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by jardino
Thu Aug 29, 2013 8:37 pm
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

James: No video - just "big data". It is data about biological cells, proteins, amino acids and genomes - human and other. The developing science of bioinformatics analyses this data for medical and other purposes. The University of St. Andrews is using RPis rather than traditional computer networks...
by jardino
Thu Aug 29, 2013 3:51 pm
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

I spent many hours today re-building my 32 GB card from scratch - while carefully documenting the steps - only to have script 6 fail after 2 hours 12 minutes because of no space on disk! :cry:

Further analysis is needed.

Fortunately, I'd backed up the previous version.

Alan.
by jardino
Wed Aug 28, 2013 9:54 am
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

inder:

It's not really difficult, but does take a long time. Much of the apparent complexity is due to Daniel's need to connect to the University's network, which the home user doesn't need.

I'll put some details up later, but have some other work to do first.

Alan.
by jardino
Tue Aug 27, 2013 10:05 am
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

inder:

Why don't you create your own image by following Daniel's "Work Instruction", as I did. It fits easily on to a crippled 32 GB card.

With a freshly-installed copy of wheezy-rasbian, start at "Obtain BLAST database" at the foot of page 3 of the Instruction.

Alan.
by jardino
Mon Aug 26, 2013 2:21 pm
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Daniel: Success! I followed your "Work Instruction" (more or less), but downloaded the course material directly to my freshly-formatted 32 GB SD Card. See the attached fragment of output from blastall. ENSLAFP00000000422 gi|62899704|sp|Q5NU32.1|AOFA_HORSE 90.93 518 47 0 1 518 5 522 0.0 931 ENSLAFP00...
by jardino
Fri Aug 23, 2013 8:56 am
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Glad it's now flagged as a known problem! Regarding your options: 1) Trying different cards would be an expensive option, if it's pot luck seeing what size each formats to! 2) I don't mind waiting for a fix, since I have a lot of catching up in bioinformatics to do. 3) I've only skimmed your "work i...
by jardino
Thu Aug 22, 2013 12:15 pm
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Daniel, The "Intenso" brand SDHC card, nominally 32 GB, that I bought from Maplin last week formats to just under 30 GB. I don't think that the formatted size is manufacturer-related. The shortfall is probably within the manufacturing spread of each card. (If you were using the card for its intended...
by jardino
Thu Aug 22, 2013 10:57 am
Forum: General discussion
Topic: 4273pi: Bioinformatics education on low cost ARM hardware
Replies: 30
Views: 6034

Re: 4273pi: Bioinformatics education on low cost ARM hardwar

Daniel: I certainly know of no other scientific paper that mentions the Raspberry Pi. Yours has certainly rekindled my interest in cell biology and Perl! However, it would be good to point out that the downloaded image file very nearly fills a true 32 Gbyte SD card. Some nominal 32 Gbyte cards deliv...
by jardino
Mon Jul 22, 2013 3:48 pm
Forum: General discussion
Topic: Raspberry Pi Camera Module
Replies: 16
Views: 2690

Re: Raspberry Pi Camera Module

Try ModMyPi:

https://www.modmypci.com/raspberry-pi-e ... mera-board

At 16:45 today (22nd July), they were still saying "In stock", but no indication of stock levels.
Good supplier, in my experience.
Alan.
by jardino
Fri Jul 19, 2013 9:36 am
Forum: General discussion
Topic: Camera boards back in stock at element14
Replies: 27
Views: 3152

Re: Camera boards back in stock at element14

I ordered my camera board from ModMyPi, together with some other goodies, around 07:00 yesterday (July 18th) and everything arrived intact at 10:00 today. I call that first class service. My camera cable is gently folded, not creased in any way. I'm looking forward to plugging it in! We don't hear m...
by jardino
Mon Jul 15, 2013 9:10 am
Forum: General discussion
Topic: Computing Pioneer Doug Englebart Has Passed Away
Replies: 10
Views: 1843

Re: Computing Pioneer Doug Englebart Has Passed Away

There's a nice obituary about Doug in the current issue of "The Economist". See
http://www.economist.com/news/obituary/ ... -engelbart .

I don't think you need to subscribe to read it.

Alan.
by jardino
Thu Mar 07, 2013 8:38 am
Forum: HATs and other add-ons
Topic: Purchasing Straps
Replies: 11
Views: 2745

Re: Purchasing Straps

by jardino
Thu Jan 31, 2013 3:30 pm
Forum: HATs and other add-ons
Topic: Farnell assembled Gertboard
Replies: 27
Views: 5694

Re: Farnell assembled Gertboard

ianajo said: "...the assembled board can also plug straight onto the Pi." I know - that's the way I've been working since mine arrived a few days ago. However, I'd like to separate them and wanted to make sure I got the right cable. And one supplier (who currently offers only f-to-f cables) is adver...
by jardino
Thu Jan 31, 2013 11:40 am
Forum: HATs and other add-ons
Topic: Farnell assembled Gertboard
Replies: 27
Views: 5694

Re: Farnell assembled Gertboard

Difference between kit and assembled board? As far as I can tell from photographs, the kit's GPIO header (J1) extends through to the top of the board with pins - meaning that a female-to-female cable can be used to connect the board to the RPi. Yet my assembled board has only the socket on the botto...
by jardino
Sun Jan 27, 2013 11:38 am
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

You could however use this single line to build apple_serial: mpicc -O3 apple_serial.c invar.c -o apple_serial Thanks for that - it worked! Here are my results using the "time" parameter: real 0m46.164s user 0m45.950s sys 0m0.070s. Onwards and upwards! (Just curious: why do you refer to "mandelbrot"...
by jardino
Sat Jan 26, 2013 11:32 am
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

Congratulations on getting your cluster running! I'm back up to 4 nodes again. I am interested in going through your MPI tutorial but have failed at the first hurdle - compiling the apple_serial.c program. I get compiler messages like "undefined references to initRanges / XPIX / YPIX" and so on (11 ...
by jardino
Wed Jan 16, 2013 2:25 pm
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

Very good, Marco-Luis.

I assume this was the Fortran program?

Let me know if you need help getting the C version to compile. However, I'm not very strong in C.

Alan.
by jardino
Fri Jan 04, 2013 5:33 pm
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

OK - grand-daughter gone home :( and Beowulf restored to two working nodes :) , so here goes. The following assumes that you have followed the U. of Southampton instructions - including installing the Fortran compiler - and got as far as running the cpi program on two nodes. I'm focussing on Fortran...
by jardino
Wed Jan 02, 2013 11:30 am
Forum: General discussion
Topic: Thank you Foundation
Replies: 7
Views: 1406

Re: Thank you Foundation

Amidst all the "it dont work", "it should work like this" we often forget to say thank you. So thank you for a fantastic product, I havent had so much fun since I used a BBC B to boot the Z80 add-on pack that was available to push code back to the BBC B to run an 800 channel lighting system many ye...
by jardino
Wed Jan 02, 2013 11:09 am
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

Hello Marco-Luis: I'll be delighted to post my examples. However, there will be a short delay. First, my Beowulf is currently down. Not for any technical reason, but because I keep cannibalising it to build other interesting RPi projects. Time to buy more Pi, I think! Secondly, my keyboard and mouse...
by jardino
Tue Jan 01, 2013 4:33 pm
Forum: General discussion
Topic: A faster CPU
Replies: 41
Views: 12718

Re: A faster CPU

A few days ago I started to play with my brand new Model B 512 MB and just ordered 4 additional units. I plan to build a little cluster to run MPI programs on. Surely I do not do that because the Pi is the best platform for the purpose - cause it is not. The whole point for me is to see what one ca...
by jardino
Sat Nov 17, 2012 5:39 pm
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

Node 3 (a.k.a. Slave02) of my Beowulf was installed with only one slight difficulty - I'd cloned its SD card from my Master image, rather than from my Slave01 image, so it declined to accept MPI requests. Repeating the last item in Step 33 of the "Southampton" instructions quickly fixed this. Perhap...
by jardino
Sat Nov 10, 2012 4:33 pm
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

Well, after another few dozen false starts, I'm now documenting where I've got to and my various blind alleys – in the hope that it may help fellow Beowulf builders along the way. (By the way, when friends ask me what I'm doing these days, I've stopped replying that I'm building a Beowulf from Raspb...
by jardino
Mon Oct 22, 2012 7:42 pm
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

Thanks for your reply.

It's good to see that someone is looking in here!

I propose to, first, write a simple "cookbook" set of instructions, then later fill it in with some rationale for what is going on.

What do you think?

Alan.
by jardino
Mon Oct 22, 2012 3:56 pm
Forum: Other projects
Topic: Cluster (Bramble...) Design Discussion (Advanced)
Replies: 170
Views: 83029

Re: Cluster (Bramble...) Design Discussion (Advanced)

Since my last post, I've learned how to take my Bramble (still 2 nodes, but node 3 with 512 Mb has just arrived!) beyond the point where Professor Cox left us (http://www.southampton.ac.uk/~sjc/raspberrypi/ ). I can now compile and run the demo programs from Argonne - in C and Fortran - and even wri...

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