I am considering adding a small parallel file system ~(5-10TB) my small
cluster (~32 2x dual core Opteron nodes) that is used mostly by a handful of
regular users. Currently the only storage accessible to all nodes is home
directory space which is provided by the Lab's IT department (this is a
Glen Beane wrote:
I am considering adding a small parallel file system ~(5-10TB) my small
cluster (~32 2x dual core Opteron nodes) that is used mostly by a handful of
regular users. Currently the only storage accessible to all nodes is home
directory space which is provided by the Lab's IT
On 9/25/08 10:19 AM, Joe Landman [EMAIL PROTECTED] wrote:
Glen Beane wrote:
I am considering adding a small parallel file system ~(5-10TB) my small
cluster (~32 2x dual core Opteron nodes) that is used mostly by a handful of
regular users. Currently the only storage accessible to all nodes
Glen Beane wrote:
[...]
Hi Glen:
BLAST uses mmap'ed IO. This has some interesting ... interactions
... with parallel file systems.
for what its worth, we use Paracel BLAST and are also considering
mpiBLAST-pio to take advantage of a parallel file system
Cool.
On Sep 25, 2008, at 10:19 AM, Joe Landman wrote:
We have measured NFSoverRDMA speeds (on SDR IB at that) at 460 MB/s,
on an RDMA adapter reporting 750 MB/s (in a 4x PCIe slot, so ~860 MB/
s max is what we should expect for this). Faster IB hardware should
result in better performance,
On 25 Sep 2008, at 3:19 pm, Joe Landman wrote:
BLAST uses mmap'ed IO. This has some interesting ...
interactions ... with parallel file systems.
It's not *too* bad on Lustre. We use it in production that way.
Are there other recommendations for fast scratch space (it doesn't
have to
Scott Atchley wrote:
On Sep 25, 2008, at 10:19 AM, Joe Landman wrote:
We have measured NFSoverRDMA speeds (on SDR IB at that) at 460 MB/s,
on an RDMA adapter reporting 750 MB/s (in a 4x PCIe slot, so ~860 MB/s
max is what we should expect for this). Faster IB hardware should
result in
On Thu, 2008-09-25 at 09:40 -0400, Glen Beane wrote:
I am considering adding a small parallel file system ~(5-10TB) my small
cluster (~32 2x dual core Opteron nodes) that is used mostly by a handful of
regular users. Currently the only storage accessible to all nodes is home
directory space
On Thu, Sep 25, 2008 at 10:19:26AM -0400, Joe Landman wrote:
BLAST uses mmap'ed IO. This has some interesting ... interactions ...
with parallel file systems.
The PathScale compilers use mmap on their temporary files. This led to
some interesting bugs being reported... fortunately, we were
Greg Lindahl wrote:
On Thu, Sep 25, 2008 at 10:19:26AM -0400, Joe Landman wrote:
BLAST uses mmap'ed IO. This has some interesting ... interactions ...
with parallel file systems.
The PathScale compilers use mmap on their temporary files. This led to
some interesting bugs being reported...
On Thu, Sep 25, 2008 at 02:08:23PM -0400, Joe Landman wrote:
It looks like people use mmap files to explicitly avoid seeks,
replacing semantics of file IO with memory access semantics.
Well, it explicitly avoids having to call I/O functions all the time
as you skip around a file. It also
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