similar to: MPI-Blast + Lustre

Hello, I am experiencing some strange behaviour that I am hoping someone can shed some light on. OS and kernel: Red Hat Enterprise Linux AS release 4 (Nahant Update 5) Linux host135 2.6.9-67.9hp.7sp.XCsmp #1 SMP Thu Jul 3 18:55:59 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux built both openssh-5.0p1 and openssh-5.1p1 with the following options: ./configure --prefix=/usr

Hi, I''m seeing what can only be described as dismal striped write performance from lustre 1.6.3 clients :-/ 1.6.2 and 1.6.1 clients are fine. 1.6.4rc3 clients (from cvs a couple of days ago) are also terrible. the below shows that the OS (centos4.5/5) or fabric (gigE/IB) or lustre version on the servers doesn''t matter - the problem is with the 1.6.3 and 1.6.4rc3 client kernels

https://bugzilla.mindrot.org/show_bug.cgi?id=1549 Summary: change in remote command execution behavior Product: Portable OpenSSH Version: 5.1p1 Platform: amd64 OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: sshd AssignedTo: unassigned-bugs at mindrot.org ReportedBy:

on our cluster that has been running lustre for about 1 month. I have 1 MDT/MGS and 1 OSS with 2 OST''s. Our cluster uses all Gige and has about 608 nodes 1854 cores. We have allot of jobs that die, and/or go into high IO wait, strace shows processes stuck in fstat(). The big problem is (i think) I would like some feedback on it that of these 608 nodes 209 of them have in dmesg

Hi, I am trying to work with the ape package, and there is one thing I am struggling with. When calling the *read.GenBank()* function, I can get it to work with an object created like this: *>x <- c("AY395554","AY611035", ...)* *>read.GenBank(x)* However, I am trying to use the function to fetch several hundred sequences at once. So I have been testing with small

So basically I have made a HTML file with a table in it. Column 3 contains a GenBank number and is always proceeded by "=GenBank">". I want to read the file and return the number which comes directly after this (the contents of column 3). Ideally I would like to save this number as a string for use later in the script, but any help is good help. Been at this for HOURS and

Hi All, I have use the BLAST program provided by NCBI to compare large databases and have generated a lot of output in one long text file. I was looking for a way to parse out the results in a nice way so that it could be easily visualized. I was thinking of trying to write something in R, but I wanted to check in with the help group to make sure I am not re-inventing the wheel. Any help

hello if there is a package can do blast in R? [[alternative HTML version deleted]]

Dear R users, I would like to align two protein sequences using BLAST (bl2seq). The question is whether this programm have been implemented in R. Thank you for your help, Alla.

Hi I am trying to read genbank est flat files. Is there any function in R to do that. I was looking for something similar to SeqIO.parse(input_handle, "genbank") in bioPython that convert the genebank sequence into fasta sequence. (One option is to call biopython from R but I am not familiar with python functions so I want to avoid that and I am keeping it as last resort) Thanks and

Hi all, I am learning R by "doing". And this is my first post. I want to use R: 1- to fetch a DNA sequence from a databank (see bellow) and 2- store it as FASTA file. The problem: neither an error is prompted nor the fasta file is created. Testing the code (see bellow), I notice that everything works until the *"write.dna" *command - which is not creating the fasta file.

I just ran this again and got this error: leelab/NCBI_Data_old/GenBank/htg write failed on leelab/NCBI_Data_old/GenBank/htg : Error 0 rsync error: error in file IO (code 11) at receiver.c(243) Received signal 16. (no core) rsync error: received SIGUSR1 or SIGINT (code 20) at rsync.c(229) The command I am running is: /usr/local/bin/rsync -auv --delete --rsh=/usr/bin/ssh lpgfs104:/share/group/*

I suspect you meant WD <- "~/Documents/Scripting/R_Studio/Sequences/" but I am entirely unfamiliar with the packages you are using, and know nothing about what is on your hard drive. For future reference: A) Read the Posting Guide. This is a plain text email list, and your html formatting gets removed leaving a mess that is not always readable. B) Most frequent users of R

Can anyone recommend software that will allow me to utilize my VoIP provider and send fax over IP? I use Asterisk now for my phone system. Thanks! Wiley E. Siler Director of Information Technology Education 2020 4110 N. Scottsdale Rd. Ste 110 Scottsdale, Arizona 85251 (480) 296.0260 (866) 320.2083 ext. 1003 mailto:wsiler@education2020.com <mailto:wsiler@education2020.com>

Hi, I'm helping out with a political campaign and would like to use asterisk to blast out about 200,000 calls with a short message from the candidate. Provider: I'm thinking voipjet may be a good solution? Hardware setup: I will have access to several T-1 lines so I would just want to set up the dialers to limit the number of concurrent calls and so forth. I found teleyapper on

I've done a little digging, but I haven't been able to find an MPI or snow (or any other distributed processing) implementation of fanny (from cluster) or cmeans. Is anyone aware of some implementations or addons which I've missed? [I know of doi://10.1007/978-3-540-71351-7; but that's not for R] Don Armstrong [Currently not subscribed; M-F-T: set accordingly.] -- Certainly

Dear R users, did anybody hack MPI bindings for R? (hoping somebody did that for me before :) Otherwise I might do that soonish. Anybody out there who has some special wishes for that? If yes, please email me directly.. as I'll spend a few days thinking about how to do that best and then do it. (Note: I'm not producing a parallel, thread-safe version of R) Armin

Hi, I would like to compile a shared C++ library but using MPI. Is there away to compile shared libraries using the functionality of mpiexec supplied with MPICH-2. Thanks for any help, Jarrod

Hi, I am a rookie to xen. So far i have managed to install Cent OS -5.1 Xen images over two different nodes of my cluster. The cluster uses infiniband(IB) interconnect. Now ive already tested the bandwidth and latency of IB over those two nodes. But my aim now is to see the overhead that xen adds to the bandwidth and latency values. So, i am actually not sure how i can install mpi over the

Hello, I'm using R on a 10 blade dual quad core Rocks Cluster, and trying to use Rpmi and snow. I basically wondered if at the moment I ought to install Rmpi against another form of mpi (not openmpi) and wondered whether anyone could pass on any experience. I'm mainly worried about (a) the R server taking up 100% cpu time (I think this is a known issue with Rmpi and openmpi) and (b)