Hi Bill- I'd like to try YDL. Glen On Jul 14, 2005, at 7:18 PM, William Harman wrote: > If there are interested parties that would like to try Yellow Dog > Linux, and > the corresponding cluster distro, Y-HPC, let me know off line, and > I will > arrange for a 30-45 days, no cost evaluation, will also provide > technical > support if required. Supported are ext3, XFS, PVFS2. > http://www.terrasoftsolutions.com/products/y-hpc/applications.shtml > > I would also suggest that you might want to check our web site in > early > August for an announcement concerning a Bio package which Terra > Soft will > release for a PowerPC - Linux platform, as well as some new PowerPC > products. www.terrasoftsolutions.com > > > Bill Harman, > Director of Sales > Terra Soft Solutions > Salt Lake City office > P - (801) 572-9252 F - (801) 571-4927 > wharman at terrasoftsolutions.com > wharman at prism.net > billharman at comcast.net > skype: harman8015729252 > > > -----Original Message----- > From: bioclusters-bounces+wharman=prism.net at bioinformatics.org > [mailto:bioclusters-bounces+wharman=prism.net at bioinformatics.org] > On Behalf > Of John H. Lee > Sent: Thursday, July 14, 2005 4:38 PM > To: Clustering, compute farming & distributed computing in life > science > informatics > Subject: Re: [Bioclusters] OS X and NFS > > > Since Juan's system is OS X, can anyone offer a suggestion for OS X? > Cluster filesystems like Lustre and PVFS sound promising for Linux, > but what > options do we have on Macs? Any experience with Xsan? With a > fibre channel > limit of 64 endpoints, can Xsan even be considered for systems as > large as > Tim's? > > We have a 16-node Xserve cluster with one Xserve RAID. The RAID is > connected via FC to one server, which exports the volumes via AFP > and NFS > over gigabit ethernet. As expected, the AFP/NFS server is a > bottleneck. > > -John > > On Jul 14, 2005, at 1:32 AM, Tim Cutts wrote: > > >> On 13 Jul 2005, at 7:01 pm, M. Michael Barmada wrote: >> >> >> >>> Hi Carlos, >>> >>> If its any help, we also had similar problems with our cluster. >>> Our solution >>> was to train the users to include code in their scripts that would >>> create >>> local directories (on the compute node - in /tmp) and copy the >>> files they >>> needed to those directories, then do their computing locally and >>> copy back >>> the results. >>> >>> >> >> Absolutely. And preferably do the copying with something other >> than NFS too - rcp or rsync work well, or the scheduler's built-in >> mechanism. >> Most batch schedulers have built in abilities to this - LSF >> certainly does, in the form of lsrcp and various options to bsub. >> I don't know about SGE - I'm not familiar with it, but I imagine >> the same sort of features are available. >> >> It really is quite amazing how badly NFS scales. I remember having >> serious problems with it on the first Linux cluster I built at >> Incyte's UK office about 6 years ago, and that was just 7 dual-CPU >> nodes talking to a Sun E3000 NFS server. It didn't crash, but it >> got *really* slow - and that was deliberately caching the data >> locally (I wrote wrapper scripts around blastall and other >> applications to cache the databases locally, blowing them away by a >> least-recently-used method if there wasn't room). >> >> Sanger's current 1100 node cluster still has NFS in places, and it >> regularly causes us grief. Our medium-term aim is to remove pretty >> much all NFS from the cluster altogether, with the possible >> exception of automounted home directories, and use cluster >> filesystems like Lustre for shared data. >> >> Tim >> >> -- >> Dr Tim Cutts >> Informatics Systems Group, Wellcome Trust Sanger Institute >> GPG: 1024D/E3134233 FE3D 6C73 BBD6 726A A3F5 860B 3CDD 3F56 E313 >> 4233 >> >> _______________________________________________ >> Bioclusters maillist - Bioclusters at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bioclusters >> >> > > -- > John H. Lee > Berkeley Phylogenomics Group > http://phylogenomics.berkeley.edu > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters > > > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters > >