will help:
Kappy's Personal Suggestions for OS X Maintenance
For disk repairs use Disk Utility.  For situations DU cannot handle the best third-party utilities are: Disk Warrior;  DW only fixes problems with the disk directory, but most disk problems are caused by directory corruption; Disk Warrior 4.x is now Intel Mac compatible. TechTool Pro provides additional repair options including file repair and recovery, system diagnostics, and disk defragmentation.  TechTool Pro 4.5.1 or higher are Intel Mac compatible;  Drive Genius is similar to TechTool Pro in terms of the various repair services provided.  Versions 1.5.1 or later are Intel Mac compatible.
OS X performs certain maintenance functions that are scheduled to occur on a daily, weekly, or monthly period. The maintenance scripts run in the early AM only if the computer is turned on 24/7 (no sleep.) If this isn't the case, then an excellent solution is to download and install a shareware utility such as Macaroni, JAW PseudoAnacron, or Anacron that will automate the maintenance activity regardless of whether the computer is turned off or asleep.  Dependence upon third-party utilities to run the periodic maintenance scripts had been significantly reduced in Tiger and Leopard.  These utilities have limited or no functionality with Snow Leopard and should not be installed.
OS X automatically defragments files less than 20 MBs in size, so unless you have a disk full of very large files there's little need for defragmenting the hard drive. As for virus protection there are few if any such animals affecting OS X. You can protect the computer easily using the freeware Open Source virus protection software ClamXAV. Personally I would avoid most commercial anti-virus software because of their potential for causing problems.
I would also recommend downloading the shareware utility TinkerTool System that you can use for periodic maintenance such as removing old logfiles and archives, clearing caches, etc.  Other utilities are also available such as Onyx, Leopard Cache Cleaner, CockTail, and Xupport, for example.
For emergency repairs install the freeware utility Applejack.  If you cannot start up in OS X, you may be able to start in single-user mode from which you can run Applejack to do a whole set of repair and maintenance routines from the commandline.  Note that AppleJack 1.5 is required for Leopard. AppleJack 1.6 is compatible with Snow Leopard.
When you install any new system software or updates be sure to repair the hard drive and permissions beforehand. I also recommend booting into safe mode before doing system software updates.
Get an external Firewire drive at least equal in size to the internal hard drive and make (and maintain) a bootable clone/backup. You can make a bootable clone using the Restore option of Disk Utility. You can also make and maintain clones with good backup software. My personal recommendations are (order is not significant):
Backuplist
Carbon Copy Cloner
Data Backup
Deja Vu
iBackup
JaBack
Silver Keeper
MimMac
Retrospect
Super Flexible File Synchronizer
SuperDuper!
Synchronize Pro! X
SyncTwoFolders
Synk Pro
Synk Standard
Tri-Backup
Visit The XLab FAQs and read the FAQs on maintenance, optimization, virus protection, and backup and restore.
Additional suggestions will be found in Mac Maintenance Quick Assist.
Referenced software can be found at CNet Downloads or MacUpdate.

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