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  • Submitting R jobs using PBS

    - by Tony
    I am submitting a job using qsub that runs parallelized R. My intention is to have R programme running on 4 different cores rather than 8 cores. Here are some of my settings in PBS file: #PBS -l nodes=1:ppn=4 .... time R --no-save < program1.R > program1.log I am issuing the command "ta job_id" and I'm seeing that 4 cores are listed. However, the job occupies a large amount of memory(31944900k used vs 32949628k total). If I were to use 8 cores, the jobs got hang due to memory limitation. top - 21:03:53 up 77 days, 11:54, 0 users, load average: 3.99, 3.75, 3.37 Tasks: 207 total, 5 running, 202 sleeping, 0 stopped, 0 zombie Cpu(s): 30.4%us, 1.6%sy, 0.0%ni, 66.8%id, 0.0%wa, 0.0%hi, 1.2%si, 0.0%st Mem: 32949628k total, 31944900k used, 1004728k free, 269812k buffers Swap: 2097136k total, 8360k used, 2088776k free, 6030856k cached Here is a snapshot when issuing command ta job_id PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 1794 x 25 0 6247m 6.0g 1780 R 99.2 19.1 8:14.37 R 1795 x 25 0 6332m 6.1g 1780 R 99.2 19.4 8:14.37 R 1796 x 25 0 6242m 6.0g 1784 R 99.2 19.1 8:14.37 R 1797 x 25 0 6322m 6.1g 1780 R 99.2 19.4 8:14.33 R 1714 x 18 0 65932 1504 1248 S 0.0 0.0 0:00.00 bash 1761 x 18 0 63840 1244 1052 S 0.0 0.0 0:00.00 20016.hpc 1783 x 18 0 133m 7096 1128 S 0.0 0.0 0:00.00 python 1786 x 18 0 137m 46m 2688 S 0.0 0.1 0:02.06 R How can I prevent other users to use the other 4 cores? I like to mask somehow that my job is using 8 cores with 4 cores idling. Could anyone kindly help me out on this? Can this be solved using pbs? Many Thanks

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  • Syntax error when using "with open" in Python (python newbie)

    - by Tony
    [root@234571-app2 git]# ./test.py File "./test.py", line 4 with open("/home/git/post-receive-email.log",'a') as log_file: ^ SyntaxError: invalid syntax The code looks like this: [root@234571-app2 git]# more test.py #!/usr/bin/python from __future__ import with_statement with open("/home/git/post-receive-email.log",'a') as log_file: log_file.write("hello world") and I am using Python 2.5.5 [root@234571-app2 git]# python -V Python 2.5.5

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  • Searching a document for multiple terms in VBA?

    - by Tony
    I'm trying to create a macro to be used in Microsoft Word 2007 that will search a document for multiple keywords (string variables) located in an external Excel file (the reason for having it in an external file is that the terms will often be changed and updated). I've figured out how to search a document paragraph by paragraph for a single term and color every instance of that term, and I assumed that the proper method would be to use a dynamic array as the search term variable. The question is: how do I get the macro to create an array containing all the terms from an external file and search each paragraph for each and every term? This is what I have so far: Sub SearchForMultipleTerms() ' Dim SearchTerm As String 'declare search term SearchTerm = InputBox("What are you looking for?") 'prompt for term. this should be removed, as the terms should come from an external XLS file rather than user input. Selection.Find.ClearFormatting Selection.Find.Replacement.ClearFormatti… With Selection.Find .Text = SearchTerm 'find the term! .Forward = True .Wrap = wdFindStop .Format = False .MatchCase = False .MatchWholeWord = False .MatchWildcards = False .MatchSoundsLike = False .MatchAllWordForms = False End With While Selection.Find.Execute Selection.GoTo What:=wdGoToBookmark, Name:="\Para" 'select paragraph Selection.Font.Color = wdColorGray40 'color paragraph Selection.MoveDown Unit:=wdParagraph, Count:=1 'move to next paragraph Wend End Sub Thanks for looking!

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  • Conditional ESC, ideas?

    - by Tony
    I often need to enter insert mode just to make changes on a specific line, and would like know if there is a way to enter insert mode in a way that when I am done editing on that line, hitting [Return] gets me back to normal mode. I am aware of the 'r' command for replacing a single character, I guess what I want is something like that but for a line.

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  • How do you create application preferences page?

    - by Tony
    I see some application that uses the settings bundle for their app. Example: http://knol.google.com/k/usman-ismail/iphone-sdk-application-preferences#. I was wondering how to do that without it appearing at the user main settings. I see some application managed to do that. Is there any tutorial around?

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  • Best practice for DAO pattern ?

    - by Tony
    I've seen a lot of codes use a service-dao pattern , I don't know the origin of this pattern . It force the front layer call service , then delegates some of the service task to dao. I want to ask : Does DAO layer do purely data access related task ? What about exception encapsulation ? Is there other pattern can be used to replace this ?

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  • Flex project architecture ?

    - by Tony
    What's the best way to organize functionality modules in a flex project? I saw some people put all modules in one view stack ,and so the application interface is only load once, but when the application get larger, the whole compiled swf would be very big. If we put swfs in different pages, we pass request parameters through HTTP request, we lost the benefits from flex RPC services, slow loading, and we can't see any superior comparing to php,asp,jsp... what's the best practice to organize front end architecture?

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  • What languages, preprocessors, and toolkits will Apple not allow you to develop iPhone OS 4.0 Apps w

    - by Tony Lambert
    According to articles on web Apple will not approve Apps that have code that is not originally developed in Objective C, C or C++. Found on the Web: 3.3.1 Applications may only use Documented APIs in the manner prescribed by Apple and must not use or call any private APIs. Applications must be originally written in Objective-C, C, C++, or JavaScript as executed by the iPhone OS WebKit engine, and only code written in C, C++, and Objective-C may compile and directly link against the Documented APIs (e.g., Applications that link to Documented APIs through an intermediary translation or compatibility layer or tool are prohibited). Can we build a list of things developer use that will and won't be allowed under these possible new rules? We can use: C, C++, Objective C We can't use: Flash, Monotouch C#, Pascal, Fortran, Perl, Python, Lex, Yacc, Unity (games engine), Java What others?

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  • SIMPLE reverse geocoding using Nominatim

    - by tony gil
    i am developing an online mapping application using OpenLayers + OpenStreetMaps. i need help implementing a simple reverse geocoding function in javascript (or php) that receives Latitude and Longitude and returns an Address. i would like to work with Nominatim, if possible. i do NOT want to use Google, Bing or CloudMade or other proprietary solutions. this link returns a reasonable response and i used simple_html_dom.php to break down the result but it is sort of an ugly solution. <?php include('simple_html_dom.php'); $url = "http://nominatim.openstreetmap.org/reverse?format=xml&lat=-23.56320001&lon=-46.66140002&zoom=27&addressdetails=1"; $html = file_get_html($url); foreach ($html->find('road') as $element ) { echo $element; } ?> any suggestions of a more elegant solution?

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  • 'SImple' 2 class Java calculator doesn't accept inputs or do calculations

    - by Tony O'Keeffe
    Hi, I'm trying to get a two class java calculator working (new to java) to work but so far i'm having no success. the two classes are outlined below, calcFrame is for the interface and calEngine should do the actual calculations but i can't get them to talk to one another. i'd really appreciate any assistance on same. Thanks. CalcFrame Code - import java.awt.; import javax.swing.; import javax.swing.border.; import java.awt.event.; /** *A Class that operates as the framework for a calculator. *No calculations are performed in this section */ public class CalcFrame implements ActionListener { private CalcEngine calc; private JFrame frame; private JTextField display; private JLabel status; /** * Constructor for objects of class GridLayoutExample */ public CalcFrame() { makeFrame(); //calc = engine; } /** * This allows you to quit the calculator. */ // Alows the class to quit. private void quit() { System.exit(0); } // Calls the dialog frame with the information about the project. private void showAbout() { JOptionPane.showMessageDialog(frame, "Group Project", "About Calculator Group Project", JOptionPane.INFORMATION_MESSAGE); } private void makeFrame() { frame = new JFrame("Group Project Calculator"); makeMenuBar(frame); JPanel contentPane = (JPanel)frame.getContentPane(); contentPane.setLayout(new BorderLayout(8, 8)); contentPane.setBorder(new EmptyBorder( 10, 10, 10, 10)); /** * Insert a text field */ display = new JTextField(); contentPane.add(display, BorderLayout.NORTH); //Container contentPane = frame.getContentPane(); contentPane.setLayout(new GridLayout(4, 4)); JPanel buttonPanel = new JPanel(new GridLayout(4, 4)); contentPane.add(new JButton("1")); contentPane.add(new JButton("2")); contentPane.add(new JButton("3")); contentPane.add(new JButton("4")); contentPane.add(new JButton("5")); contentPane.add(new JButton("6")); contentPane.add(new JButton("7")); contentPane.add(new JButton("8")); contentPane.add(new JButton("9")); contentPane.add(new JButton("0")); contentPane.add(new JButton("+")); contentPane.add(new JButton("-")); contentPane.add(new JButton("/")); contentPane.add(new JButton("*")); contentPane.add(new JButton("=")); contentPane.add(new JButton("C")); contentPane.add(buttonPanel, BorderLayout.CENTER); //status = new JLabel(calc.getAuthor()); //contentPane.add(status, BorderLayout.SOUTH); frame.pack(); frame.setVisible(true); } /** * Create the main frame's menu bar. * The frame that the menu bar should be added to. */ private void makeMenuBar(JFrame frame) { final int SHORTCUT_MASK = Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(); JMenuBar menubar = new JMenuBar(); frame.setJMenuBar(menubar); JMenu menu; JMenuItem item; // create the File menu menu = new JMenu("File"); menubar.add(menu); // create the Quit menu with a shortcut "Q" key. item = new JMenuItem("Quit"); item.setAccelerator(KeyStroke.getKeyStroke(KeyEvent.VK_Q, SHORTCUT_MASK)); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { quit(); } }); menu.add(item); // Adds an about menu. menu = new JMenu("About"); menubar.add(menu); // Displays item = new JMenuItem("Calculator Project"); item.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { showAbout(); } }); menu.add(item); } /** * An interface action has been performed. * Find out what it was and handle it. * @param event The event that has occured. */ public void actionPerformed(ActionEvent event) { String command = event.getActionCommand(); if(command.equals("0") || command.equals("1") || command.equals("2") || command.equals("3") || command.equals("4") || command.equals("5") || command.equals("6") || command.equals("7") || command.equals("8") || command.equals("9")) { int number = Integer.parseInt(command); calc.numberPressed(number); } else if(command.equals("+")) { calc.plus(); } else if(command.equals("-")) { calc.minus(); } else if(command.equals("=")) { calc.equals(); } else if(command.equals("C")) { calc.clear(); } else if(command.equals("?")) { } // else unknown command. redisplay(); } /** * Update the interface display to show the current value of the * calculator. */ private void redisplay() { display.setText("" + calc.getDisplayValue()); } /** * Toggle the info display in the calculator's status area between the * author and version information. */ } CalcEngine - public class CalcEngine { // The calculator's state is maintained in three fields: // buildingDisplayValue, haveLeftOperand, and lastOperator. // The current value (to be) shown in the display. private int displayValue; // The value of an existing left operand. private int leftOperand; /** * Create a CalcEngine. */ public CalcEngine() { clear(); } public int getDisplayValue() { return displayValue; } /** * A number button was pressed. * Either start a new operand, or incorporate this number as * the least significant digit of an existing one. * @param number The number pressed on the calculator. */ public void numberPressed(int number) { if(buildingDisplayValue) { // Incorporate this digit. displayValue = displayValue*10 + number; } else { // Start building a new number. displayValue = number; buildingDisplayValue = true; } } /** * The 'plus' button was pressed. */ public void plus() { applyOperator('+'); } /** * The 'minus' button was pressed. */ public void minus() { applyOperator('-'); } /** * The '=' button was pressed. */ public void equals() { // This should completes the building of a second operand, // so ensure that we really have a left operand, an operator // and a right operand. if(haveLeftOperand && lastOperator != '?' && buildingDisplayValue) { calculateResult(); lastOperator = '?'; buildingDisplayValue = false; } else { keySequenceError(); } } /** * The 'C' (clear) button was pressed. * Reset everything to a starting state. */ public void clear() { lastOperator = '?'; haveLeftOperand = false; buildingDisplayValue = false; displayValue = 0; } /** * @return The title of this calculation engine. */ public String getTitle() { return "Java Calculator"; } /** * @return The author of this engine. */ public String getAuthor() { return "David J. Barnes and Michael Kolling"; } /** * @return The version number of this engine. */ public String getVersion() { return "Version 1.0"; } /** * Combine leftOperand, lastOperator, and the * current display value. * The result becomes both the leftOperand and * the new display value. */ private void calculateResult() { switch(lastOperator) { case '+': displayValue = leftOperand + displayValue; haveLeftOperand = true; leftOperand = displayValue; break; case '-': displayValue = leftOperand - displayValue; haveLeftOperand = true; leftOperand = displayValue; break; default: keySequenceError(); break; } } /** * Apply an operator. * @param operator The operator to apply. */ private void applyOperator(char operator) { // If we are not in the process of building a new operand // then it is an error, unless we have just calculated a // result using '='. if(!buildingDisplayValue && !(haveLeftOperand && lastOperator == '?')) { keySequenceError(); return; } if(lastOperator != '?') { // First apply the previous operator. calculateResult(); } else { // The displayValue now becomes the left operand of this // new operator. haveLeftOperand = true; leftOperand = displayValue; } lastOperator = operator; buildingDisplayValue = false; } /** * Report an error in the sequence of keys that was pressed. */ private void keySequenceError() { System.out.println("A key sequence error has occurred."); // Reset everything. clear(); } }

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  • DateTime.Now question

    - by Tony
    Hello, I am using a couple varaibles that have value of DateTime.now for both database and web services purpose. Now, if someone asks you that how I am handling non-machine timezone, is that question refering that how the code will handle in case if the application gets deployed to machines in different time zones? To give more information, the application will manipulate data from different time zones. Thank you.

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  • Java Swing - Drawing markers on JSlider.

    - by Tony Day
    Hi, I have a progress bar which inherits from JSlider to provide highlighting functionality. Highlights can be added to the slider at a point (and a Color) and these are then painted onto the control. As follows: The problem is that I cannot get the highlights in the right place, they need to be in the same location as the markers. I also do not know how to retrieve the left and right margins to where the markers start and end. Is there anyway to get the coordinates of each marker? Or perhaps a better way of performing this task? Many Thanks!

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  • OutOfMemory during paging

    - by Tony
    Hi I am using ObjectDataSource, ListView, CustomPaging If the total number of rows is too big, I got OutOfMemory exception, it seems that it caused by some array, I don't get it, because total number of rows should never make any array to be filled with elements, the page size do!! This is the logger. ****EXCEPTION # 3 : 4/30/2010 9:43:07 PM System.Web.HttpUnhandledException: Exception of type 'System.Web.HttpUnhandledException' was thrown. --- System.OutOfMemoryException: Exception of type 'System.OutOfMemoryException' was thrown. at System.Web.UI.WebControls.ListView.CreateChildControls() at System.Web.UI.Control.EnsureChildControls() at System.Web.UI.WebControls.ListView.get_Controls() at System.Web.UI.Control.LoadChildViewStateByIndex(ArrayList childState) at System.Web.UI.Control.LoadViewStateRecursive(Object savedState) at System.Web.UI.Control.LoadChildViewStateByIndex(ArrayList childState) at System.Web.UI.Control.LoadViewStateRecursive(Object savedState) at System.Web.UI.Control.LoadChildViewStateByIndex(ArrayList childState) at System.Web.UI.Control.LoadViewStateRecursive(Object savedState) at System.Web.UI.Control.LoadChildViewStateByIndex(ArrayList childState) at System.Web.UI.Control.LoadViewStateRecursive(Object savedState) at System.Web.UI.Control.LoadChildViewStateByIndex(ArrayList childState) at System.Web.UI.Control.LoadViewStateRecursive(Object savedState) at System.Web.UI.Control.LoadChildViewStateByIndex(ArrayList childState) at System.Web.UI.Control.LoadViewStateRecursive(Object savedState) at System.Web.UI.Page.LoadAllState() at System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) --- End of inner exception stack trace --- at System.Web.UI.Page.HandleError(Exception e) at System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) at System.Web.UI.Page.ProcessRequest(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) at System.Web.UI.Page.ProcessRequest() at System.Web.UI.Page.ProcessRequestWithNoAssert(HttpContext context) at System.Web.UI.Page.ProcessRequest(HttpContext context) at ASP.default_aspx.ProcessRequest(HttpContext context) in c:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\flickrdemo\15752207\c63ea96c\App_Web__8yxn9sb.0.cs:line 0 at System.Web.HttpApplication.CallHandlerExecutionStep.System.Web.HttpApplication.IExecutionStep.Execute() at System.Web.HttpApplication.ExecuteStep(IExecutionStep step, Boolean& completedSynchronously)

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  • preg_replace only part of match

    - by Tony Vipros
    Hi, I'm using preg_replace to create urls for modrewrite based paging links. I use: $nextURL = preg_replace('%/([\d]+)/%','/'.($pageNumber+1).'/',$currentURL); which works fine, however I was wondering if there is a better way without having to include the '/' in the replacement parameter. I need to match the number as being between two / as the URLs can sometimes contain numbers other than the page part. These numbers are never only numbers however, so have /[\d]+/ stops them from getting replaced.

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  • jquery content slider

    - by tony noriega
    this content slider works fine in IE8, and i just tested on FF with FireBug 1.5 and could not find why it doesnt work in FireFox... can anyone else find why its not working in FF? https://www.bcidaho.com/about_us/reduce-healthcare-costs.asp

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  • Multiple Table Inheritance vs. Single Table Inheritance in Ruby on Rails

    - by Tony
    I have been struggling for the past few hours thinking about which route I should go. I have a Notification model. Up until now I have used a notification_type column to manage the types but I think it will be better to create separate classes for the types of notifications as they behave differently. Right now, there are 3 ways notifications can get sent out: SMS, Twitter, Email Each notification would have: id subject message valediction sent_people_count deliver_by geotarget event_id list_id processed_at deleted_at created_at updated_at Seems like STI is a good candidate right? Of course Twitter/SMS won't have a subject and Twitter won't have a sent_people_count, valediction. I would say in this case they share most of their fields. However what if I add a "reply_to" field for twitter and a boolean for DM? My point here is that right now STI makes sense but is this a case where I may be kicking myself in the future for not just starting with MTI? To further complicate things, I want a Newsletter model which is sort of a notification but the difference is that it won't use event_id or deliver_by. I could see all subclasses of notification using about 2/3 of the notification base class fields. Is STI a no-brainer, or should I use MTI? Thanks!

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  • Logging which is the best way

    - by Tony
    Hi People who talk about loggers here never talke about EventLog, I think this is good for windows system. Is it reliable, or I found it dead in some bad morning? Why not logging everything at SQLServer, I am creating E-Commerce website, if SQL server down the website will be down anyway. but I am worry about temporally connection failure, what do u think? Why everyone like files, it can be in great size, too big to handle, or maybe I will create another file when a file is too big, and I can create a file with a date. Some one tried MS Enterprise library? talk to me about it. Thanks

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  • The fastest way to do a collection subtraction

    - by Tony
    I have two Sets. Set<B> b is the subset of Set<A> a. they're both very huge Sets. I want to subtract b from a , what's the best practice to do this common operation ? I've written to many codes like this , and I don't think it's efficient. what's your idea ? for(int i = 0 ; i < a.size(); i++) { for (int j=0 ; j < b.size() ;j++) { // do comparison , if found equals ,remove from a break; } } And I want to find an algorithm , not only applies to Sets, also works for Array.

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  • How does one decrypt a PDF with an owner password, but no user password?

    - by Tony Meyer
    Although the PDF specification is available from Adobe, it's not exactly the simplest document to read through. PDF allows documents to be encrypted so that either a user password and/or an owner password is required to do various things with the document (display, print, etc). A common use is to lock a PDF so that end users can read it without entering any password, but a password is required to do anything else. I'm trying to parse PDFs that are locked in this way (to get the same privileges as you would get opening them in any reader). Using an empty string as the user password doesn't work, but it seems (section 3.5.2 of the spec) that there has to be a user password to create the hash for the admin password. What I would like is either an explanation of how to do this, or any code that I can read (ideally Python, C, or C++, but anything readable will do) that does this so that I can understand what I'm meant to be doing. Standalone code, rather than reading through (e.g.) the gsview source, would be best.

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  • In terms of loss of volume or corruption, is failure probability of an Amazon EBS volume 'x', indepe

    - by Tony Morgan
    In terms of loss of volume or corruption, is failure probability of an Amazon EBS* volume 'x', independent of the failure of another volume 'y'. Amazon states[1] AFR** of between 0.1%-0.5%, lets say 0.5%, 0.005. To restate the question is the AFR composed of two EBSs mirrored actually 0.005*0.005 = 0.000025? To be clear I'm not interested in high availability here, just very high durability. *EBS = elastic block storage (amazons persistant disks) **AFR = annual failure rate. [1] http://aws.amazon.com/ebs/

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  • GenericIdentity not FormsIdentity

    - by Tony
    H Regarding this URL http://www.codeproject.com/KB/aspnet/FlashUpload.aspx User.Identity as System.Web.Security.FormsIdentity is always null, because the Identity is GenericIdentity, I assumed it will be as in the tutorial FormsIdentity, what is chances. Thanks

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