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Full Discussion: File System inconsistency
Top Forums UNIX for Dummies Questions & Answers File System inconsistency Post 65464 by Perderabo on Saturday 5th of March 2005 09:12:55 AM
Old 03-05-2005
I'm not following all of this, but here are a few comments. Are you sure that /usr is mounted? Are you sure that you don't know the device name? It's not easy to find out that a file system is mounted without also obtaining the device name. For example, with the "df" command, the device name is the first field. You can just examine /etc/fstab to get the device name. But you should not actually need the device name. Modern versions of fsck will look it up in /etc/fstab. So simply:
fsck /usr
really should work.

Ideally you should find some way to umount /usr or arrange that it was never mounted prior to fsck. A boot cd (can linux really boot from a diskette?) would be a good option. You're right that running fsck on a mounted filesystem is very dangerous. This is because some of the data from that filesystem is sitting in buffer cache. When this cache is written out, it will intermix with the data written by fsck and scramble the filesystem. So you need to do the following sequence of commands:
sync
<wait 10 seconds or so>
fsck /usr
reboot -n

The first sync will flush out any changed data in / or any other mounted filesystems. You need to wait until the disk writes complete. Then run fsck.
Then immediately reboot without syncing. Also during this entire procedure, almost nothing else must be happening. It is relatively safe in single user mode. This is not completely safe, but your system is not usuable anyway, so it is what I would try. There is a risk of damaging other mounted filesystems. The first sync together with minimizing activity should mitigate this danger. If you decide to try it, please post back and let us know how it works.

However, even if this does work, you may not be home free. fsck may not be able to repair your disk. "attempt to read blocks from filesystem resulted in short read" make me think that your disk may be bad in a hardware sense. fsck cannot repair broken hardware.

Whether or not fsck seems to work, you must immediately do the "reboot -n". Good luck.
 

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LEARN ABOUT DEBIAN

ompi-clean

orte-clean(1)							     Open MPI							     orte-clean(1)

NAME

       orte-clean - Cleans up any stale processes and files leftover from Open MPI jobs.

SYNOPSIS

       orte-clean [--verbose]
       mpirun --pernode [--host | --hostfile file] orte-clean [--verbose]

OPTIONS

       [-v | --verbose] This argument will run the command in verbose mode and print out the universes that are getting cleaned up as well as pro-
       cesses that are being killed.

DESCRIPTION

       orte-clean attempts to clean up any processes and files left over from Open MPI jobs that were run in the past as  well	as  any  currently
       running jobs.  This includes OMPI infrastructure and helper commands, any processes that were spawned as part of the job, and any temporary
       files.  orte-clean will only act upon processes and files that belong to the user running the orte-clean command.  If run as root, it  will
       kill off processes belonging to any users.

       When run from the command line, orte-clean will attempt to clean up the local node it is run from.  When launched via mpirun, it will clean
       up the nodes selected by mpirun.

EXAMPLES

       Example 1: Clean up local node only.

       example% orte-clean

       Example 2: To clean up on a specific set of nodes specified on command line, it is recommended to use the pernode option.   This  will  run
       one orte-clean for each node.

       example% mpirun --pernode --host node1,node2,node3 orte-clean

       To clean up on a specific set of nodes from a file.

       example% mpirun --pernode --hostfile nodes_file orte-clean

       Example 3: Within a resource managed environment like N1GE, SLURM, or Torque.  The following example is from N1GE.

       First, we see that we have two nodes with two CPUs each.

       example% qsh -pe orte 4
       example% mpirun -np 4 hostname
       node1
       node1
       node2
       node2

       Clean up all the nodes in the cluster.

       example% mpirun --pernode orte-clean

       Clean up a subset of the nodes in the cluster.

       example% mpirun --pernode --host node1 orte-clean

SEE ALSO

       orterun(1), orte-ps(1)

1.4.5								   Feb 10, 2012 						     orte-clean(1)
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