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• Support-function in the GJK-algorithm.

  - by Marcus Johansson

  I am trying to implement the GJK-algorithm but I got stuck instantly. The problem is to implement the Support-function that isn't O(n^2). As it is now I'm computing the complete Minkowski difference, and then there is really no point in doing the GJK-algorithm. (or is it?) What I mean by Support-function is the function that returns the point in the Minkowski difference that is furthest away in a specified direction. I assume this shouldn't be O(n^2) as it is in my current implementation.

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• gcc options for fastest code

  - by rwallace

  I'm distributing a C++ program with a makefile for the Unix version, and I'm wondering what compiler options I should use to get the fastest possible code (it falls into the category of programs that can use all the computing power they can get and still come back for more), given that I don't know in advance what hardware, operating system or gcc version the user will have, and I want above all else to make sure it at least works correctly on every major Unix-like operating system. Thus far, I have g++ -O3 -Wno-write-strings, are there any other options I should add? On Windows, the Microsoft compiler has options for things like fast calling convention and link time code generation that are worth using, are there any equivalents on gcc? (I'm assuming it will default to 64-bit on a 64-bit platform, please correct me if that's not the case.)

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• How to save the world from your computer?

  - by Francisco Garcia

  Sometimes I miss the "help other people" factor within computer related careers. Sure that out there I could find many great projects improving society, but that is not common. However there are little things that we all can do to make this a better place beyond trying to erradicate annoynig stuff such as Visual Basic. You could join a cloud computing network such as World Community Grid to fight cancer. Write a charityware application such as Vim, improve an office IT infrastructure to support telecommuting and reduce CO2 emissions, use an ebook reader for saving paper... what else would you? which projects do you think can have an impact?

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• Count of memory copies in *nix systems between packet at NIC and user application?

  - by Michael_73

  Hi there, This is just a general question relating to some high-performance computing I've been wondering about. A certain low-latency messaging vendor speaks in its supporting documentation about using raw sockets to transfer the data directly from the network device to the user application and in so doing it speaks about reducing the messaging latency even further than it does anyway (in other admittedly carefully thought-out design decisions). My question is therefore to those that grok the networking stacks on Unix or Unix-like systems. How much difference are they likely to be able to realise using this method? Feel free to answer in terms of memory copies, numbers of whales rescued or areas the size of Wales ;) Their messaging is UDP-based, as I understand it, so there's no problem with establishing TCP connections etc. Any other points of interest on this topic would be gratefully thought about! Best wishes, Mike

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• Whats the deal with python?

  - by gmatt

  My interests in programming lie mainly in algorithms, and lately I have seen many reputable researchers write a lot of their code in python. How easy and convenient is python for scientific computing? Does it have a library of algorithms that compares to matlab's? Is Python a scripting language or does it compile? Is it a great language for prototyping an algorithm? How long would it take me to learn enough of it to be productive provided I know C well and OO programming somewhat? Is it OO based? Sorry for the condensed format of questions, but I'm very curious and was hoping a more experienced programmer could help me out.

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• Expanding iSCSI LUNs (NTFS)

  - by Fatih

  I have a 4TB iSCSI LUN that formated as NTFS in Windows 2008. I've shared this formated volume as a folder over SMB. When the capacity of this volume is not enough, I have to add more iSCSI LUNs, but the end-users must see only the folder that I've shared before. So, when I expand the NTFS volume that is currently 4TB, with more iSCSI LUNS(for example 2 more 4TB LUN), if one of the luns is failed, or missing, will all of my data in the folder be lost? I imagine that the expanding ntfs volume is like RAID 0(striped). if it is like RAID 0, then all my data will be lost when one of the luns is failed, or missing. In brief, there are two questions in here: 1- What will be happened, if one of the luns is missing in an expanded ntfs volume? 2- Is there another way to merge all of iscsi luns as only a folder, in that way the users don't see any extra folder even if I add extra iscsi luns to the file server.(I don't mention about DFS) Regards.

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• Can't mount hard drive. Ubuntu 12.04

  - by Sam

  I am trying to recover some pictures on my 320 GB Hard Disk, so I put in a Live Ubuntu CD and am in that right now. In the devices list, it shows my USB drive, but not my 320 GB Hard Disk. I can see the disk in Disk Utility (it says it's on /dev/sda), but it's not mounted, and it says it has a few bad sectors but it is OK. In Disk Usage Analyzer, it says my maximum capacity is 13.4 GB, so it's definitely not using the 320 GB Hard Disk. I tried the following: sudo mkdir /media/newhd (worked) sudo mount /dev/sda /media/newhd (didn't work. it says I must specify the filesystem type) I then tried: fsck.ext4 -f /dev/sda (didn't work. Said: Superblock invalid, trying to backup blocks. then: Bad magic number in super-block while trying to open /dev/sda. The superblock could not be read or does not describe a correct ext2 filesystem. If the device is valid and it contains an ext2 filesystem (and not swap or ufs or something else), then the superblock is corrupt, and you might try running e2fsck with an alternate superblock) Does anyone have any ideas? The whole problem started when my Windows Vista said "Can't find operating system". Any ideas on how I can get on to my hard drive at /dev/sda?

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• How to use your computer to save the world?

  - by Francisco Garcia

  Sometimes I miss the "help other people" factor within computer-related fields. However, there are little things that we all can do to make this a better place—beyond trying to eradicate annoying stuff such as Visual Basic. You could join a cloud computing network such as World Community Grid to fight cancer, write a charityware application such as Vim, improve office IT infrastructure to support telecommuting and reduce CO2 emissions, use an ebook reader to save paper, ... What else can we do to help others? Which projects can have the biggest impact?

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• disk space keeps filling up on EC2 instance with no apperent files/directories

  - by sasher

  How come os shows 6.5G used but I see only 3.6G in files/directories? Running as root on an Amazon Linux AMI (seems like Centos), lots of free memory available, no swapping going on, no apparent file descriptors issue. The only thing I can think of is a log file that was deleted while applications append to it. Disk space usage is slowly but continuously rising towards full capacity (~1k/min with very small decreases from time to time) Any explanation? Solution? du --max-depth=1 -h / 1.2G /usr 4.0K /cgroup 22M /lib64 11M /sbin 19M /etc 52K /dev 2.1G /var 4.0K /media 0 /sys 4.0K /selinux du: cannot access /proc/14024/task/14024/fd/4': No such file or directory du: cannot access<br/> /proc/14024/task/14024/fdinfo/4': No such file or directory du: cannot access /proc/14024/fd/4': No such file or directory du: cannot<br/> access/proc/14024/fdinfo/4': No such file or directory 0 /proc 18M /home 4.0K /logs 8.1M /bin 16K /lost+found 12M /tmp 4.0K /srv 35M /boot 79M /lib 56K /root 67M /opt 4.0K /local 4.0K /mnt 3.6G / df -h Filesystem Size Used Avail Use% Mounted on /dev/xvda1 7.9G 6.5G 1.4G 84% / tmpfs 3.7G 0 3.7G 0% /dev/shm sysctl fs.file-nr fs.file-nr = 864 0 761182

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• Cannot get at data in my NAS

  - by Ben

  I've got a bit of an issue that I'm hoping you can help me with. I have an Iomega ix4 as my NAS. This runs Linux and each drive in the box has 2 partitions: one for the OS and RAID info, and the second for the actual data. I had it configured as RAID5. Recently one of the drives failed. At this point all of the data was available, it was just reporting a failed drive. I had a drive of the same capacity (although not the exact same spec) which I swapped in place of the failed drive. It recognised it, and started to rebuild the data protection. So far so good ... or so I thought. The next day, after data protection had finished reconstructing, the NAS was telling me that 4 new drives had been added, and wanted confirmation to overwrite the data. Obviously I declined to do this. I swapped the failed drive back in again, in the hope that it would return to its previous state of the data being accessible, but one failed disk. However it didn't - it still tells me that the NAS has 4 new drives in it. I am hopeful that the actual data is untouched, so what I need to do is get it to rebuild the RAID without touching the data on the disks. I have ssh access, and have run stuff like mdadm --examine to see what I can find. The mdadm.conf file has no entry in the "definitions of existing MD arrays" section. I have not run any actual rebuilding commands as yet, because this is entering an area which I am out of my depth in. Please can someone advise the best way of getting my data? Thanks.

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• SRAM Cell Diagram - Can someone explain this a bit more clearly? ( From COMP1917 @ UNSW: Lecture 2 o

  - by Kristina

  I've begun watching a series of first year lectures from the University of New South Wales (UNSW) in Australia, and I'm a bit perplexed by the instructors explanation of how an SRAM gate works. I realize this isn't exactly "programming-related" but since it comes from a series of lectures relating to computing and programming, I thought StackOverflow may be able to help (reddit failed me entirely). In this lecture beginning at around 32:12, Richard (the lecturer) tries to explain how a "latch gate" works within SRAM. Although his students seem to keep up, I feel I'm missing something crucial which is preventing the concept from really "clicking" in my brain. For convenience, I've added the image from the video below: Thanks in advance for any help you can provide, but if this question doesn't fit your view of "programming-related" could you please provide an alternate forum for this in a comment when you cast your close vote? Thanks!

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• Backtrack, Wi-Fi not working

  - by hradecek

  I've installed Backtrack 5R3 KDE, and I realized that my wireless is not working, but wired is working fine. Here's the lshw output: *-network description: Ethernet interface product: RTL8101E/RTL8102E PCI Express Fast Ethernet controller vendor: Realtek Semiconductor Co., Ltd. physical id: 0 bus info: pci@0000:02:00.0 logical name: eth0 version: 05 serial: 04:7d:7b:b7:46:f8 size: 100MB/s capacity: 100MB/s width: 64 bits clock: 33MHz capabilities: pm msi pciexpress msix vpd bus_master cap_list ethernet physical tp mii 10bt 10bt-fd 100bt 100bt-fd autonegotiation configuration: autonegotiation=on broadcast=yes driver=r8169 driverversion=2.3LK-NAPI duplex=full firmware=rtl_nic/rtl8105e-1.fw ip=192.168.2.2 latency=0 link=yes multicast=yes port=MII speed=100MB/s resources: irq:42 ioport:2000(size=256) memory:f0404000-f0404fff memory:f0400000-f0403fff lspci output: 00:00.0 Host bridge: Intel Corporation 2nd Generation Core Processor Family DRAM Controller (rev 09) 00:02.0 VGA compatible controller: Intel Corporation 2nd Generation Core Processor Family Integrated Graphics Controller (rev 09) 00:14.0 USB Controller: Intel Corporation Panther Point USB xHCI Host Controller (rev 04) 00:16.0 Communication controller: Intel Corporation Panther Point MEI Controller #1 (rev 04) 00:1a.0 USB Controller: Intel Corporation Panther Point USB Enhanced Host Controller #2 (rev 04) 00:1b.0 Audio device: Intel Corporation Panther Point High Definition Audio Controller (rev 04) 00:1c.0 PCI bridge: Intel Corporation Panther Point PCI Express Root Port 1 (rev c4) 00:1c.1 PCI bridge: Intel Corporation Panther Point PCI Express Root Port 2 (rev c4) 00:1d.0 USB Controller: Intel Corporation Panther Point USB Enhanced Host Controller #1 (rev 04) 00:1f.0 ISA bridge: Intel Corporation Panther Point LPC Controller (rev 04) 00:1f.2 SATA controller: Intel Corporation Panther Point 6 port SATA AHCI Controller (rev 04) 00:1f.3 SMBus: Intel Corporation Panther Point SMBus Controller (rev 04) 02:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd. RTL8101E/RTL8102E PCI Express Fast Ethernet controller (rev 05)

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• Interrupting `while loop` with keyboard in Cython

  - by linello

  I want to be able to interrupt a long function with cython, using the usual CTRL+C interrupt command. My C++ long function is repeatedly called inside a while loop from Cython code, but I want to be able, during the loop, to send an "interrupt" and block the while loop. The interrupt also should wait the longFunction() to finish, so that no data are lost or kept in unknown status. This is one of my first implementation, which obviously doesn't work: computed=0; print "Computing long function..." while ( computed==0 ): try: computed = self.thisptr.aLongFunction() except (KeyboardInterrupt, SystemExit): computed=1 print '\n! Received keyboard interrupt.\n' break; (p.s. self.thisptr is the pointer to the current class which implements aLongFunction() )

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• why don't more programming languages have builtin interfaces to the window manager?

  - by Naveen

  Programming is at the heart about automating tasks on a computer. Presumably those tasks would normally be done manually by a human. Humans use the computer through the keyboard, mouse, and interaction with the console or the window manager. But very few languages have built in functions that provide an interface to these basic computing objects. A notable exception is autohotkey, an open source language on windows, providing builtin functions that allow the following simple tasks: * Get Pixel Information * Get mouse position * Keyboard macros * Simulate key strokes * Simulate mouse click * Window management See examples on rosettacode. There have been various attempts on linux, many of which were stopped without explanation. One is the inactive tcl library: android. Search google code for android, lang:tcl

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• Recovering data from an external hard drive

  - by CCallaghan

  I have a WD Elements 2GB hard drive (formatted NTFS). I accidentally kicked out the USB cable while writing data to the disk, and now I can't access most of the data. Although this was ostensibly my backup drive, there is a great deal of important material on there which was only on there. I realise how idiotic this makes me. (So, formatting is not an option.) Things I've tried/information I've gathered: Windows Explorer will recognise the drive itself. However, it will not access most directories therein (and will sometimes crash when exploring). I can access all of the directories through the command line, but the dir command will often report that it can't read any files in most of the directories. The situation was similar when I hooked it up to an Ubuntu machine: the file explorer crashed, but I could access directories - but not files in those directories - via terminal commands. Several files I tried to copy out either resulted in an I/O error being reported or resulted in the command line crashing. The Disk Management utility on Windows reports a healthy disk formatted as NTFS and not RAW. It also indicates the correct amount of space used up and its capacity (so it seems that the files are not deleted). I've tried to run chkdsk, but that hangs on Step 2 (checking indexes) at 74%. Step 1 reported no bad sectors. I tried Recuva, but that didn't seem to work (stalled at 0% for half an hour). I should also note that the disk doesn't seem to be spinning smoothly; it seems to be chopping back, like it's reading the same sector over and over again. I noticed this after I kicked out the cable. Any help would be greatly appreciated. Update: It would seem the problem has taken a turn for the worse. The external hard drive now shows up on my computer as a local disk and is not mountable by Linux.

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• Binomial test in Python for very large numbers

  - by Morlock

  I need to do a binomial test in Python that allows calculation for 'n' numbers of the order of 10000. I have implemented a quick binomial_test function using scipy.misc.comb, however, it is pretty much limited around n = 1000, I guess because it reaches the biggest representable number while computing factorials or the combinatorial itself. Here is my function: from scipy.misc import comb def binomial_test(n, k): """Calculate binomial probability """ p = comb(n, k) * 0.5**k * 0.5**(n-k) return p How could I use a native python (or numpy, scipy...) function in order to calculate that binomial probability? If possible, I need scipy 0.7.2 compatible code. Many thanks!

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• mysql - moving to a lower performance server, how small can I go?

  - by pedalpete

  I've been running a site for a few years now which really isn't growing in traffic, and I want to save some money on hosting, but keep it going for the loyal users of the site and api. The database has one a nearly 4 million row table, and on a 4gb dual xeon 5320 server. When I check server stats on this server with ps -aux, i get returns of mysql running at about 11% capacity, so no serious load. The main query against mysql runs in about 0.45 seconds. I popped over to linode.com to see what kind of performance I could get out of one of their tiny boxes, and their 360mb ram XEN vps returns the same query in 20 seconds. Clearly not good enough. I've looked at the mysql variables, and they are both very similar (I've included the show variables output below, if anybody is interested). Is there a good way to decide on what size server is needed based on what I'm coming from? Is it RAM that is likely making the difference with the large table size? Is there a way for me to figure out how much ram would be ideal?? Here's the output of the show variables (though I'm not sure it is important). +---------------------------------+------------------------------------------------------------+ | Variable_name | Value | +---------------------------------+------------------------------------------------------------+ | auto_increment_increment | 1 | | auto_increment_offset | 1 | | automatic_sp_privileges | ON | | back_log | 50 | | basedir | /usr/ | | bdb_cache_size | 8384512 | | bdb_home | /var/lib/mysql/ | | bdb_log_buffer_size | 262144 | | bdb_logdir | | | bdb_max_lock | 10000 | | bdb_shared_data | OFF | | bdb_tmpdir | /tmp/ | | binlog_cache_size | 32768 | | bulk_insert_buffer_size | 8388608 | | character_set_client | latin1 | | character_set_connection | latin1 | | character_set_database | latin1 | | character_set_filesystem | binary | | character_set_results | latin1 | | character_set_server | latin1 | | character_set_system | utf8 | | character_sets_dir | /usr/share/mysql/charsets/ | | collation_connection | latin1_swedish_ci | | collation_database | latin1_swedish_ci | | collation_server | latin1_swedish_ci | | completion_type | 0 | | concurrent_insert | 1 | | connect_timeout | 10 | | datadir | /var/lib/mysql/ | | date_format | %Y-%m-%d | | datetime_format | %Y-%m-%d %H:%i:%s | | default_week_format | 0 | | delay_key_write | ON | | delayed_insert_limit | 100 | | delayed_insert_timeout | 300 | | delayed_queue_size | 1000 | | div_precision_increment | 4 | | keep_files_on_create | OFF | | engine_condition_pushdown | OFF | | expire_logs_days | 0 | | flush | OFF | | flush_time | 0 | | ft_boolean_syntax | + - For some reason, that table formats properly in the preview, but apparently not when viewing the question. Hopefully it isn't needed anyway.

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• Generating a beveled edge for a 2D polygon

  - by Metaphile

  I'm trying to programmatically generate beveled edges for geometric polygons. For example, given an array of 4 vertices defining a square, I want to generate something like this. But computing the vertices of the inner shape is baffling me. Simply creating a copy of the original shape and then scaling it down will not produce the desired result most of the time. My algorithm so far involves analyzing adjacent edges (triples of vertices; e.g., the bottom-left, top-left, and top-right vertices of a square). From there, I need to find the angle between them, and then create a vertex somewhere along that angle, depending on how deep I want the bevel to be. And because I don't have much of a math background, that's where I'm stuck. How do I find that center angle? Or is there a much simpler way of attacking this problem?

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• Perl: Fastest way to get directory (and subdirs) size on unix - using stat() at the moment

  - by ivicas

  I am using Perl stat() function to get the size of directory and it's subdirectories. I have a list of about 20 parent directories which have few thousand recursive subdirs and every subdir has few hundred records. Main computing part of script looks like this: sub getDirSize { my $dirSize = 0; my @dirContent = <*>; my $sizeOfFilesInDir = 0; foreach my $dirContent (@dirContent) { if (-f $dirContent) { my $size = (stat($dirContent))[7]; $dirSize += $size; } elsif (-d $dirContent) { $dirSize += getDirSize($dirContent); } } return $dirSize; } The script is executing for more than one hour and I want to make it faster. I was trying with the shell du command, but the output of du (transfered to bytes) is not accurate. And it is also quite time consuming. I am working on HP-UNIX 11i v1.

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• Oracle: 1 Large Server vs. 2 Smaller Servers?

  - by nvahalik

  We are in the planning stages of setting up our production Oracle 10gR2 environment. Our budget gives us the ability to buy 2 processor licenses of Oracle DB Standard Edition. We have minimal experience with Oracle so I'll defer to anyone who has used it. We are trying to decide if we should set up a single dual quad-core box or 2 individual quad-core boxes in a RAC configuration. Our DB right now is about 60 GB, and at our peak, we'll have up to 150 concurrent users. Most of the big stuff is done via batch processing at night. My gut tells me that having 2 boxes in a RAC configuration can't be a bad thing because it provides a true hardware failover solution. DB stored in a shared LUN on a SAN via iSCSI. Plus if we ever need to add capacity, we already have boxes in place that can be upgraded with extra procs (I assume with zero downtime, since it's set up in a RAC config) if we add extra licenses, or RAM. Does RAC have any performance penalties? Will it add extra latency? Is there any true advantage for having dual processor boxes running these systems? If we build out the Oracle boxes with special hardware: hardware iSCSI cards, TOE NICs, will these boxes be solid? We are deploying on 64-bit Windows. So what would you do? One box or two?

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• RAIDs with a lot of spindles - how to safely put to use the "wasted" space

  - by kubanczyk

  I have a fairly large number of RAID arrays (server controllers as well as midrange SAN storage) that all suffer from the same problem: barely enough spindles to keep the peak I/O performance, and tons of unused disk space. I guess it's a universal issue since vendors offer the smallest drives of 300 GB capacity but the random I/O performance hasn't really grown much since the time when the smallest drives were 36 GB. One example is a database that has 300 GB and needs random performance of 3200 IOPS, so it gets 16 disks (4800 GB minus 300 GB and we have 4.5 TB wasted space). Another common example are redo logs for a OLTP database that is sensitive in terms of response time. The redo logs get their own 300 GB mirror, but take 30 GB: 270 GB wasted. What I would like to see is a systematic approach for both Linux and Windows environment. How to set up the space so sysadmin team would be reminded about the risk of hindering the performance of the main db/app? Or, even better, to be protected from that risk? The typical situation that comes to my mind is "oh, I have this very large zip file, where do I uncompress it? Umm let's see the df -h and we figure something out in no time..." I don't put emphasis on strictness of the security (sysadmins are trusted to act in good faith), but on overall simplicity of the approach. For Linux, it would be great to have a filesystem customized to cap I/O rate to a very low level - is this possible?

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• Replacing Failing RAID 1 Drive

  - by mrduclaw

  I hope this is a simple question, but I simply don't know anything about RAID. Some time ago I received a machine that, as I understand it, has two drives in it under RAID 1 (or so that one drive is mirrored on the other and appears as just 1 drive to the OS). Recently, one of these drives has started marking a clicking noise and I would like to replace it. I believe the machine has a hardware RAID controller on the motherboard that handles the RAID stuff, but if it matters the Operating System is Windows XP 32-bit. Is the solution to my problem as simple as buying another drive that is of the same capacity and plugging it in where the clicking drive is currently? Or could I possibly lose everything if the drive that's clicking is the one being mirrored on to the other drive? Is there some menu I need to find before unhooking things? Any best practices out there? I'm sure I'm leaving out some required information, so please just tell me what I'm missing. Thanks!

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• thought about shared storage (NFS, Lustre) [closed]

  - by user134880

  Possible Duplicate: Can you help me with my capacity planning? Now I habe small cluster with total of 8 nodes. 6 of them are computing nodes (apache and vmware) and 2 nodes are for storage. 2 storage nodes are identical. Each storage server is linux box with 8 x 1Tb WD RE4 in soft raid 10. 1st box is master and 2nd is slave. Data is mirrored with DRDB. We export NFSv4 shares to Apache (for document root) and iSCSI to Vmware. Now all is working pretty good and stable. But it will be soon time to upgrade our system. I have been thinking of Lustre. Does some one has any real experience with Lustre or NFS medium clusters? Will it be good idea just to upgrade server and change hdd's to 3Tb ? With NFS we will always have only 2 servers to maintain (one primary and one slave). Thanks. QUESTIONS: 1) Does some one used Lustre? In production? I have seen a lot of info about how it is hard to setup Lustre because you need to compile own kernel and patches. It's answers from newbies. Is there some one who has used Lustre for some period of time? 2) About disk upgrades - it's only description of strategy. I'm not asking if it is enough 3Tb or not. I just ask if it is right just to replace hdds instead of adding new server (like with Lustre) Thanks again.

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• Faking a Single Address Space

  - by dsimcha

  I have a large scientific computing task that parallelizes very well with SMP, but at too fine grained a level to be easily parallelized via explicit message passing. I'd like to parallelize it across address spaces and physical machines. Is it feasible to create a scheduler that would parallelize already multithreaded code across multiple physical computers under the following conditions: The code is already multithreaded and can scale pretty well on SMP configurations. The fact that not all of the threads are running in the same address space or on the same physical machine must be transparent to the program, even if this comes at a significant performance penalty in some use cases. You may assume that all of the physical machines involved are running operating systems and CPU architectures that are binary compatible. Things like locks and atomic operations may be slow (having network latency to deal with and all) but must "just work".

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• How do I profile memory usage in my project

  - by Gacek

  Are there any good, free tools to profile memory usage in C# ? Details: I have a visualization project that uses quite large collections. I would like to check which parts of this project - on the data-processing side, or on the visualization side - use most of the memory, so I could optimize it. I know that when it comes to computing size of the collection the case is quite simple and I can do it on my own. But there are also certain elements for which I cannot estimate the memory usage so easily. The memory usage is quite big, for example processing a file of size 35 MB my program uses a little bit more than 250 MB of RAM.

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