Re: [Beowulf] [EXTERNAL] server lift

2021-10-22 Thread David Mathog
where the lifted computer would be. In a narrow aisle situation a person working alone would have to walk all the way around to reach the other side to install/remove the server after having set the height. Regards, David Mathog ___ Beowulf mailing list

Re: [Beowulf] server lift

2021-10-20 Thread David Mathog
nd act of yoga by a superhero > If the prongs are level couldn't you attach a shelf of sorts to it? Then you would only have to slide the computer onto or off of the level smooth shelf. Consider the big industrial forklifts, they are usually lifting palettes, rathan than the objects them

Re: [Beowulf] Odd NFS write issue for commands issued in a script

2020-12-11 Thread David Mathog
On 8 Dec 2020 17:30:14 -0800 David Mathog wrote Can anybody suggest why a script which causes writes to an NFS mounted directory like so ssh remotenode 'command >/usr/common/tmp/outfile.txt' could somehow fail that write silently, but this variant ssh remotenode 'com

[Beowulf] Odd NFS write issue for commands issued in a script

2020-12-11 Thread David Mathog
or dmesg. The client's fstab has: server:/usr/common /usr/common nfs bg,hard,intr,rw 1 1 and the server's /etc/exports has: /usr/common *.cluster(rw,sync,no_root_squash) Thanks, David Mathog mat...@caltech.edu Man

Re: [Beowulf] RIP CentOS 8

2020-12-11 Thread David Mathog
rward. Gregory Kurtzer indicated in that thread that he was thinking along similar lines. One must also wonder how many of the CentOS developers are going to want to ride this ship down. It always seemed likely that CentOS would come to a bad end when Red Hat took over, and now it has.

Re: [Beowulf] perl with OpenMPI gotcha?

2020-11-23 Thread David Mathog
erate only on files on an NFS file system (for input, output, and status) and compute node local (scratch files, if any). No data is fed in through stdin or returned through stdout. Thanks for your help, David Mathog ___ Beowulf mailing list, Be

Re: [Beowulf] perl with OpenMPI gotcha?

2020-11-20 Thread David Mathog
On Fri, 20 Nov 2020, David Mathog wrote: I should add that passwordless ssh and regular OpenMPI (simple bash script via mpirun) both work fine on the test machine: ssh localhost hostname #poweredge.cluster cat >/tmp/test.sh <https://beowulf.org/cgi-bin/mailman/listinfo/beowulf

[Beowulf] perl with OpenMPI gotcha?

2020-11-20 Thread David Mathog
anager but I would prefer not to use it in this case. Is there some library/method other than MPI which people typically use these days for this sort of compute cluster process control with Perl from the head node? Thanks, David Mathog ___ Beowulf m

Re: [Beowulf] OT, RAID controller replacement replacement batteries?

2020-11-18 Thread David Mathog
EM options are like this one might as well buy some of the ancient Dell batteries and rebuild them oneself. At least then there would be a record of what was in it! Regards, David Mathog ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Pen

[Beowulf] ***UNCHECKED*** Re: OT, RAID controller replacement batteries?

2020-11-04 Thread David Mathog
hild=1&keywords=3.7v+lithium+ion+battery&qid=1604510929 The NU209 has a 5 pin connector, and the card can identify the battery. There must be some electronics in there (besides +,-, and Thermistor pins, although there could be two or more ground pins.) Thanks, David Mathog ___

[Beowulf] OT, RAID controller replacement batteries?

2020-11-02 Thread David Mathog
there any batteries out there which are both new and reliable enough to buy? Thanks, David Mathog ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsubscribe) visit https://beowulf.org/cgi-bin/mailman/listinfo/beowulf

Re: [Beowulf] Lmod question

2020-06-19 Thread David Mathog
On 18 Jun 2020 16:18:53 -0700 (PDT) David Mathog wrote: module --config 2>&1 | grep -i cache number of cache dirs 0 Ignore Cache no Cached loads no User cache valid time(sec) 86400 Write cache after (sec)2

[Beowulf] Lmod question

2020-06-18 Thread David Mathog
Ideally I would like to prevent it from making those cache files again, kind of hard to do not knowing what made them in the first place! This is on CentOS 8, Lmod 8.2.7-1. Thanks, David Mathog ___ Beowulf mailing list, Beowulf@beowulf.org spon

Re: [Beowulf] ganglia on CentOS 8?

2020-04-02 Thread David Mathog
g for _another_ firewall. So the solution is to stop firewalld and then disable it. Otherwise, add rules to firewalld allowing gmond/gmetad connections. The RPMs that were rebuilt from the Fedora src.rpm did not contain commands to set these rules, apparently. Regards, David

Re: [Beowulf] ganglia on CentOS 8?

2020-04-02 Thread David Mathog
ion they are. A thread on this problem has been started here: https://forums.centos.org/viewtopic.php?f=54&t=73893 Regards, David Mathog mat...@caltech.edu ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your

Re: [Beowulf] ganglia on CentOS 8?

2020-04-01 Thread David Mathog
ble, but not "icinga". Presumably those work. They are both massive overkill as I only use gmond and gstat in ganglia. Which of those two other monitoring systems is simplest/lightest? At first glance, they both look a lot more complicated than g

Re: [Beowulf] ganglia on CentOS 8?

2020-04-01 Thread David Mathog
ms to be logging all the right sorts of data, but it won't show any host information to gstat. (A gstat which can very well obtain that information from gmond running on Ubuntu.) Regards, David Mathog mat...@caltech.edu ___ Beowulf mailing lis

[Beowulf] ganglia on CentOS 8?

2020-03-30 Thread David Mathog
est was received and serviced. This: telnet 192.168.0.121 8649 elicits a well formed XML response, but one devoid of data. Here is the end part of it: -- David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___

Re: [Beowulf] ganglia on CentOS 8?

2020-03-30 Thread David Mathog
On 2020-03-30 12:25, David Mathog wrote: (Sorry, the paste somehow sent the email prematurely) Here is the end part of it: int32 | uint32 | float | double | timestamp) #REQUIRED> unspecified) #IMPLIED> ]>

Re: [Beowulf] Power per area

2020-03-10 Thread David Mathog
s are still available. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsubs

Re: [Beowulf] Power per area

2020-03-10 Thread David Mathog
ta center is on the ground floor sitting right on a concrete slab with no voids beneath it I would expect the latter value to be huge and not a real concern, but it might be less than (500 pounds per square foot) X (total area) on the 2nd or higher floors. Regards, David Mathog mat...@calt

[Beowulf] First cluster in 20 years - questions about today

2020-02-03 Thread David Mathog
rograms. When that is available it can be a significant performance enhancement. Will each of your nodes be able to support a GPU? Plan ahead as these often have quite large power requirements which may overload your supply circuits or overwhelm a room's A/C. Regards, David Matho

Re: [Beowulf] Interactive vs batch, and schedulers

2020-01-17 Thread David Mathog
e with run times going way way up when page faulting occurs or jobs crashing when the system runs out of memory. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beow

Re: [Beowulf] 10G and rsync

2020-01-02 Thread David Mathog
On Thu, 2 Jan 2020 13:32:17 Michael Di Domenico wrote: On Thu, Jan 2, 2020 at 12:44 PM David Mathog wrote: 1. Is a single large file transfer rate reasonable? 2. Ditto for several large files? yes, if i transfer files outside of rsync performance is reasonable Are you sure there is not a

Re: [Beowulf] 10G and rsync

2020-01-02 Thread David Mathog
gt; /sys/kernel/mm/redhat_transparent_hugepage/defrag Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscripti

Re: [Beowulf] Is Crowd Computing the Next Big Thing?

2019-11-27 Thread David Mathog
seems likely that if the application was only running when the phone was plugged into its charger that level of payment could cover those extra electricity costs. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech __

Re: [Beowulf] software for activating one of many programs but not the others?

2019-08-23 Thread David Mathog
tOS/vanilla 2) augustus/3.3.2-CentOS-vanilla augustus 2>&1 | head -2 AUGUSTUS (3.3.2) is a gene prediction tool written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech __

Re: [Beowulf] software for activating one of many programs but not the others?

2019-08-21 Thread David Mathog
le to make these run, sometimes, using the matlab run time library, but it is a PITA. Using the matlab run time library isn't all that different than using a container - it is a huge block of code needed to run what is often a very small block of code. Regards, David Mathog mat...@c

Re: [Beowulf] software for activating one of many programs but not the others?

2019-08-20 Thread David Mathog
g system environment and then building within it. That is another variation on this theme: https://xkcd.com/927/ Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list,

Re: [Beowulf] software for activating one of many programs but not the others?

2019-08-20 Thread David Mathog
On 2019-08-20 13:33, David Mathog wrote: Turns out EasyBuild has many of the software packages in question, so EasyBuild+Lmod looks like the winner here. Easybuild - simple to use - not very quick though. scl enable devtoolset-7 'eb Jellyfish-1.1.12-foss-2018b.eb --robot' has be

Re: [Beowulf] software for activating one of many programs but not the others?

2019-08-20 Thread David Mathog
On 2019-08-20 10:40, Alex Chekholko wrote: Other examples include RPM or EasyBuild+Lmod or less common tools like Singularity or Snap/Snappy or Flatpak. Turns out EasyBuild has many of the software packages in question, so EasyBuild+Lmod looks like the winner here. Thanks, David Mathog

Re: [Beowulf] software for activating one of many programs but not the others?

2019-08-20 Thread David Mathog
paths to their data or other programs. (Consider Jellyfish again - many programs use it, a lot of them ship with their own copies, and they expect to find the one they want in their own specified directory.) Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biol

[Beowulf] software for activating one of many programs but not the others?

2019-08-20 Thread David Mathog
at this time. Docker is already available if the user wants to go that route, which avoids this whole issue, but at the cost of moving big images around. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech __

Re: [Beowulf] Containers in HPC

2019-05-22 Thread David Mathog
piler, and a few test cases to verify that the binary is working properly. Unfortunately distributing a program in a Docker image seems to have become the latest excuse for not writing portable code (in the bioinformatics arena, anyway). Regards, David Mathog mat...@caltech.edu Manager, Seq

[Beowulf] Dell rack rails - standardization?

2019-05-08 Thread David Mathog
tion of server then I may keep them for possible future use. But if Dell moves the slots around so that they are effectively keyed for specific models, so that they never fit new models, there wouldn't be much point. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analys

Re: [Beowulf] Anybody here still use SystemImager?

2019-04-22 Thread David Mathog
On 21-Mar-2019 16:14, David Mathog wrote: Hi all, Just in case anybody ever needs this, or has followed this thread to its end and wants to see the final result, I packaged up my BOEL replacement. Since it was meant to install Centos 7 it has the uninspiring and uninformative name "C7knl&q

Re: [Beowulf] Anybody here still use SystemImager?

2019-03-21 Thread David Mathog
r disks and set up xfs file systems. There are some instructions included for rebuilding the initrd, kernel, and binaries.tar.gz file. Hopefully they are clear enough so that it shouldn't be too hard for others to start from this and modify it as needed. Regards, David Mathog mat...

Re: [Beowulf] live free SGE descendent (for Centos 7)?

2019-03-06 Thread David Mathog
tested yet, need to set up some compute nodes to use this version. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To

Re: [Beowulf] live free SGE descendent (for Centos 7)?

2019-03-06 Thread David Mathog
rt is excellent. Regards, Alex On Tue, Mar 5, 2019 at 10:39 AM David Mathog wrote: Are any of the free SGE derived projects still alive? If so, buildable on Centos 7? Son of grid engine, for instance, has not had a release since 2016 https://arc.liv.ac.uk/downloads/SGE/releases/8.1.9/

[Beowulf] live free SGE descendent (for Centos 7)?

2019-03-05 Thread David Mathog
made long ago (Mandriva 2010 or Mageia 3?) and still uses /etc/rc.d/init.d/sgemaster to start/stop rather than a systemd method. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Be

Re: [Beowulf] Anybody here still use SystemImager?

2019-03-01 Thread David Mathog
Joe Landman wrote On 2/27/19 9:08 PM, David Mathog wrote: Joe Landman wrote: [...] I'm about 98% of the way there now, with a mashup of parts from boel and Centos 7. The initrd is pretty large though. Wasted most of a day on a mysterious issue with "sh" (busybox) not re

Re: [Beowulf] Anybody here still use SystemImager?

2019-02-27 Thread David Mathog
n /dev, just not the SATA. This is on a Dell poweredge T110, maybe there is some driver for the SATA controller which isn't loading. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech __

[Beowulf] Anybody here still use SystemImager?

2019-02-26 Thread David Mathog
ear 3.10, with an initrd which loads a target script (by nodename) into busybox and runs it? Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsore

Re: [Beowulf] Oh.. IBM eats Red Hat

2018-10-29 Thread David Mathog
h the one (often very small) program I actually want to run. (See "bioconda".) Most of these programs will build just fine from source even on CentOS 6, but often the only way to download a binary for them is to accept an additional 1Gb (or more) of other stuff. Regards, D

Re: [Beowulf] Hacked MBs It was only a matter of time

2018-10-04 Thread David Mathog
call "national security" when implementing a policy like that and actually have a good case. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org

[Beowulf] emergent behavior - correlation of job end times

2018-07-24 Thread David Mathog
for 40 "CPUs", NUMA with even cpus on node0 and odd on node1, 512Gb RAM, RAID5 with 4 disks for 11.7Tb. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowu

Re: [Beowulf] GLIBC_3.4.x/GLIBCXX_3.4.x not found on CentOS 7.x?

2018-06-20 Thread David Mathog
On 20-Jun-2018 10:21, Ryan Novosielski wrote: On Jun 19, 2018, at 6:25 PM, David Mathog wrote: What software would that be? Where we’ve run into something similar before was the NCI gdc-client. #on centos 6.9 cd /tmp wget https://gdc.cancer.gov/system/files/authenticated%20user/0/gdc

Re: [Beowulf] GLIBC_3.4.x/GLIBCXX_3.4.x not found on CentOS 7.x?

2018-06-19 Thread David Mathog
a problem. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsu

Re: [Beowulf] Avoiding/mitigating fragmentation of systems by small jobs?

2018-06-08 Thread David Mathog
ly disable saving process accounting records for "all children of process PID". Accounting is either on or off. Now when I run scripts prone to this accounting is turned off first. This was on Centos 6.9, on machines reporting (via /proc/cpuinfo) 48 and 56 cpus. Regards, David Matho

Re: [Beowulf] OT, X11 editor which works well for very remote systems

2018-06-07 Thread David Mathog
using that, or there isn't one (headless server)? Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your su

Re: [Beowulf] OT, X11 editor which works well for very remote systems?

2018-06-07 Thread David Mathog
So far it looks like the best bet for any major editing is to download the file, edit locally, and upload. Be that explicitly or via some remote mount file system. Thanks all, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech _

Re: [Beowulf] OT, X11 editor which works well for very remote systems?

2018-06-06 Thread David Mathog
On 06-Jun-2018 15:28, Fred Youhanaie wrote: Does enabling ssh compression with -C help? The local side is over putty from a Windows machine. Enabled its ssh compression option, which I think is the same thing. It didn't make a noticeable difference. Thanks, David Matho

Re: [Beowulf] OT, X11 editor which works well for very remote systems?

2018-06-06 Thread David Mathog
oadcasting Company's enormous web footprint. Yes, nedit. It is old but it still works (especially for column operations, which I use a lot). Admittedly it is useless with utf encoded text, but 99.999% of what I do is ANSI, so that is rarely an issue. Regards, David Mathog mat...@calt

[Beowulf] OT, X11 editor which works well for very remote systems?

2018-06-06 Thread David Mathog
GUI editors that are less sensitive to these issues? If not I will just use nano or vim. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by

Re: [Beowulf] Slow RAID reads, no errors logged, why?

2018-03-22 Thread David Mathog
map 1:1 with those slots. My best guess is that the problem is in the disk firmware, so changing the controller most likely would not help with the SMART issue. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility,

Re: [Beowulf] Slow RAID reads, no errors logged, why?

2018-03-21 Thread David Mathog
t running. The disks are 2Tb 6.0Gb/s SAS with 128Mb cache and 4.16ms latency. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Pengu

Re: [Beowulf] Slow RAID reads, no errors logged, why?

2018-03-19 Thread David Mathog
M0005 There are a bunch of small differences between the two systems so it is hard to say for sure which is the actual culprit. I will put this out on the smartmontools list and see if anybody has seen it before. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Bi

Re: [Beowulf] Slow RAID reads, no errors logged, why?

2018-03-19 Thread David Mathog
n the system. Checked the speed on a third similar machine, H370P controller and again SAS disks. This one is all SEAGATE ST4000NM0005. It was as fast as the 'A' machine (more or less.) Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Di

Re: [Beowulf] Slow RAID reads, no errors logged, why?

2018-03-19 Thread David Mathog
On 19-Mar-2018 13:58, David Mathog wrote: The only oddness of late on "B" is that a few days ago it loaded too many memory hungry processes so the OS killed some. I have had that happen before on other systems without them doing anything odd afterwards. Sorry, hit return to soo. Th

[Beowulf] Slow RAID reads, no errors logged, why?

2018-03-19 Thread David Mathog
systems without them doing anything odd afterwards. Any ideas what this slowdown might be? Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored

Re: [Beowulf] Theoretical vs. Actual Performance

2018-02-22 Thread David Mathog
can eliminate this variable. Perhaps wherever they keep that they also have a detailed description of the test system? Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list,

[Beowulf] Large Dell, odd IO delays

2018-02-14 Thread David Mathog
ee any other jobs using up CPU time when this was going on, but perhaps the defrag processes sometimes run in a mode where they don't rise much in "top" yet bogs down the IO. In any case, set the problem system to match the other two. Does this sound like a reasonab

Re: [Beowulf] slow jobs when run through queue

2017-12-06 Thread David Mathog
. Super frustrating to set something like '--cpus=40' and then watch the resulting heap of programs sit for long periods of time (hours, not seconds) running only on a single CPU. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Divisio

Re: [Beowulf] materials for air shroud?

2011-08-31 Thread David Mathog
scratch components off the motherboard if it falls out of position. I'm thinking perhaps 1/16" polypropylene, that may be stiff enough for this, and it is similar to the shroud material we have in another server. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis

Re: [Beowulf] materials for air shroud?

2011-08-31 Thread David Mathog
ng sparks, but that is a real possibility when a power supply fails. Maybe even a brief flame. Of course paper won't hold up well compared to plastic if it gets wet. Moisture resistance is not important here though - if the insides of the computer are dripping, air shroud failure is the least of my wor

[Beowulf] materials for air shroud?

2011-08-31 Thread David Mathog
ly work, but I'm about 90% confident that taping a sheet of plastic onto the back of the existing shroud would work as well - if I can find a plastic that won't flap around or melt. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis

Re: [Beowulf] OT: public random numbers?

2011-08-15 Thread David Mathog
olute score in a high scoring game like basketball, would be exceedingly difficult, and would likely be obvious to even the casual observer. To rig every digit in the final score of every game played on a given day should be pretty close to impossible. Regards, David Mathog mat...@caltech.edu Manag

Re: [Beowulf] OT: public random numbers?

2011-08-12 Thread David Mathog
should be plenty. (More wouldn't hurt, of course.) Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscr

Re: [Beowulf] OT: public random numbers?

2011-08-12 Thread David Mathog
to change some digits. When I get some time I still need to look and see if the high/low/close values for individual stocks are also variable from web site to web site. These numbers might be more reliable for single stocks since they might all trace back to the data feed from the exchange where t

Re: [Beowulf] OT: public random numbers?

2011-08-12 Thread David Mathog
s discovered it would be easy enough to resolve. There is no intrinsic order to the scores, and some scheduled games might be canceled, so it would have to be something like "sort the scores from all NBA teams who played on 4/4/11 into ascending order and concatenate the digits". Regards,

Re: [Beowulf] OT: public random numbers?

2011-08-12 Thread David Mathog
es themselves have MD5 checksums (but are not signed). They also support https. It comes up a little short on criteria 1 (we really don't know what is going on behind the scenes) and 6 (it is a single site.) Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Bi

[Beowulf] OT: public random numbers?

2011-08-11 Thread David Mathog
sed to charge to recover distribution costs. Criteria 4-6 are typical of software distributed on mirror sites, but so far I have not found any physical measurements which are distributed in a similar manner. Thanks, David Mathog mat...@caltech.edu Manager, Sequence A

Re: [Beowulf] PetaBytes on a budget, take 2

2011-07-22 Thread David Mathog
and in between migrations, to test read the archives periodically so as to detect unforeseen longevity issues early, while there is still a chance to recover the data. David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech __

Re: [Beowulf] [tt] One million ARM chips challenge Intel bumblebee

2011-07-08 Thread David Mathog
mulating a bee brain, it is a worker bee brain, and a worker bee is lucky if it lives a couple of months. Did it say anywhere that the emulation was real time? Very common for emulations to run orders of magnitude slower than real time, so processor loss could still be an issue during runs. David

Re: [Beowulf] Facebook's servers

2011-06-27 Thread David Mathog
ubnet and some method that can remotely force the attacked system to do an orderly shutdown. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponso

Re: [Beowulf] PathScale EKOPath goes open source

2011-06-14 Thread David Mathog
he real history) is here: http://en.wikipedia.org/wiki/Open64 More useful than the history would be a performance comparison of the current versions of the Open64 variants vs. gcc vs. Intel vs. Portland compilers. Anybody seen a comparison that is not several years old? Thanks, David Mathog mat

Re: [Beowulf] Curious about ECC vs non-ECC in practice

2011-05-24 Thread David Mathog
management a memory glitch wouldn't have been too terrible, but now that some of them control automatic parking and other "higher" functions, and with around 100M units in circulation just in the USA, if they aren't ECC then memory glitches in running vehicles would have to be h

Re: [Beowulf] Execution time measurements

2011-05-24 Thread David Mathog
11.1 gives the same time for 1 and 2 simultaneously runnung jobs. Mon, 23 May 2011 12:32:33 -0700 письмо от "David Mathog" : > Mon, 23 May 2011 09:40:13 -0700 письмо от "David Mathog" > : > > > On Fri, May 20, 2011 at 02:26:31PM -

Re: [Beowulf] Curious about ECC vs non-ECC in practice

2011-05-24 Thread David Mathog
m" after the most significant bit in the int32 value has flipped. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing T

Re: [Beowulf] Execution time measurements

2011-05-23 Thread David Mathog
Mikhail Kuzminsky sent this to me and asked that it be posted: BEGIN FORWARD Mon, 23 May 2011 09:40:13 -0700 письмо от "David Mathog" : > > On Fri, May 20, 2011 at 02:26:31PM -0400, Mark Hahn forwarded a message: > > > When I run 2 identical examp

Re: [Beowulf] Execution time measurements - clarification

2011-05-23 Thread David Mathog
ally cannot be run safely at the same time. That is, they run faster together, but they run incorrectly. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.o

Re: [Beowulf] Grid Engine build machine

2011-04-18 Thread David Mathog
er to autoconf, automake? As I recall aimk was really touchy the last time I built this (4 years ago), with lots of futzing around to convince it to use library files it should have found on its own. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facil

[Beowulf] Random numbers (was Re: /dev/random entropy on stateless/headless nodes)

2011-02-28 Thread David Mathog
will all receive different blocks, and these can be stuffed into the ioctl to keep /dev/urandom happy. Probably less work to keep the cluster behind a firewall and dispense with applications (or application modes) that need /dev/urandom. Regards, David Mathog mat...@caltech.edu Manager, Sequence

Re: [Beowulf] 9 traits of the veteran Unix admin

2011-02-17 Thread David Mathog
Editors are like cars, there are lots of them http://en.wikipedia.org/wiki/Comparison_of_text_editors and one person's preference may be incomprehensible to another. So do we really need to talk about editors? Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Fac

Re: [Beowulf] IBM's Watson on Jeopardy tonight

2011-02-16 Thread David Mathog
as famous), might have listed somebody like Robert Hooke, who was better known than either of them, and more likely to be remembered by somebody with a good background in Science, but not a PhD in the history of mathematics. Regards, David Mathog mat...@caltech.edu Manager, Sequence

Re: [Beowulf] IBM's Watson on Jeopardy tonight

2011-02-15 Thread David Mathog
on with a mechanical plunger. Unless they built a typical human reaction delay into that mechanism one would expect the plunger to be much faster than a thumb. In terms of score/watt the humans had the machine beat by a mile :-). David Mathog mat...@caltech.edu Manager, Sequence Analysis Facili

Re: [Beowulf] Advice on 4 CPU node configurations

2011-02-10 Thread David Mathog
60Gbases of raw sequence and expands it 31X. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your sub

Re: [Beowulf] Memory stress testing tools

2010-12-10 Thread David Mathog
wn to 1 CPU then you could swap that with another and see if the issue moves with it. You probably already did this, but be sure both machines have the same BIOS release. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Divisi

Re: [Beowulf] Memory stress testing tools.

2010-12-07 Thread David Mathog
Prentice Bisbal wrote: > When the system seems > stable, I let the users back on it, and sure enough, they get it to > start reporting SBEs in short order. Sounds like you already have a good tool for triggering memory errors on that system - your user's code. Regards, Da

[Beowulf] Re: Interesting

2010-10-28 Thread David Mathog
nothingness in less than a year. Which wouldn't be a problem except one must present these same receipts in order to return any "lifetime guarantee" tools that did not, in fact, last a lifetime. Regards, David Mathog mat...@caltech.edu

Re: [Beowulf] 48-port 10gig switches?

2010-09-02 Thread David Mathog
ation shuts down, so it is a good thing it has redundant fans. I could not find a price for the Voltaire, but it isn't going to be cheap. Somewhere above $20K maybe? Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility,

[Beowulf] Re: Top of the Green 500

2010-07-26 Thread David Mathog
rack, which appears to be about 10cm. high by 1m wide. Maybe the heat is carried away by the rats nest of cables? Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf

[Beowulf] Re: OT: recoverable optical media archive format?

2010-07-21 Thread David Mathog
neighborhood, isn't going to be as trivial to split into threads, and that could be rate limiting. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org spons

[Beowulf] instances where a failed storage block is not all zero?

2010-07-07 Thread David Mathog
ftware out there... Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing list, Beowulf@beowulf.org sponsored by Penguin Computing To change your subscription (digest mode or unsubscr

Re: [Beowulf] dollars-per-teraflop : any lists like the Top500?

2010-07-01 Thread David Mathog
This thread brings to mind the punch line from the second of the SNL "Citiwide Change Bank" ads. Here is a link to the transcript: http://snltranscripts.jt.org/88/88achangebank2.phtml Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Divisio

[Beowulf] Re: Peformance penalty when using 128-bit reals on AMD64

2010-06-25 Thread David Mathog
e scaled up or down by some constant factor so that the numbers once again fit into the range of exponents supported by R*8? Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf mailing lis

Re: [Beowulf] OT: recoverable optical media archive format?

2010-06-10 Thread David Mathog
eds a bit of work to sand the rough edges off. I will have a look at it, but won't have a chance to do so for a couple of weeks. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ Beowulf ma

Re: [Beowulf] OT: recoverable optical media archive format?

2010-06-10 Thread David Mathog
difference, for the smaller test file the restored files were 240842 bytes bigger, not 97535 like before. My guess is that since the program dates back to the age of very small media it may be using "int" or "long" in locations where "long long" is needed today. R

[Beowulf] OT: recoverable optical media archive format?

2010-06-08 Thread David Mathog
n two copies should be enough to recover all of an .img.gz so long as the same data wasn't lost on both media, and if bad DVD sectors always come back as "failed read", never ever showing up as a good read but actually containing bad data. Perhaps the frame checksum on a DVD

[Beowulf] Choosing pxelinux.cfg DEFAULT via dhcpd.conf?

2010-04-22 Thread David Mathog
ption on the pxelinux.cfg list, using just the one file, other than by editing that file changing DEFAULT, and reloading the dhcpd daemon. Thanks, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___

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