Hi guys...
Joe Landman wrote:
Hi Chris
Christopher Dwan wrote:
* Hack MPIBlast code to change the file permissions on the MBF files
(seems reasonable, but there must be some reason why it's not
already done. Probably concerns about users stepping on each
other's jobs).
This is something I ran into ~3 years ago with early versions. Users
would stamp all over others runs, and complain that the cluster was
broken.
There is no satisfactory solution other than isolation. Isolation
effectively defeats caching. If we break out the file distribution
(or more accurately, the chunk distribution) from mpiblast, you may
be able to have another lower layer work on it, but that layer would
need to be designed.
An alternative (but a very bad one for a number of reasons) is to have
all users have the same group, and give every one group read/write
permission into the cache directory. You want to avoid any scenario
which does this due to the potential for users to step on each other,
and the complete lack of access control that such a scheme requires to
function.
I think the problem of users stepping on each other can be avoided
through file locking. When one user's mpiblast job wants to change the
.mbf it should get a read/write lock on the file, and likewise, when
another user's mpiblast job simply wants to read the .mbf it can get a
read lock.
We actually tried to implement that in the 1.3.0 release of mpiblast but
ran into trouble when the "local" storage directory was set to an NFS
mount. NFS supposedly supports file locking but it turned out to be
very flakey in our experience, occasionally locking up the NFS server
completely. Whether the problem was on our end (e.g. we didn't
understand the NFS file locking API) or their end (bugs in linux nfs
lockd) was something we never sorted out completely. In any case, the
locking code is still in mpiblast and can be enabled with the --lock option.
File locking doesn't really solve the access control problem, however
perhaps the file permissions could be configured such that any user can
add to the cache, but only an admin can clear the cache? This could
potentially be done with finer grained ACLs such as those offered by AFS...
-Aaron
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