[mira_talk] Re: NFS and log file
- From: Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Tue, 08 Feb 2011 15:52:25 -0500
Dear Sven,
I do not have control over the Linux cluster environment that I
described earlier. My point was that Mira will work acceptably in that
environment.
However, if I had control over the environment, I would use an SSD
for the log directory. That would improve performance for the I/O
limited parts of Mira.
Managing storage for NGS is a challenge!
Regards,
Bob
Sven Klages wrote:
That's probably a matter of Euros ...
For the Isilon data storage system Illumina recommends for their
Hiseq2000 systems I can buy a few 48core servers with loads of RAM and
TB of local diskspace :-)
It is probably not a bad idea to have enough local (cheap) disk space
for the usual assembly tasks. Roche's Newbler gets more sensitive to
fast IO as well and will probably run into problems with huge datasets
on slow IO (standard) NFS mounts or heavy loaded disks ..
my 2p,
Sven
2011/2/8 Robert Bruccoleri <bruc@xxxxxxxxxxxxxxxxxxxxx
<mailto:bruc@xxxxxxxxxxxxxxxxxxxxx>>
Dear Mira Users,
I'm using Mira in a Linux cluster environment with Isilon
storage provided via NFS and Infiniband. In our environment, using
NFS works reasonably well. I do some delays relative to locally
mounted storage, but it's not significant. Most of the time, Mira
is CPU limited.
Your mileage may vary.
Bob
Bastien Chevreux wrote:
On Tuesday 08 February 2011 19:12:48 CRISTINA FRIAS LOPEZ wrote:
I have read in the manual and search in the foro about NFS.
You have to force Mira to write the log file in the NFS or better if you
can specify that this file was wrote in a local disk.
Quite correct.
So, my question is that these solution are fine or is better use
another network system file?
Whenever possible, try to have input/output operations on local disks. This is
not only valid for MIRA, but for all programs which have to move around
gigabytes of data.
Any kind of networking layer (NFS or whatever) will slow down input / output.
Perhaps with the exception of specialised high-end gear from vendors who'll
charge you the equivalent of several hundreds harddisks worth to get the
network up and running. Though I cannot really vouch for it as I never tested
MIRA on such an environment.
B.
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