LinuxQuestions.org
Share your knowledge at the LQ Wiki.
Go Back   LinuxQuestions.org > Forums > Linux Forums > Linux - Newbie
User Name
Password
Linux - Newbie This Linux forum is for members that are new to Linux.
Just starting out and have a question? If it is not in the man pages or the how-to's this is the place!

Notices


Reply
  Search this Thread
Old 11-13-2010, 02:00 PM   #1
yaximik
Member
 
Registered: Nov 2010
Posts: 87

Rep: Reputation: 0
Lost in space


[FONT="Courier New"]Hello all,

My 64bit Dell box with RHEL5.5 came with 4 500GB HDs (SCSI), so I expected to have 2TB of storage space. So I was surprized that I run out of storage space when I tried to download human genome data (about 10 GB) . Since then I am trying to figure out where is all this extra space. Here what I tried:

Check physical presence of disks - dmesg report shows presence of 4 Seagate 500GB disks

Check partitions - parted print shows the following output:
Number--Start-----End------Size-----Type------File System--Flags
1-------32.3kB----82.3MB---82.2MB---primary---fat16
2-------82.3MB----5453MB---5371MB---primary----------------lvm
3-------5651MB----5914MB---263MB----primary---ext3---------boot
4-------5914MB----1499GB---1493GB---extended
5-------5980MB----38.2GB---32.2GB---logical----------------lvm
So, it comes to about 1.5TB total, not 2TB, but it still should be plenty.

Checking LVM - this is the summary what is shown in the LVM vindows:

VolGroup00 has 2 Physical Volumes

sda2 (5GB, all Unused space, 160 Physical Extents, Allocated 0)
sda5 (30GB, 960 Physical Extents, Allocated 960)

sda2 holds 6 Logical Volumes:
LogVol00 (4GB, 1 segment, /root filesystem, ext3)
LogVol01 (3.69GB, 1 segment, unmounted, swap)
LogVol02 (4GB, 1 segment, /usr, ext3)
LogVol03 (3GB, 1 segment, /tmp, ext3)
LogVol04 (4GB, 1 segment, /var, ext3)
LogVol05 (11.31GB, 1 segment, /home, ext3)

Uninitialized Entities:
/dev/sda

partition 1 (/dev/sda1, 0.08GB, Dell Utility, unmounted, no filesystem)

Partition 3 (/dev/sda3, 0.25GB, Linux, /boot, no filesystem, Not Initializable:Foreign boot partition)

Partition 4 (/dev/sda4, 1390.24GB, Extended, unmounted, no filesystem, Not Initializable:Extended partition)

Unpartitioned Space (/dev/sda, 1360.17GB, no partition, unmounted, no filesystem, Not Initializable:Partition manually)

Unpartitioned Space (/dev/sda, 0.06GB, no partition, unmounted, no filesystem, Not Initializable:Partition manually)

Unpartitioned Space (/dev/sda, 0.18GB, no partition, unmounted, no filesystem, Not Initializable:Partition manually)

First - how much is the total space?

dmesg report - 2TB (4x 500GB HD)
parted report - ~1.5TB
LVM report - ~1.4TB (partitioned) + ~1.4TB (unpartitioned) = 2.8TB ??

Second - I tried to follow RedHat Deployment Guide (LVM section) with no avail. Uninitialized partition 4 is not initializable (already initialized as Extended?), but it is not shown as Unallocated, so I cannot do anything with it - it just sits there with all buttons greyed out. Cannot do anything with Unpartitioned space either - all buttons greyed out; and where these extra 0.8TB came from? For making a new LogVol I have only 5GB free space and migrating Extents is allowed only within the allocated ~35GB space.

Perhaps there is no issue at all, but I cannot quite figure it out by myself, so I would appreciate someone more experienced shows me a way out of this maze. If this is not of a general interest, please use my e-mail.

Thanks,

yaximik
 
Old 11-13-2010, 04:04 PM   #2
stress_junkie
Senior Member
 
Registered: Dec 2005
Location: Massachusetts, USA
Distribution: Ubuntu 10.04 and CentOS 5.5
Posts: 3,873

Rep: Reputation: 332Reputation: 332Reputation: 332Reputation: 332
This is definitely of general interest. This is an LVM issue.

I'm not an expert in LVM but here's what I noticed when I read your post.

Quote:
VolGroup00 has 2 Physical Volumes
That accounts for two of the four disks. The other two aren't mentioned. That's half of your space right there.

Quote:
Unpartitioned Space (/dev/sda, 1360.17GB, no partition, unmounted, no filesystem, Not Initializable:Partition manually)

Unpartitioned Space (/dev/sda, 0.06GB, no partition, unmounted, no filesystem, Not Initializable:Partition manually)

Unpartitioned Space (/dev/sda, 0.18GB, no partition, unmounted, no filesystem, Not Initializable:Partition manually)
Maybe you need to create partitions in this space using LVM. Or maybe you can extend an existing partition into this space.

My limited understanding of LVM includes the notion that you can dynamically resize LVM partitions without losing data. Maybe these uninitialized spaces are part of the LVM smoke and mirrors that allows dynamic partition resizing.

http://www.tcpdump.com/kb/os/linux/l...ide/intro.html
 
Old 11-13-2010, 05:00 PM   #3
yaximik
Member
 
Registered: Nov 2010
Posts: 87

Original Poster
Rep: Reputation: 0
I assumed that too at first, but I cannot figure out how to make usable both the partitioned and unpartitioned space. Even if I am logged in as root all options are greyed out...
 
Old 11-13-2010, 05:17 PM   #4
stress_junkie
Senior Member
 
Registered: Dec 2005
Location: Massachusetts, USA
Distribution: Ubuntu 10.04 and CentOS 5.5
Posts: 3,873

Rep: Reputation: 332Reputation: 332Reputation: 332Reputation: 332
Have you tried using EVMS? It is an extension of LVM. EVMS is compatible with LVM.
 
Old 11-14-2010, 08:20 AM   #5
hughetorrance
Member
 
Registered: Aug 2009
Location: London North West
Distribution: x86_64 Slack 13.37 current : +others
Posts: 459

Rep: Reputation: 59
Talking What does it look like .... ?

here is mine,take a screen shot of yours and post it here.
Attached Thumbnails
Click image for larger version

Name:	Partitions.jpg
Views:	19
Size:	124.2 KB
ID:	5178  
 
Old 11-14-2010, 09:33 AM   #6
AwesomeMachine
Senior Member
 
Registered: Jan 2005
Location: USA and Italy
Distribution: Debian testing/sid; OpenSuSE; Fedora
Posts: 1,832

Rep: Reputation: 259Reputation: 259Reputation: 259
An extended partition is used to create more than four partitions on a physical drive. Each partition table has room for four primary partitions. So, the extended partition allows you to make logical volumes while using only one primary partition. You must make logical volumes inside the extended partition, and then format them with whichever file system you want to use--which is another discussion. Gparted or qtparted should help you out. Then, if you want to add the new storage to the volume group, you use special tools designed for that purpose.
 
Old 11-14-2010, 10:33 AM   #7
catkin
LQ 5k Club
 
Registered: Dec 2008
Location: Tamil Nadu, India
Distribution: Debian
Posts: 8,576
Blog Entries: 31

Rep: Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195
Quote:
Originally Posted by yaximik View Post
Check partitions - parted print shows the following output:
Code:
Number--Start-----End------Size-----Type------File System--Flags
1-------32.3kB----82.3MB---82.2MB---primary---fat16
2-------82.3MB----5453MB---5371MB---primary----------------lvm
3-------5651MB----5914MB---263MB----primary---ext3---------boot
4-------5914MB----1499GB---1493GB---extended
5-------5980MB----38.2GB---32.2GB---logical----------------lvm
That looks like incomplete information about a single storage volume. Are the physical HDDs being combined into a single volume? RAID? What was the exact parted command line? Please post all the output of parted -l. BTW, it is easier to read that sort of output when it is posted in code tags (that's a link to instructions or you may prefer to use "Advanced Edit" mode which has a # button for code tags).
Quote:
Originally Posted by yaximik View Post
Checking LVM - this is the summary what is shown in the LVM vindows:

VolGroup00 has 2 Physical Volumes

sda2 (5GB, all Unused space, 160 Physical Extents, Allocated 0)
sda5 (30GB, 960 Physical Extents, Allocated 960)

sda2 holds 6 Logical Volumes:
LogVol00 (4GB, 1 segment, /root filesystem, ext3)
LogVol01 (3.69GB, 1 segment, unmounted, swap)
LogVol02 (4GB, 1 segment, /usr, ext3)
LogVol03 (3GB, 1 segment, /tmp, ext3)
LogVol04 (4GB, 1 segment, /var, ext3)
LogVol05 (11.31GB, 1 segment, /home, ext3)
That doesn't make sense; it says there's ~30 GB of LVs in 5GB of space! Please post the output of pvdisplay and vgdisplay (in code tags!).
Quote:
Originally Posted by yaximik View Post
Uninitialized partition 4 is not initializable (already initialized as Extended?)
The extended partition is simply a container for the logical partition table so has no usable storage space.
Quote:
Originally Posted by yaximik View Post
For making a new LogVol I have only 5GB free space and migrating Extents is allowed only within the allocated ~35GB space.
That is correct but there's a lot of unused space which could be used -- either directly, or given that LVM is already in use, for the LVM storage "pool".

Quote:
Originally Posted by yaximik View Post
For making a new LogVol I have only 5GB free space and migrating Extents is allowed only within the allocated ~35GB space.
The simplest, most flexible configuration would be to have a single partition for LVM, using all the space in the extended partition. The steps to get there would be (subject to verification, especially you may not have the pvresize command; IDK RHEL5.5):
  1. Extend the logical partition (sda5) to take up the whole of the extended partition.
  2. pvresize it.
  3. lvmove the LVs from the sda2 PV to the sda5 PV.
  4. pvremove sda2.
It is always prudent to have a tested backup (one you have restored from); it is especially prudent when manipulating LVM which very occasionally goes wrong.
 
Old 11-14-2010, 02:11 PM   #8
yaximik
Member
 
Registered: Nov 2010
Posts: 87

Original Poster
Rep: Reputation: 0
Oops, that was mistake, /dev/sda5 has 6 logical volumes, not sda2. Certaily it did not make sense.
I have no previous exposure to Linux, so perhaps one cannot be newbeer than I am. Our IT folks do not support Linux, so I am banging my head as I am learning on fly how to deploy RHEL5.5 that came preinstalled on the 64-bit Dell box. It certanly would be more informative to post screenshoots or command outputs, but I need to learn first how to do all that on the Linux box. Right now I communicate from my Windows laptop simply repeating what I see on Linux screen.

I know what should be done, the problem I do not yet know HOW to do that. I have no idea what factory folks were thinking when making partitions the box came with - why only 35 GB out of 2TB was allocated the way it is, and the rest of space is visible but unreachable. Like I said, I followed RedHat deployment guide, which says how to use LVM to manage space. But the problem is that instruction in the guide seem useless since all the buttons and menus in the LVM window are greyed out. There would not be a need to come here for help if I could proceed as instructed. I used parted with default options to get that output I provided - /sbin/parted -I followed by pprint produces the same output. I just omitted the following top lines of the output:

Model: DELL PERC 6/1 (scsi)
Disk /de/sda: 1499GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Then goes the table I provided above. Why only 1499GB is listed instead of 2000GB? Perhaps one of four 500GB HDs is not partitioned, but in the LVM window Unpartitioned space is ~1400GB in total, not 500GB. In total, it looks like Uninitialized Entities (partitionad and unpartitioned) hold ~2800GB space (as per LVM window), but the box came with four 500GB HDs, so numbers do not add up. Any advice?

Anyway I downloaded Gparted, so I try it first after I install it and figure out how to use it. I also found the qtparted site, so I am going have more headbanging fun today.

Thanks for your input, folks. Please be patient with my naivety.
 
Old 11-14-2010, 02:44 PM   #9
catkin
LQ 5k Club
 
Registered: Dec 2008
Location: Tamil Nadu, India
Distribution: Debian
Posts: 8,576
Blog Entries: 31

Rep: Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195Reputation: 1195
Quote:
Originally Posted by yaximik View Post
Our IT folks do not support Linux, so I am banging my head as I am learning on fly how to deploy RHEL5.5 that came preinstalled on the 64-bit Dell box. It certanly would be more informative to post screenshoots or command outputs, but I need to learn first how to do all that on the Linux box. Right now I communicate from my Windows laptop simply repeating what I see on Linux screen.
Hopefully we can help you along and you will enjoy the learning adventure. Interesting to learn this is a default factory installation. Ouch! Hard work typing all that -- the sooner you find out how to copy and paste the better. In most graphical terminal emulators you highlight the text with the mouse. Sometimes that alone automatically copies it to the paste buffer, sometimes you need something like Ctrl+Shift+C to copy it. Once in a web browser it's the usual Ctrl+V to paste.
Quote:
Originally Posted by yaximik View Post
I have no idea what factory folks were thinking when making partitions the box came with - why only 35 GB out of 2TB was allocated the way it is, and the rest of space is visible but unreachable. Like I said, I followed RedHat deployment guide, which says how to use LVM to manage space. But the problem is that instruction in the guide seem useless since all the buttons and menus in the LVM window are greyed out.
They probably did it that way to give the customer choice in how to use the remaining space. IDK RHEL5.5 but graphical LVM front ends generally are not very robust. Mostly VM is advantageous on high-availability servers and sysadmins on that type of machine tend to use the command line so the graphical LVM front ends don't get that much testing and, if they don't work as expected, it's no big deal. The greyed out extended partition is correctly greyed out.
Quote:
Originally Posted by yaximik View Post
I used parted with default options to get that output I provided - /sbin/parted -I followed by pprint produces the same output. I just omitted the following top lines of the output:

Model: DELL PERC 6/1 (scsi)
Disk /de/sda: 1499GB
Sector size (logical/physical): 512B/512B
Partition Table: msdos

Then goes the table I provided above. Why only 1499GB is listed instead of 2000GB? Perhaps one of four 500GB HDs is not partitioned, but in the LVM window Unpartitioned space is ~1400GB in total, not 500GB. In total, it looks like Uninitialized Entities (partitionad and unpartitioned) hold ~2800GB space (as per LVM window), but the box came with four 500GB HDs, so numbers do not add up. Any advice?
So the physical HDDs have been agglomerated into a single volume which is normally done for resilience using RAID but taking 4x500 physical HDDs and ending up with a 1500 volume is strange. Is there anything in the documentation about this for this specific model? Could it be that the missing capacity is used for parity-checking?
Quote:
Originally Posted by yaximik View Post
Anyway I downloaded Gparted, so I try it first after I install it and figure out how to use it. I also found the qtparted site, so I am going have more headbanging fun today.
Many people are happy with gparted but I have found it unreliable and prefer the command line tools.
Quote:
Originally Posted by yaximik View Post
Thanks for your input, folks. Please be patient with my naivety.
Patience mode on (we all had to start once).
 
Old 12-29-2010, 04:52 PM   #10
dynamphorous
LQ Newbie
 
Registered: Dec 2010
Posts: 1

Rep: Reputation: 0
Has anyone figured this out?
I got a redhat system from Dell for the first time yesterday, so I am a complete noob when it comes to RedHat. I have been using Gentoo for years and years now, and have never had to deal with this "logical volume" stuff. Fdisk is out of the question becuase if you change the type of partition 4, it destroys partition 5. I cant believe that right out of the box they would give you a system where most of the primary drive is tied up in a format where you cant get to it, and they dont leave you even basic instructions or tools for how to access it!
 
  


Reply


Thread Tools Search this Thread
Search this Thread:

Advanced Search

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is Off
HTML code is Off



Similar Threads
Thread Thread Starter Forum Replies Last Post
Lost space kd5pbo Slackware 9 12-27-2006 05:05 PM
Lost space on HD Mitsuhashi Linux - General 7 08-01-2006 05:32 PM
lost space to partitioning? chipmonk010 Linux - Hardware 1 09-04-2005 09:38 PM
ccd - lost space? hw-tph *BSD 4 08-12-2005 06:58 PM
3Gb of disk space lost! Disk space problem or mother board conflicts with HDD Mistreated Linux - Hardware 4 12-06-2004 04:58 PM


All times are GMT -5. The time now is 06:39 AM.

Main Menu
Advertisement
My LQ
Write for LQ
LinuxQuestions.org is looking for people interested in writing Editorials, Articles, Reviews, and more. If you'd like to contribute content, let us know.
Main Menu
Syndicate
RSS1  Latest Threads
RSS1  LQ News
Twitter: @linuxquestions
Facebook: linuxquestions Google+: linuxquestions
Open Source Consulting | Domain Registration