Re: newbie problems

From: Rayson Ho <no email>
Date: Mon, 21 May 2012 16:09:15 -0400

Hi Manal & Ron,

The StarCluster way to partition & format an EBS vol is documented at:

"Create and Format a new EBS Volume"

http://web.mit.edu/star/cluster/docs/latest/manual/volumes.html#create-and-format-a-new-ebs-volume


And Ron mentioned the /dev/sda -> /dev/xvd mapping. If you want to
mount the EBS volume manually, you will need to read this in the
Amazon documentation, "... if the kernel has xvd drivers, then the
devices will be mapped to xvd[a-p]. If the kernel does not have xvd
drivers, then the devices will be mapped to sd[a-z][1-15]":

http://docs.amazonwebservices.com/AWSEC2/latest/UserGuide/ebs-attaching-volume.html

Since the kernels we run have the xvd driver (Xen Virtual Disk - the
virtual block-device), you will find that the mapping is different
than the one you see in the AWS Management Console.

Rayson

================================
Open Grid Scheduler / Grid Engine
http://gridscheduler.sourceforge.net/

Scalable Grid Engine Support Program
http://www.scalablelogic.com/




On Mon, May 21, 2012 at 3:44 PM, Ron Chen <ron_chen_123_at_yahoo.com> wrote:
> Manal,
>
> Note: I am only a developer of Open Grid Scheduler, the open source Grid Engine. I am not exactly a EC2 developer yet, and may be there are better ways to do it in StarCluster.
>
> Did you format your EBS? Like a new harddrive, you need to fdisk & format it before you can use it.
>
> - So first, logon to the EC2 Management Console. Then go to your EBS Volumes.
>
> - Then check the state, if it is in-use then it is already attached to an instance. If it is available, then StarCluster has not attached it yet.
>
> - After you are sure it is attached, the Attachment section should show something similar to the following:
>
>    Attachment: i-39586e5f (master):/dev/sdf1 (attached)
>
>
>
> And now you need to partition the disk.
>
> - If you see /dev/sdf1 above, you need to partition /dev/xvdf as the AMIs have the xvd drivers:
>
> # fdisk /dev/xvdf
>
>
> Then you can format the disk using mkfs.
>
> # mkfs -t ext4 /dev/xvdf1
>
>
> So finally, you can mount the disk, and if you specify the volume in the StarCluster config correctly, then it will be mounted next time you boot StarCluster.
>
>  -Ron
>
>
>
>
>
> ________________________________
> From: Manal Helal <manal.helal_at_gmail.com>
> To: Justin Riley <jtriley_at_mit.edu>
> Cc: starcluster_at_mit.edu
> Sent: Monday, May 21, 2012 7:41 AM
> Subject: Re: [StarCluster] newbie problems
>
>
> Hello,
> I hate being a headache, but this didn't go smooth as I was hoping, and I appreciate your support to get moving,
>
> I finally successfully attached the volume I created, but didn't see where it should be on the cluster, and how my data will be saved from session to session,
>
> The volume I created is a 30 GB, I first mounted it to /mydata, and didn't see this when I started the cluster, this is what I get:
>
> root_at_ip-10-16-3-102:/dev# fdisk -l
>
> Disk /dev/sda: 8589 MB, 8589934592 bytes
> 255 heads, 63 sectors/track, 1044 cylinders, total 16777216 sectors
> Units = sectors of 1 * 512 = 512 bytes
> Sector size (logical/physical): 512 bytes / 512 bytes
> I/O size (minimum/optimal): 512 bytes / 512 bytes
> Disk identifier: 0x00000000
>
>    Device Boot      Start         End      Blocks   Id  System
> /dev/sda1   *       16065    16771859     8377897+  83  Linux
>
> Disk /dev/xvdb: 901.9 GB, 901875499008 bytes
> 255 heads, 63 sectors/track, 109646 cylinders, total 1761475584 sectors
> Units = sectors of 1 * 512 = 512 bytes
> Sector size (logical/physical): 512 bytes / 512 bytes
> I/O size (minimum/optimal): 512 bytes / 512 bytes
> Disk identifier: 0x00000000
>
> Disk /dev/xvdb doesn't contain a valid partition table
>
> Disk /dev/xvdc: 901.9 GB, 901875499008 bytes
> 255 heads, 63 sectors/track, 109646 cylinders, total 1761475584 sectors
> Units = sectors of 1 * 512 = 512 bytes
> Sector size (logical/physical): 512 bytes / 512 bytes
> I/O size (minimum/optimal): 512 bytes / 512 bytes
> Disk identifier: 0x00000000
>
> Disk /dev/xvdc doesn't contain a valid partition table
>
> root_at_ip-10-16-3-102:/dev# df -h
> Filesystem            Size  Used Avail Use% Mounted on
> /dev/sda1             7.9G  5.1G  2.5G  68% /
> udev                   12G  4.0K   12G   1% /dev
> tmpfs                 4.5G  216K  4.5G   1% /run
> none                  5.0M     0  5.0M   0% /run/lock
> none                   12G     0   12G   0% /run/shm
> /dev/xvdb             827G  201M  785G   1% /mnt
>
>
>
> no 30GB volume attached, then I terminated and followed the suggestions in this page:
>
> http://web.mit.edu/star/cluster/docs/latest/manual/configuration.html
>
> making it mount to /home thinking it will be used in place of the /home folder, and this way all my installations and downloads will be saved after I terminate the session,
>
> however, when I started the cluster this is what I get:
>
> root_at_ip-10-16-24-98:/home# df -h
> Filesystem            Size  Used Avail Use% Mounted on
> /dev/sda1             7.9G  5.1G  2.5G  68% /
> udev                   12G  4.0K   12G   1% /dev
> tmpfs                 4.5G  216K  4.5G   1% /run
> none                  5.0M     0  5.0M   0% /run/lock
> none                   12G     0   12G   0% /run/shm
> /dev/xvdb             827G  201M  785G   1% /mnt
>
>
> There is no 30 GB volume as well, and neither / nor /mnt are getting bigger,
>
> here is what I am having in my config file:
>
> [cluster mycluster]
> VOLUMES = mydata
>
>
> [volume mydata]
> # attach vol-c9999999 to /home on master node and NFS-shre to worker nodes
> VOLUME_ID = vol-c9999999 #(used the volume ID I got from the AWS console)
> MOUNT_PATH = /home  #(not sure if this is true or not, I used /mydata in the first run and didn't work as well)
>
> also when I was running before attaching the volume, I had starcluster put and starcluster get commands working very well. After attaching the volume, I had them working and saying 100% complete on my local machine, but when I log in to the cluster, I find the paths where I was uploading the files to, empty, no files went through! I am not sure if this is related to attaching the volume and whether there should be anything I need to do
> P.S. I noticed in the ec2 command line tools to attach a volume to an instance, I should define the volume ID, the instance ID and the device ID (/dev/sdf), same as found in the aws online console. However, the mount path in the starcluster configuration file, doesn't seem to be a device ID that should have been (/dev/sdf) for linux as far as I understand. Not sure where to define this in starcluster if this is the missing point,
>
> I appreciate your help  very much,
>
> thanks again,
>
> Manal
>
>
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Received on Mon May 21 2012 - 16:09:20 EDT