[Beowulf] Project Planning: Storage, Network, and Redundancy Considerations

Brian R. Smith brs at usf.edu
Mon Mar 19 12:49:34 PDT 2007


Mike Davis wrote:
> Brian,
> My personal preference is to keep scratch on the compute nodes 
> whenever possible. This reduces network traffic dramatically. The 
> method that we use for this is to write wrappers for our more common 
> applications (VASP, G03, DeMon) setting scratch to /tmp on the nodes. 
> For interactive work such as abaqus the env variables are set to you 
> /tmp as well.
I usually provide both.  Some parallel applications that we run write
simultaneously to one file or another and others don't (maybe each
process writes out multiple files or simply hits the file system really
hard).  We have PVFS2 for parallel scratch and we provide /slocal as a
local disk alternative (apps like Schrodinger's Jaguar & Qsite run very
well under a local scratch configuration).  The solution I'm looking for
will (hopefully) replace our need for an independent parallel scratch
and /home storage. It would be good if we could run both off of one
filesystem (you know, administrative overhead and stuff).

> We do not make use of Myranet or infiniband at this time and we have 
> 120 current nodes on one HP modular switch (combo of dual single and 
> dual dual opterons). I have another 70 dual duals and one 8way dual to 
> add this year.
> One thing that you might consider for performance is a completely 
> separate nfs network. Connecting all nodes to a switch with a 10gb 
> gbic that connects to the thumper or other storage device.
This is a possibility...  It would be easy to roll out and would provide
great benefit for file system use (that and all of our nodes now have
dual GigE links).
> We use zfs for some purposes (/home on a number of research machines 
> sharing a 5.6TB storage unit with a v40z frontend and nfs) but until 
> now the clusters still use ext3 (yes, I know that there are problems).
I was looking into zfs, but the linux "client" appears to run via FUSE.
I've heard good things but I've also heard a couple not-so-good things
about the performance of userspace file system access.  Your thoughts?
> I've thought that Mississippi State's design with individual rack 
> gigabit switches connected by 10gb gbics was interesting. But we are 
> getting good performance with all of the nodes connected at 1gb to a 
> single switch and I think that it is easier to manage.
I agree with this point about the single switch.  If its possible for us
to do this, I would prefer to go that route.  Otherwise, we have a
couple other plans up our sleeves.
Thanks for your suggestions!

> Mike Davis
> Brian R. Smith wrote:
>> Hey list,
>> I am seeking some advice regarding our latest project.  Currently, 
>> our shop runs 5 different clusters of varying size and handles the 
>> maintenance and administration of each.  I've been planning for some 
>> time to finally consolidate all of these machines together under a 
>> single head-node with a common storage pool (for /home, /opt, 
>> /usr/local), utilizing SGE for our resource management.  A lot of 
>> times on this list, the point comes up that many things depend upon 
>> your applications so I'll make it clear here:  Our "application" is 
>> quite varied.  Our users come from a wide variety of disciplines and 
>> the nature of our group is as a sort of tier-2 scientific computing 
>> lab where we provide hardware, development environments, and support 
>> for developing and running applications of various nature hence 
>> general-purpose.
>> We have fairly robust systems in place for node provisioning (an 
>> in-house system that utilizes kickstart and anaconda that supports 
>> multiple architectures), resource management (SGE has proven 
>> extremely reliable and more than capable of managing our fairly 
>> quaint resources).
>> Currently, my two largest problems are figuring out our storage needs 
>> (in terms of device bandwidth and throughput) and our network needs.  
>> When all is said and done, this is the hardware I expect to have:
>> ~60x 16GiB RAM, Dual-Dual-Core AMD Opterons, IB-connected, 
>> GigE-connected, with modest local storage
>> 8x 16GiB RAM, Dual-Dual-Core AMD Opterons & 24x 8GiBRAM, 
>> Dual-Opterons, Myrinet-connected, GigE-connected, modest storage 
>> (cluster1)
>> We wish to add to this cluster the following existing configurations:
>> 12x AMD Opteron 246, 4GiB RAM, Myrinet-connected, etc. (cluster2)
>> 38x AMD Opteron 246, 4GiB RAM, GigE-connected (clusters 3 & 4)
>> ~40x Intel P4 Xeon @2.66GHz, 2GiB RAM, GigE-connected (cluster5)
>> Yes, I know the last sets of machines are approaching (or already 
>> are) legacy status (especially the last batch), but these machines 
>> are still useful at running the problems they were originally 
>> purchased for (especially the Opterons), and are still very good at 
>> some other general tasks (Distributed Matlab, commercial FE codes, 
>> instructional use, etc).
>> Currently, each cluster has its own local storage, averaging about a 
>> 1TB on each.  We've currently got about 4TB of total data across all 
>> of these machines but anticipate this number possibly doubling with 
>> in the next 12-18 months.  The first phase of this plan (which must 
>> occur in concert with the second) is to consolidate all of these 
>> disparate arrays into one volume that is accessible by every node in 
>> the cluster.  I know that some of the supercomputing centers like 
>> NCSA have dealt with much larger-scale storage issues than this so 
>> I'd love to hear from one of you.  The current ideas that we have 
>> been floating around include the following:
>> 1. Proprietary parallel storage systems (like Panasas, etc.):  It 
>> provides the per-node bandwidth, aggregate bandwidth, caching 
>> mechanisms, fault-tolerance, and redundancy that we require (plus 
>> having a vendor offering 24x7x365 support & 24 hour turnover is quite 
>> a breath of fresh air for us).  Price point is a little high for the 
>> amount of storage that we will get though, little more than doubling 
>> our current overall capacity.  As far as I can tell, I can use this 
>> device as a permanent data store (like /home) and also as the user's 
>> scratch space so that there is only a single point for all data needs 
>> across the cluster.  It does, however, require the installation of 
>> vendor kernel modules which do often add overhead to system 
>> administration (as they need to be compiled, linked, and tested 
>> before every kernel update).
>> 2. Separate /home and /scratch volumes.  /home would be NFS exported 
>> read-only to all hosts (to prevent writes during run-time).  The 
>> volume would reside on one or two file servers (Sun's Thumper/X4500, 
>> etc. either on JFS or GFS (or perhaps ZFS???), depending on hardware) 
>> and at current prices, we would be able to acquire around 20TB.  We 
>> would double this purchase and provide the same setup off-site for 
>> redundancy (including our tape-backup regime).  Bandwidth for reads 
>> is more than sufficient for the needs of our current users.  The 
>> scratch space would be comprised of 8-12 nodes with 0.5 TB RAID1 
>> storage utilizing either PVFS2 (which has worked exceptionally well 
>> for us previously) or Lustre (which we have not tested very well 
>> yet).  Both require separate kernel modules (this seems to be a 
>> recurring theme) and hence some additional administration.  Neither 
>> are well-suited for general tasks such as compiling (though there are 
>> ways around this) or problems involving many short writes, but most 
>> of the applications being run do not fit this profile.  8-12 nodes 
>> should provide us between 3-6TB of usable scratch.  We would like a 
>> little more, but again, this is sufficient for our current usage 
>> patterns.  The pricing for this might be somewhat less than the 
>> proprietary system described above.
>> Can anyone suggest any other approaches to this problem?
>> We also have a problem regarding how to link these clusters together 
>> over a single network fabric (GigE).  It will be possible for all 
>> nodes to utilize this network for Message Passing, but it is highly 
>> improbable that such a scenario will ever be played out since almost 
>> all of our MPI jobs will no doubt run on either the Infiniband our 
>> Myrinet nodes (there are SGE policies in place to help ensure this).
>> Currently, each cluster has its own GigE network for provisioning, 
>> administration, and resource management.  Some of these hosts utilize 
>> it for communications (clusters 3, 4, & 5) and all of them will no 
>> doubt need to utilize it for filesystem access.  Clusters 3 and 4 can 
>> be consolidated to a single GigE HP switch that will have a couple of 
>> ports left over.  Cluster 5 will have to be kept as-is and clusters 1 
>> and 2 will fit on a single switch as well.  I have discussed with our 
>> campus network admin the possibility of using two recent cisco 
>> switches that would support failover and load balancing as a 
>> redundant and high-bandwidth "trunk" for each of these networks, 
>> obviously with the capacity to grow in the future.  Each of our 
>> existing 3 switches would have up to two links to each "trunk" switch 
>> and our file servers (in which ever configuration we eventually 
>> choose) would also be attached to these switches.  There should be 
>> enough bandwidth to go around under this plan.  I'm just curious if 
>> this seems doable and if it is, are there any obvious pitfalls that I 
>> have overlooked?  Is there perhaps a better way to approach this 
>> (perhaps a single, large switch instead)?
>> Our final problem is a relatively simple one though I am definitely a 
>> newbie to the H.A. world.  Under this consolidation plan, we will 
>> have only one point of entry to this cluster and hence a single point 
>> of failure.  Have any beowulfers had experience with deploying 
>> clusters with redundant head nodes in a pseudo-H.A. fashion 
>> (heartbeat monitoring, fail-over, etc.) and what experiences have you 
>> had in adapting your resource manager to this task?  Would it simply 
>> be more feasible to move the resource manager to another machine at 
>> this point (and have both headnodes act as submit and administrative 
>> clients)?  My current plan is unfortunately light on the details of 
>> handling SGE in such an environment.  It includes purchasing two 
>> identical 1U boxes (with good support contracts).  They will monitor 
>> each other for availability and the goal is to have the spare take 
>> over if the master fails.  While the spare is not in use, I was 
>> planning on dispatching jobs to it.
>> There are a number of unfilled blanks in this plan currently (and I 
>> have a month with which to fine-tune the rest of this) and so if 
>> anyone would be kind enough to offer suggestions on how to fill in a 
>> few I'd appreciate it.
>> Thanks to all in advance for any help!
>> Brian Smith

+ Brian R. Smith                                       +
+ HPC Systems Analyst & Programmer                     +
+ Research Computing, University of South Florida      +
+ 4202 E. Fowler Ave. LIB618                           +
+ Office Phone: 1 (813) 974-1467                       +
+ Mobile Phone: 1 (813) 230-3441                       +
+ Organization URL: http://rc.usf.edu                  +

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