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  • Which OS should I boot into for virtualization?

    - by acidzombie24
    This might be a silly question. I use windows 7 99% of the time. I run linux 10% of the time and XP 5% of the time. I am thinking about getting a Intel® Core™ i7-2600 Processor which has hardware support for virtualization. I dont think i want more than one partition. May have a swap partition. Which OS should I make my primary (and only) partition? I suspect windows7 if i am always using it as going through a linux layer would slow it down. Does it matter much which OS i use if i have hardware support for virtualization? At the moment I am using VMWare player. I suspect software doesnt effect performance?

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  • Timing startup processes?

    - by acidzombie24
    My Windows 7 use to boot up fast and now its getting rather slow. I suspect one program is eating up all the time yet i cant tell what it is since task manager shows <40% of the cpu being used. What can i use to track how long each process takes when my computer boots/starts up? Note: Except for launchy which i used before my comp became slow, all my startup and services are all signed and known (broadcom, VMWare, Google Inc, Intel, etc) Note2: I am mostly considering the time it takes after i login but i suspect the time before that is slightly slower (i dont think very much though)

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  • sticky bit on NFS file system

    - by Kris_R
    I have a system where to the main server (homes, nfs, ntp, queue...) can log-in only root – all the other users use front-end host with NFS-mounted home directories (RW) and all other software directories (read-only). My problem is, that time to time, if root or normal user with sudo makes some administrative works on front-end some homes of normal users getting sticky bits (drwsr-sr-x). If it happens usually the user can't log-in (as long as permission for his home are not changed to drwxr-xr-x). The last time I saw it after compiling some new software (normal user configure;make) and installation from the same directory as root (su and make install or direct as normal user sudo make install). Can somebody explain me why it happens and what should I do to get rid of this problem? p.s. I'm using CentOS 5.7

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  • Windows 2003 Server Suddenly Drops Connections to everything but PING and port 80 (webserver)

    - by Urda
    Hi, I'm running a Windows 2003 Dedicated server, and the box has been rock solid for more than 2 years now. Just recently, I have had an issue where after a certain ammount of time the server will just stop accepting connections on all ports except 80, and still responds to pings. If you surf to a static HTML page on the box, you can display it. If you pull up a PHP file that has an outside database connection, it fails. RDP refuses to connect, and LogMeIn reports that "The connection was reset" The only fix at this time is to have the provider physically reboot my box to correct the issue. The event log doesn't seem to be leaving helpful messages, and I am at a lost to what is causing this error since I have not installed any new software in months on it. Any tips or help would be appreciated to tracking down this issue. I don't mind updating the question as responses come in, I just do not know where to start troubleshooting because it seems random at this time.

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  • Nvidia driver on Windows 7 causing black screen

    - by inKit
    I have just installed Windows 7 on a desktop machine and for the first time ever have had a really tough time doing so, its normally a nice smooth install. This time I found that the monitor would simply go black after completing the installation. I tried reinstalling about 3 times and this did not help. After much searching I discovered that it was the nvidia drivers that were playing up with win 7, so i booted into safe mode, disabled the device, then rebooted to complete the installation. Windows 7 now works fine as long as the nvidia 9600 gt video card is disabled. The moment I enable it, the system requires a reboot and the screen will go black before even getting to the log in screen. I have tried downloading the latest driver and installing it manually, I have also tried uninstalling the device and allowing windows 7 to install it itself. Nothing seems to work. any clues?

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  • How to remove permanent map of a network drive on OS X Lion?

    - by Flijfi
    Some time ago I mapped a network drive on my Snow Leopard Mac, which was upgraded to Lion. The network drive is not active any more and I receive popups all the time with the error: There was a problem connecting to the server XXXX. I have no idea how I configured at the time. I may have included a mount command, in a config file but I don't know any more where I did it. I reviewed the Preferences/Account/Login items and there is no permanent mapping there. OSX is updated as Nov 27,2011 and the issue is not related to the upgrade to Lion itself but to a misconfiguration. Any help will be greatly appreciated. (If you have the opposite problem, here is the link to solve it: Permanently map a network drive on Mac OS X Leopard)

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  • Windows Virtual Machine ping reply fails the first few times

    - by user28471
    I am running a windows Web Server 2008 virtual machine. When I try to ping it from another windows machine the ping reply comes straight back with 100% success. But when I try to ping it from one of the Linux boxes, the ping reply fails with partial or 100% loss the first couple of time and succeeds the third time onwards. I know it is quite strange but can any one think anything that could be causing it. Could anything in the Windows Domain Security or Firewall be "taking time" to allow responding to the ping request? In fact even the firewall is turned off on the virtual machine.

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  • Does multi-platter hard-drive use all of their heads to read simultaneously?

    - by WiSaGaN
    Suppose we have a harddisk with 2 platters with characteristics below: Rotational rate: 10, 000 RPM Avg sectors/track: 1000 Surfaces: 4 Sector size: 512 bytes I was reading "Computer Systems: A Programmer's Perspective 2ed" when I found that it calculates transfer time as if it only uses ONE head to read a sector. If that's the case, why not use 4 heads to write(read) on 4 surfaces? So when I write a 2K bytes file, each head should only need to wait for the platters to rotate just one sector length instead of 4, thus reducing the transfer time by a factor of 4. Or even redesign sector to make each sector on one cylinder but on 4 tracks residing same position respectively on 4 surfaces. Each one of (512/4) bytes. So when the hd needs to read a sector of 512 bytes, we only need the disk to rotate roughly 1/4 compare to original time. The idea looks like RAID 0.

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  • Is LDAP typically used in conjunction with SAP?

    - by michael
    I have potential clients that all use SAP. To avoid silent push back from IT, we want to make sure we don't add extra complexity to their job if the client (our client internal to the company is not IT) wants to adopt our SaaS. One way to avoid headaches is to add support for LDAP in our SaaS (a bit of work, but nothing major) ahead of time and make sure to mention that to IT. I really know nothing about SAP. Does SAP use an internal or external LDAP server usually? Updated question: A Company relies on an Asset management product from SAP. If I wanted to provide a SaaS that shares space in their workflow, is it advisable to use the SAP product authentication service (if it exists), and if so, do they provide an API?

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  • What are the most likely reasons an application would fail on only one of my servers?

    - by Rising Star
    I have several servers to test new code on. I primarily push out asp.NET web applications. Last week, I had an issue where I installed a newly developed web application on three servers. The three servers all run in separate environments. The application worked fine on two of them, but consistently crashed on the third server with each web request. The problem was eventually traced to an in-house developed .dll file being out of date on the third server. I'm certain that this kind of thing happens all the time. However, there are numerous things that could go wrong to cause this kind of behavior. I spent quite a bit of time tracing this problem. I would like to make a list of things to be suspicious of next time this happens. What are the most likely reasons that a web application would crash on one of my servers while identical code runs fine on another server?

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  • Router for Infrastructure Network

    - by amfortas
    We have an HPC operation that down the years has grown to several racks of gear at three sites, hooked up via Gigabit fiber and Catalyst 2960s (we control the links and switches). Thus far all machines have been on a flat RCF1918 10/8 but we are looking to segment the network in order to streamline matters for iSCSI and generally keep infrastructure equipment away from our end-users. We have now reached a point where we need to consider introducing VLANs for specific subnets and are wondering if it would be worthwhile in the longer run to acquire a small router to keep to keep track of all this stuff and cut down on the complexity of netmasks and routes on host machines, etc. Has anyone here had a similar experience? Suggestions as to suitable equipment would be welcome.

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  • Windows XP occasionally hangs for 2-3 minutes as the splash screen fades in.

    - by marcusw
    This is a bit of a rare problem, I have not been able to debug or fix it or find anyone else with the issue. I hope someone here can help me out. Once in a while, I boot up Windows XP from the first partition of the first disk (using grub, the computer dual-boots ubuntu) and it hangs as the Windows XP splash image fades in, leaving the screen with a dim image of the splash screen. After 2-3 minutes, it continues to boot as normal, no error messages or strange behavior. I have noticed that this happens about 75% of the time when the last time the computer was shut down it was from Ubuntu, and maybe 5-10% of the time otherwise. I have looked at system logs as far as I was able, and did not find anything the miss. What is causing this and how can I fix it?

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  • Looking for a product configurator

    - by Netsrac
    I am looking for a product configurator for products with high complexity. The main goal is to allow a sales person to configure the product in a correct and working manner. The product is a combination of hard- and software options. The options for sure have dependecies (so option A needs B and C) and can also exclude each other. The performance requirements of the software related to the hardware need to be considered. So some rules need to be defineable. Does anybody know a tool (preferred open source) doing that job? Thanks for your help.

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  • Why my backup to USB Drive is too slow?

    - by Jonas
    I have tried several backup solutions for my data and none of them was good enough. I basically want to make a copy of my files to an attached USB Drive from time to time. I don't mind starting my backups manually, since the USB Drive is not always connected. My problem is that my data contains a lot of files (a huge amount), so backing up takes forever (more than 20 hours). Using "rsync" an other similar solutions is not working because the I/O needed to check the file for changes takes longer than the time to actually copy it. Any suggestions?

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  • My microphone is too quiet

    - by AmitM9S6
    I've been chatting with skype for a long time.. and I don't know why, but for X time it's fine, and then it's too quiet.. Here how it goes : I'm booting the PC - getting into a skype call with friends - talking with friends on skype - (everything goes well) - Closing the skype call - Going back to a skype call like a hour after -. They can't hear me well, I have to shout so they'll hear me, and in the settings, it's on 100% + 30 DECIBELS, so I can't raise it higher... and if I'll re-boot my PC, it'll be well until I'll close the skype call again.. Every time I'm skyping with friends well, and then when I close the call and come back after a while, they hear me really low(volume).. I've been trying to fix this problem for about 2 months! If you'll be able to help me, I'd be so happy. (btw It's connected not through USB, but through a microphone connection and headphone connection...) Also, I got Windows 7..

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  • Remote location's status "Disconnected", how to keep it connected (OK)? [net-use-command]

    - by AZ
    I have an script that keeps running, under some scenarios, it needs to contact a server (\\us-sign). From time to time, if this server remains uncontacted for a while, the next time my script needs it, it will ask for my credentials. What I found is that, after such thing happening and using net use, such server will be displayed as disconnected. if I type "net use \\us-sign", it won't ask me neither user nor password, what makes me believe, my credentials for such server are still "valid", nonetheless, its status will remain "disconnected". This script is supposed to help us automate some procedures, but the need to keep a watch on it shall it request for credentials, it kind of defeats the purpose. How can I keep its status "OK" no matter how long it is not being contacted?

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  • My microphone is too quiet (seems to be connected with Skype)

    - by AmitM9S6
    I've been chatting with skype for a long time.. and I don't know why, but for X time it's fine, and then it's too quiet.. Here how it goes : I'm booting the PC - getting into a skype call with friends - talking with friends on skype - (everything goes well) - Closing the skype call - Going back to a skype call like a hour after -. They can't hear me well, I have to shout so they'll hear me, and in the settings, it's on 100% + 30 DECIBELS, so I can't raise it higher... and if I'll re-boot my PC, it'll be well until I'll close the skype call again.. Every time I'm skyping with friends well, and then when I close the call and come back after a while, they hear me really low(volume).. I've been trying to fix this problem for about 2 months! If you'll be able to help me, I'd be so happy. (btw It's connected not through USB, but through a microphone connection and headphone connection...) Also, I got Windows 7..

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  • Should Production Windows Web Servers (IIS & SQL) be in a domain?

    - by tlianza
    We have a few web servers and a few database servers. To date, they've been standalone machines that are not part of a domain. The web servers don't talk to each other, and the web servers talk to the database servers via SQL Auth. My concern with putting the machines in a domain together were added complexity - it's one more "thing" running, and doing "things" that could go wrong. risk - if a domain controller fails, am I now putting other machines at risk? However, in certain scenarios it does seem convenient for them to be on a domain, sharing credentials. For example, if I want to give the "services" control on one machine access to another machine (because Remote Desktop craps out) I need to go in and assign privileges on multiple machines - something that I believe Active Directory and Domain Accounts set to simplify. My question: I'm sure there are things I'm not considering here. Is there a best practice?

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  • HOWTO: Migrate SharePoint site from one farm to another?

    - by Ramiz Uddin
    Hi Everyone, I've a site deployed on a developed machine. The site was developed under WSS 3.0 which contains custom List, Features, Templates, Styles etc. What I've to do is to create a deployment package (setup) which I can give away to my client. I know about stsadm but I don't have the access of the production machine. Is there a way I can package all the dependencies in a single file (installation file) and run on the server which will include all the dependencies (including site content)? I've tried to experiment this with SharePoint Content Deployment Wizard. It all went well when Export the site but always fail to Import with the following message: [2/2/2010 3:43:25 PM]: Start Time: 2/2/2010 3:43:25 PM. [2/2/2010 3:43:25 PM]: Progress: Initializing Import. [2/2/2010 3:43:42 PM]: FatalError: Could not find WebTemplate #75805 with LCID 1033. at Microsoft.SharePoint.Deployment.ImportRequirementsManager.VerifyWebTemplate(SPRequirementObject reqObj) at Microsoft.SharePoint.Deployment.ImportRequirementsManager.Validate(SPRequirementObject reqObj) at Microsoft.SharePoint.Deployment.ImportRequirementsManager.DeserializeAndValidate() at Microsoft.SharePoint.Deployment.SPImport.VerifyRequirements() at Microsoft.SharePoint.Deployment.SPImport.Run() [2/2/2010 3:43:48 PM]: Progress: Import Completed. [2/2/2010 3:43:48 PM]: Finish Time: 2/2/2010 3:43:48 PM. [2/2/2010 3:43:48 PM]: Completed with 0 warnings. [2/2/2010 3:43:48 PM]: Completed with 1 errors. [2/2/2010 3:44:51 PM]: Start Time: 2/2/2010 3:44:51 PM. [2/2/2010 3:44:51 PM]: Progress: Initializing Import. [2/2/2010 3:45:08 PM]: FatalError: Could not find WebTemplate #75805 with LCID 1033. at Microsoft.SharePoint.Deployment.ImportRequirementsManager.VerifyWebTemplate(SPRequirementObject reqObj) at Microsoft.SharePoint.Deployment.ImportRequirementsManager.Validate(SPRequirementObject reqObj) at Microsoft.SharePoint.Deployment.ImportRequirementsManager.DeserializeAndValidate() at Microsoft.SharePoint.Deployment.SPImport.VerifyRequirements() at Microsoft.SharePoint.Deployment.SPImport.Run() [2/2/2010 3:45:14 PM]: Progress: Import Completed. [2/2/2010 3:45:14 PM]: Finish Time: 2/2/2010 3:45:14 PM. [2/2/2010 3:45:14 PM]: Completed with 0 warnings. [2/2/2010 3:45:14 PM]: Completed with 1 errors. [2/2/2010 3:56:17 PM]: Start Time: 2/2/2010 3:56:17 PM. [2/2/2010 3:56:17 PM]: Progress: Initializing Import. [2/2/2010 3:56:34 PM]: FatalError: Could not find WebTemplate #75805 with LCID 1033. at Microsoft.SharePoint.Deployment.ImportRequirementsManager.VerifyWebTemplate(SPRequirementObject reqObj) at Microsoft.SharePoint.Deployment.ImportRequirementsManager.Validate(SPRequirementObject reqObj) at Microsoft.SharePoint.Deployment.ImportRequirementsManager.DeserializeAndValidate() at Microsoft.SharePoint.Deployment.SPImport.VerifyRequirements() at Microsoft.SharePoint.Deployment.SPImport.Run() [2/2/2010 3:56:39 PM]: Progress: Import Completed. [2/2/2010 3:56:39 PM]: Finish Time: 2/2/2010 3:56:39 PM. [2/2/2010 3:56:39 PM]: Completed with 0 warnings. [2/2/2010 3:56:39 PM]: Completed with 1 errors. I actually couldn't find a good reference on how to use it. But, this software doesn't something I'm looking for which can create a simple deployment package (after that you don't need to do anything). I might not be correct but after two days of googling I think there is no such utility (freeware) that can create a simple package of a site and install on other farm without even need to configure anything before you run the installation package. You people might have an advise which can help me to look/think outside the box and get to the solution quickly instead adding more days working on the problem. Please, share only freewares. I can't afford to buy anything. I'm waiting to be surprised with a good share :) Have a good day! Thanks.

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  • How to implement an offline reader writer lock

    - by Peter Morris
    Some context for the question All objects in this question are persistent. All requests will be from a Silverlight client talking to an app server via a binary protocol (Hessian) and not WCF. Each user will have a session key (not an ASP.NET session) which will be a string, integer, or GUID (undecided so far). Some objects might take a long time to edit (30 or more minutes) so we have decided to use pessimistic offline locking. Pessimistic because having to reconcile conflicts would be far too annoying for users, offline because the client is not permanently connected to the server. Rather than storing session/object locking information in the object itself I have decided that any aggregate root that may have its instances locked should implement an interface ILockable public interface ILockable { Guid LockID { get; } } This LockID will be the identity of a "Lock" object which holds the information of which session is locking it. Now, if this were simple pessimistic locking I'd be able to achieve this very simply (using an incrementing version number on Lock to identify update conflicts), but what I actually need is ReaderWriter pessimistic offline locking. The reason is that some parts of the application will perform actions that read these complex structures. These include things like Reading a single structure to clone it. Reading multiple structures in order to create a binary file to "publish" the data to an external source. Read locks will be held for a very short period of time, typically less than a second, although in some circumstances they could be held for about 5 seconds at a guess. Write locks will mostly be held for a long time as they are mostly held by humans. There is a high probability of two users trying to edit the same aggregate at the same time, and a high probability of many users needing to temporarily read-lock at the same time too. I'm looking for suggestions as to how I might implement this. One additional point to make is that if I want to place a write lock and there are some read locks, I would like to "queue" the write lock so that no new read locks are placed. If the read locks are removed withing X seconds then the write lock is obtained, if not then the write lock backs off; no new read-locks would be placed while a write lock is queued. So far I have this idea The Lock object will have a version number (int) so I can detect multi-update conflicts, reload, try again. It will have a string[] for read locks A string to hold the session ID that has a write lock A string to hold the queued write lock Possibly a recursion counter to allow the same session to lock multiple times (for both read and write locks), but not sure about this yet. Rules: Can't place a read lock if there is a write lock or queued write lock. Can't place a write lock if there is a write lock or queued write lock. If there are no locks at all then a write lock may be placed. If there are read locks then a write lock will be queued instead of a full write lock placed. (If after X time the read locks are not gone the lock backs off, otherwise it is upgraded). Can't queue a write lock for a session that has a read lock. Can anyone see any problems? Suggest alternatives? Anything? I'd appreciate feedback before deciding on what approach to take.

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  • A format for storing personal contacts in a database

    - by Gart
    I'm thinking of the best way to store personal contacts in a database for a business application. The traditional and straightforward approach would be to create a table with columns for each element, i.e. Name, Telephone Number, Job title, Address, etc... However, there are known industry standards for this kind of data, like for example vCard, or hCard, or vCard-RDF/XML or even Windows Contacts XML Schema. Utilizing an standard format would offer some benefits, like inter-operablilty with other systems. But how can I decide which method to use? The requirements are mainly to store the data. Search and ordering queries are highly unlikely but possible. The volume of the data is 100,000 records at maximum. My database engine supports native XML columns. I have been thinking to use some XML-based format to store the personal contacts. Then it will be possible to utilize XML indexes on this data, if searching and ordering is needed. Is this a good approach? Which contacts format and schema would you recommend for this? Edited after first answers Here is why I think the straightforward approach is bad. This is due to the nature of this kind of data - it is not that simple. The personal contacts it is not well-structured data, it may be called semi-structured. Each contact may have different data fields, maybe even such fields which I cannot anticipate. In my opinion, each piece of this data should be treated as important information, i.e. no piece of data could be discarded just because there was no relevant column in the database. If we took it further, assuming that no data may be lost, then we could create a big text column named Comment or Description or Other and put there everything which cannot be fitted well into table columns. But then again - the data would lose structure - this might be bad. If we wanted structured data then - according to the database design principles - the data should be decomposed into entities, and relations should be established between the entities. But this adds complexity - there are just too many entities, and lots of design desicions should be made, like "How do we store Address? Personal Name? Phone number? How do we encode home phone numbers and mobile phone numbers? How about other contact info?.." The relations between entities are complex and multiple, and each relation is a table in the database. Each relation needs to be documented in the design papers. That is a lot of work to do. But it is possible to avoid the complexity entirely - just document that the data is stored according to such and such standard schema, period. Then anybody who would be reading that document should easily understand what it was all about. Finally, this is all about using an industry standard. The standard is, hopefully, designed by some clever people who anticipated and described the structure of personal contacts information much better than I ever could. Why should we all reinvent the wheel?? It's much easier to use a standard schema. The problem is, there are just too many standards - it's not easy to decide which one to use!

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  • Linq2SQL vs NHibernate performance (have I gone mad?)

    - by HeavyWave
    I have written the following tests to compare performance of Linq2SQL and NHibernate and I find results to be somewhat strange. Mappings are straight forward and identical for both. Both are running against a live DB. Although I'm not deleting Campaigns in case of Linq, but that shouldn't affect performance by more than 10 ms. Linq: [Test] public void Test1000ReadsWritesToAgentStateLinqPrecompiled() { Stopwatch sw = new Stopwatch(); Stopwatch swIn = new Stopwatch(); sw.Start(); for (int i = 0; i < 1000; i++) { swIn.Reset(); swIn.Start(); ReadWriteAndDeleteAgentStateWithLinqPrecompiled(); swIn.Stop(); Console.WriteLine("Run ReadWriteAndDeleteAgentState: " + swIn.ElapsedMilliseconds + " ms"); } sw.Stop(); Console.WriteLine("Total Time: " + sw.ElapsedMilliseconds + " ms"); Console.WriteLine("Average time to execute queries: " + sw.ElapsedMilliseconds / 1000 + " ms"); } private static readonly Func<AgentDesktop3DataContext, int, EntityModel.CampaignDetail> GetCampaignById = CompiledQuery.Compile<AgentDesktop3DataContext, int, EntityModel.CampaignDetail>( (ctx, sessionId) => (from cd in ctx.CampaignDetails join a in ctx.AgentCampaigns on cd.CampaignDetailId equals a.CampaignDetailId where a.AgentStateId == sessionId select cd).FirstOrDefault()); private void ReadWriteAndDeleteAgentStateWithLinqPrecompiled() { int id = 0; using (var ctx = new AgentDesktop3DataContext()) { EntityModel.AgentState agentState = new EntityModel.AgentState(); var campaign = new EntityModel.CampaignDetail { CampaignName = "Test" }; var campaignDisposition = new EntityModel.CampaignDisposition { Code = "123" }; campaignDisposition.Description = "abc"; campaign.CampaignDispositions.Add(campaignDisposition); agentState.CallState = 3; campaign.AgentCampaigns.Add(new AgentCampaign { AgentState = agentState }); ctx.CampaignDetails.InsertOnSubmit(campaign); ctx.AgentStates.InsertOnSubmit(agentState); ctx.SubmitChanges(); id = agentState.AgentStateId; } using (var ctx = new AgentDesktop3DataContext()) { var dbAgentState = ctx.GetAgentStateById(id); Assert.IsNotNull(dbAgentState); Assert.AreEqual(dbAgentState.CallState, 3); var campaignDetails = GetCampaignById(ctx, id); Assert.AreEqual(campaignDetails.CampaignDispositions[0].Description, "abc"); } using (var ctx = new AgentDesktop3DataContext()) { ctx.DeleteSessionById(id); } } NHibernate (the loop is the same): private void ReadWriteAndDeleteAgentState() { var id = WriteAgentState().Id; StartNewTransaction(); var dbAgentState = agentStateRepository.Get(id); Assert.IsNotNull(dbAgentState); Assert.AreEqual(dbAgentState.CallState, 3); Assert.AreEqual(dbAgentState.Campaigns[0].Dispositions[0].Description, "abc"); var campaignId = dbAgentState.Campaigns[0].Id; agentStateRepository.Delete(dbAgentState); NHibernateSession.Current.Transaction.Commit(); Cleanup(campaignId); NHibernateSession.Current.BeginTransaction(); } Results: NHibernate: Total Time: 9469 ms Average time to execute 13 queries: 9 ms Linq: Total Time: 127200 ms Average time to execute 13 queries: 127 ms Linq lost by 13.5 times! Event with precompiled queries (both read queries are precompiled). This can't be right, although I expected NHibernate to be faster, this is just too big of a difference, considering mappings are identical and NHibernate actually executes more queries against the DB.

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  • Optimizing Python code with many attribute and dictionary lookups

    - by gotgenes
    I have written a program in Python which spends a large amount of time looking up attributes of objects and values from dictionary keys. I would like to know if there's any way I can optimize these lookup times, potentially with a C extension, to reduce the time of execution, or if I need to simply re-implement the program in a compiled language. The program implements some algorithms using a graph. It runs prohibitively slowly on our data sets, so I profiled the code with cProfile using a reduced data set that could actually complete. The vast majority of the time is being burned in one function, and specifically in two statements, generator expressions, within the function: The generator expression at line 202 is neighbors_in_selected_nodes = (neighbor for neighbor in node_neighbors if neighbor in selected_nodes) and the generator expression at line 204 is neighbor_z_scores = (interaction_graph.node[neighbor]['weight'] for neighbor in neighbors_in_selected_nodes) The source code for this function of context provided below. selected_nodes is a set of nodes in the interaction_graph, which is a NetworkX Graph instance. node_neighbors is an iterator from Graph.neighbors_iter(). Graph itself uses dictionaries for storing nodes and edges. Its Graph.node attribute is a dictionary which stores nodes and their attributes (e.g., 'weight') in dictionaries belonging to each node. Each of these lookups should be amortized constant time (i.e., O(1)), however, I am still paying a large penalty for the lookups. Is there some way which I can speed up these lookups (e.g., by writing parts of this as a C extension), or do I need to move the program to a compiled language? Below is the full source code for the function that provides the context; the vast majority of execution time is spent within this function. def calculate_node_z_prime( node, interaction_graph, selected_nodes ): """Calculates a z'-score for a given node. The z'-score is based on the z-scores (weights) of the neighbors of the given node, and proportional to the z-score (weight) of the given node. Specifically, we find the maximum z-score of all neighbors of the given node that are also members of the given set of selected nodes, multiply this z-score by the z-score of the given node, and return this value as the z'-score for the given node. If the given node has no neighbors in the interaction graph, the z'-score is defined as zero. Returns the z'-score as zero or a positive floating point value. :Parameters: - `node`: the node for which to compute the z-prime score - `interaction_graph`: graph containing the gene-gene or gene product-gene product interactions - `selected_nodes`: a `set` of nodes fitting some criterion of interest (e.g., annotated with a term of interest) """ node_neighbors = interaction_graph.neighbors_iter(node) neighbors_in_selected_nodes = (neighbor for neighbor in node_neighbors if neighbor in selected_nodes) neighbor_z_scores = (interaction_graph.node[neighbor]['weight'] for neighbor in neighbors_in_selected_nodes) try: max_z_score = max(neighbor_z_scores) # max() throws a ValueError if its argument has no elements; in this # case, we need to set the max_z_score to zero except ValueError, e: # Check to make certain max() raised this error if 'max()' in e.args[0]: max_z_score = 0 else: raise e z_prime = interaction_graph.node[node]['weight'] * max_z_score return z_prime Here are the top couple of calls according to cProfiler, sorted by time. ncalls tottime percall cumtime percall filename:lineno(function) 156067701 352.313 0.000 642.072 0.000 bpln_contextual.py:204(<genexpr>) 156067701 289.759 0.000 289.759 0.000 bpln_contextual.py:202(<genexpr>) 13963893 174.047 0.000 816.119 0.000 {max} 13963885 69.804 0.000 936.754 0.000 bpln_contextual.py:171(calculate_node_z_prime) 7116883 61.982 0.000 61.982 0.000 {method 'update' of 'set' objects}

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  • Perl: Deleting multiple re-occuring lines where a certain criteria is met

    - by george-lule
    Dear all, I have data that looks like below, the actual file is thousands of lines long. Event_time Cease_time Object_of_reference -------------------------- -------------------------- ---------------------------------------------------------------------------------- Apr 5 2010 5:54PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=LUGALAMBO_900 Apr 5 2010 5:55PM Apr 5 2010 6:43PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=LUGALAMBO_900 Apr 5 2010 5:58PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 5:58PM Apr 5 2010 6:01PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:01PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:03PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=KAPKWAI_900 Apr 5 2010 6:03PM Apr 5 2010 6:04PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=KAPKWAI_900 Apr 5 2010 6:04PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSJN1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=KAPKWAI_900 Apr 5 2010 6:03PM Apr 5 2010 6:03PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:03PM NULL SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA Apr 5 2010 6:03PM Apr 5 2010 7:01PM SubNetwork=ONRM_RootMo,SubNetwork=AXE,ManagedElement=BSCC1,BssFunction= BSS_ManagedFunction,BtsSiteMgr=BULAGA As you can see, each file has a header which describes what the various fields stand for(event start time, event cease time, affected element). The header is followed by a number of dashes. My issue is that, in the data, you see a number of entries where the cease time is NULL i.e event is still active. All such entries must go i.e for each element where the alarm cease time is NULL, the start time, the cease time(in this case NULL) and the actual element must be deleted from the file. In the remaining data, all the text starting from word SubNetwork upto BtsSiteMgr= must also go. Along with the headers and the dashes. Final output should look like below: Apr 5 2010 5:55PM Apr 5 2010 6:43PM LUGALAMBO_900 Apr 5 2010 5:58PM Apr 5 2010 6:01PM BULAGA Apr 5 2010 6:03PM Apr 5 2010 6:04PM KAPKWAI_900 Apr 5 2010 6:03PM Apr 5 2010 6:03PM BULAGA Apr 5 2010 6:03PM Apr 5 2010 7:01PM BULAGA Below is a Perl script that I have written. It has taken care of the headers, the dashes, the NULL entries but I have failed to delete the lines following the NULL entries so as to produce the above output. #!/usr/bin/perl use strict; use warnings; $^I=".bak" #Backup the file before messing it up. open (DATAIN,"<george_perl.txt")|| die("can't open datafile: $!"); # Read in the data open (DATAOUT,">gen_results.txt")|| die("can't open datafile: $!"); #Prepare for the writing while (<DATAIN>) { s/Event_time//g; s/Cease_time//g; s/Object_of_reference//g; s/\-//g; #Preceding 4 statements are for cleaning out the headers my $theline=$_; if ($theline =~ /NULL/){ next; next if $theline =~ /SubN/; } else{ print DATAOUT $theline; } } close DATAIN; close DATAOUT; Kindly help point out any modifications I need to make on the script to make it produce the necessary output. Will be very glad for your help Kind regards George.

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  • How to design a C / C++ library to be usable in many client languages?

    - by Brian Schimmel
    I'm planning to code a library that should be usable by a large number of people in on a wide spectrum of platforms. What do I have to consider to design it right? To make this questions more specific, there are four "subquestions" at the end. Choice of language Considering all the known requirements and details, I concluded that a library written in C or C++ was the way to go. I think the primary usage of my library will be in programs written in C, C++ and Java SE, but I can also think of reasons to use it from Java ME, PHP, .NET, Objective C, Python, Ruby, bash scrips, etc... Maybe I cannot target all of them, but if it's possible, I'll do it. Requirements It would be to much to describe the full purpose of my library here, but there are some aspects that might be important to this question: The library itself will start out small, but definitely will grow to enormous complexity, so it is not an option to maintain several versions in parallel. Most of the complexity will be hidden inside the library, though The library will construct an object graph that is used heavily inside. Some clients of the library will only be interested in specific attributes of specific objects, while other clients must traverse the object graph in some way Clients may change the objects, and the library must be notified thereof The library may change the objects, and the client must be notified thereof, if it already has a handle to that object The library must be multi-threaded, because it will maintain network connections to several other hosts While some requests to the library may be handled synchronously, many of them will take too long and must be processed in the background, and notify the client on success (or failure) Of course, answers are welcome no matter if they address my specific requirements, or if they answer the question in a general way that matters to a wider audience! My assumptions, so far So here are some of my assumptions and conclusions, which I gathered in the past months: Internally I can use whatever I want, e.g. C++ with operator overloading, multiple inheritance, template meta programming... as long as there is a portable compiler which handles it (think of gcc / g++) But my interface has to be a clean C interface that does not involve name mangling Also, I think my interface should only consist of functions, with basic/primitive data types (and maybe pointers) passed as parameters and return values If I use pointers, I think I should only use them to pass them back to the library, not to operate directly on the referenced memory For usage in a C++ application, I might also offer an object oriented interface (Which is also prone to name mangling, so the App must either use the same compiler, or include the library in source form) Is this also true for usage in C# ? For usage in Java SE / Java EE, the Java native interface (JNI) applies. I have some basic knowledge about it, but I should definitely double check it. Not all client languages handle multithreading well, so there should be a single thread talking to the client For usage on Java ME, there is no such thing as JNI, but I might go with Nested VM For usage in Bash scripts, there must be an executable with a command line interface For the other client languages, I have no idea For most client languages, it would be nice to have kind of an adapter interface written in that language. I think there are tools to automatically generate this for Java and some others For object oriented languages, it might be possible to create an object oriented adapter which hides the fact that the interface to the library is function based - but I don't know if its worth the effort Possible subquestions is this possible with manageable effort, or is it just too much portability? are there any good books / websites about this kind of design criteria? are any of my assumptions wrong? which open source libraries are worth studying to learn from their design / interface / souce? meta: This question is rather long, do you see any way to split it into several smaller ones? (If you reply to this, do it as a comment, not as an answer)

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