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  • Embarrassingly parallel workflow creates too many output files

    - by Hooked
    On a Linux cluster I run many (N > 10^6) independent computations. Each computation takes only a few minutes and the output is a handful of lines. When N was small I was able to store each result in a separate file to be parsed later. With large N however, I find that I am wasting storage space (for the file creation) and simple commands like ls require extra care due to internal limits of bash: -bash: /bin/ls: Argument list too long. Each computation is required to run through a qsub scheduling algorithm so I am unable to create a master program which simply aggregates the output data to a single file. The simple solution of appending to a single fails when two programs finish at the same time and interleave their output. I have no admin access to the cluster, so installing a system-wide database is not an option. How can I collate the output data from embarrassingly parallel computation before it gets unmanageable?

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  • Explained shell statement

    - by Mats Stijlaart
    The following statement will remove line numbers in a txt file: cat withLineNumbers.txt | sed 's/^.......//' >> withoutLineNumbers.txt The input file is created with the following statement (this one i understand): nl -ba input.txt >> withLineNumbers.txt I know the functionality of cat and i know the output is written to the 'withoutLineNumbers.txt' file. But the part of '| sed 's/^.......//'' is not really clear to me. Thanks for your time.

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  • c++ File input/output

    - by Myx
    Hi: I am trying to read from a file using fgets and sscanf. In my file, I have characters on each line of the while which I wish to put into a vector. So far, I have the following: FILE *fp; fp = fopen(filename, "r"); if(!fp) { fprintf(stderr, "Unable to open file %s\n", filename); return 0; } // Read file int line_count = 0; char buffer[1024]; while(fgets(buffer, 1023, fp)) { // Increment line counter line_count++; char *bufferp = buffer; ... while(*bufferp != '\n') { char *tmp; if(sscanf(bufferp, "%c", tmp) != 1) { fprintf(stderr, "Syntax error reading axiom on " "line %d in file %s\n", line_count, filename); return 0; } axiom.push_back(tmp); printf("put %s in axiom vector\n", axiom[axiom.size()-1]); // increment buffer pointer bufferp++; } } my axiom vector is defined as vector<char *> axiom;. When I run my program, I get a seg fault. It happens when I do the sscanf. Any suggestions on what I'm doing wrong?

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  • Foreach File in a Folder in Flash?

    - by msandbot
    Hey, I have an image slideshow program working right now and it takes in a folder of a hard coded in number of images. I would like to change this so that it can take in a folder and will display all of them no matter the number. Is there a way to do this in flash? I'm thinking something like the foreach loop in perl or other scripting language. It is possible to store then number of images in a text file but I also don't know how to read that in flash either. I'm working in actionscript 3. Any help would be greatly appreciated. Thanks -Mike

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  • removing a line from a text file?

    - by Blackbinary
    Hi all. I am working with a text file, which contains a list of processes under my programs control, along with relevant data. At some point, one of the processes will finish, and thus will need to be removed from the file (as its no longer under control). Here is a sample of the file contents (which has enteries added "randomly"): PID=25729 IDLE=0.200000 BUSY=0.300000 USER=-10.000000 PID=26416 IDLE=0.100000 BUSY=0.800000 USER=-20.000000 PID=26522 IDLE=0.400000 BUSY=0.700000 USER=-30.000000 So for example, if I wanted to remove the line that says PID=26416.... how could I do that, without writing the file over again? I can use external unix commands, however I am not very familiar with them so please if that is your suggestion, give an example. Thanks!

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  • Error copying file from app bundle

    - by Michael Chen
    I used the FireFox add-on SQLite Manager, created a database, which saved to my desktop as "DB.sqlite". I copied the file into my supporting files for the project. But when I run the app, immediately I get the error "Assertion failure in -[AppDelegate copyDatabaseIfNeeded], /Users/Mac/Desktop/Note/Note/AppDelegate.m:32 2014-08-19 23:38:02.830 Note[28309:60b] Terminating app due to uncaught exception 'NSInternalInconsistencyException', reason: 'Failed to create writable database file with message 'The operation couldn’t be completed. (Cocoa error 4.)'.' First throw call stack: "... Here is the App Delegate Code where the error takes place -(void) copyDatabaseIfNeeded { NSFileManager *fileManager = [NSFileManager defaultManager]; NSError *error; NSString *dbPath = [self getDBPath]; BOOL success = [fileManager fileExistsAtPath:dbPath]; if (!success) { NSString *defaultDBPath = [[ [NSBundle mainBundle ] resourcePath] stringByAppendingPathComponent:@"DB.sqlite"]; success = [fileManager copyItemAtPath:defaultDBPath toPath:dbPath error:&error]; if (!success) NSAssert1(0, @"Failed to create writable database file with message '%@'.", [error localizedDescription]); } } I am very new to Sqlite, so I maybe I didn't create a database correctly in the FireFox Sqlite manager, or maybe I didn't "properly" copy the .sqlite file in? (I did check the target membership in the sqlite and it correctly has my project selected. Also, the .sqlite file names all match up perfectly.)

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  • C++ file input/output search

    - by Brian J
    Hi I took the following code from a program I'm writing to check a user generated string against a dictionary as well as other validation. My problem is that although my dictionary file is referenced correctly,the program gives the default "no dictionary found".I can't see clearly what I'm doing in error here,if anyone has any tips or pointers it would be appreciated, Thanks. //variables for checkWordInFile #define gC_FOUND 99 #define gC_NOT_FOUND -99 // static bool certifyThat(bool condition, const char* error) { if(!condition) printf("%s", error); return !condition; } //method to validate a user generated password following password guidelines. void validatePass() { FILE *fptr; char password[MAX+1]; int iChar,iUpper,iLower,iSymbol,iNumber,iTotal,iResult,iCount; //shows user password guidelines printf("\n\n\t\tPassword rules: "); printf("\n\n\t\t 1. Passwords must be at least 9 characters long and less than 15 characters. "); printf("\n\n\t\t 2. Passwords must have at least 2 numbers in them."); printf("\n\n\t\t 3. Passwords must have at least 2 uppercase letters and 2 lowercase letters in them."); printf("\n\n\t\t 4. Passwords must have at least 1 symbol in them (eg ?, $, £, %)."); printf("\n\n\t\t 5. Passwords may not have small, common words in them eg hat, pow or ate."); //gets user password input get_user_password: printf("\n\n\t\tEnter your password following password rules: "); scanf("%s", &password); iChar = countLetters(password,&iUpper,&iLower,&iSymbol,&iNumber,&iTotal); iUpper = countLetters(password,&iUpper,&iLower,&iSymbol,&iNumber,&iTotal); iLower =countLetters(password,&iUpper,&iLower,&iSymbol,&iNumber,&iTotal); iSymbol =countLetters(password,&iUpper,&iLower,&iSymbol,&iNumber,&iTotal); iNumber = countLetters(password,&iUpper,&iLower,&iSymbol,&iNumber,&iTotal); iTotal = countLetters(password,&iUpper,&iLower,&iSymbol,&iNumber,&iTotal); if(certifyThat(iUpper >= 2, "Not enough uppercase letters!!!\n") || certifyThat(iLower >= 2, "Not enough lowercase letters!!!\n") || certifyThat(iSymbol >= 1, "Not enough symbols!!!\n") || certifyThat(iNumber >= 2, "Not enough numbers!!!\n") || certifyThat(iTotal >= 9, "Not enough characters!!!\n") || certifyThat(iTotal <= 15, "Too many characters!!!\n")) goto get_user_password; iResult = checkWordInFile("dictionary.txt", password); if(certifyThat(iResult != gC_FOUND, "Password contains small common 3 letter word/s.")) goto get_user_password; iResult = checkWordInFile("passHistory.txt",password); if(certifyThat(iResult != gC_FOUND, "Password contains previously used password.")) goto get_user_password; printf("\n\n\n Your new password is verified "); printf(password); //writing password to passHistroy file. fptr = fopen("passHistory.txt", "w"); // create or open the file for( iCount = 0; iCount < 8; iCount++) { fprintf(fptr, "%s\n", password[iCount]); } fclose(fptr); printf("\n\n\n"); system("pause"); }//end validatePass method int checkWordInFile(char * fileName,char * theWord){ FILE * fptr; char fileString[MAX + 1]; int iFound = -99; //open the file fptr = fopen(fileName, "r"); if (fptr == NULL) { printf("\nNo dictionary file\n"); printf("\n\n\n"); system("pause"); return (0); // just exit the program } /* read the contents of the file */ while( fgets(fileString, MAX, fptr) ) { if( 0 == strcmp(theWord, fileString) ) { iFound = -99; } } fclose(fptr); return(0); }//end of checkwORDiNFile

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  • Cant print contents of a custom file

    - by ZaZu
    Hello, Im trying to scan contents from a random file into an array in a structure. Then I want to print those contents on screen. (NOTE: The following code is from a bigger program, this is just a sample, but all structures and arrays used are needed as declared ) The contents of the file being tested are simply: 5 4 3 2 5 3 4 2 #include<stdio.h> #define first 500 #define sec 500 struct trial{ int f; int r; float what[first][sec]; }; int trialtest(trial *test); int trialdisplay(trial *test); main(){ trial test; trialtest(&test); trialdisplay(&test); } int trialtest(trial *test){ int z,x,i; FILE *inputf; inputf=fopen("randomfile.txt","r"); for(i=0;i<5;i++){ fscanf(inputf,"%f",&(*test).what[z][x]); } fclose(inputf); return 0; } int trialdisplay(trial *test){ int i,z,x; printf("printing\n\n\n"); for (i=0;i<10;i++){ printf("%f",(*test).what[z][x]); } return 0; } The problem is, I get this error whenever I run the code .. I cant really understand whats going on : Any suggestions ? Thanks alot !

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  • Modifying File while in use using Java

    - by Marquinio
    Hi all, I have this recurrent Java JAR program tasks that tries to modify a file every 60seconds. Problem is that if user is viewing the file than Java program will not be able to modify the file. I get the typical IOException. Anyone knows if there is a way in Java to modify a file currently in use? Or anyone knows what would be the best way to solve this problem? I was thinking of using the File canRead(), canWrite() methods to check if file is in use. If file is in use then I'm thinking of making a backup copy of data that could not be written. Then after 60 seconds add some logic to check if backup file is empty or not. If backup file is not empty then add its contents to main file. If empty then just add new data to main file. Of course, the first thing I will always do is check if file is in use. Thanks for all your ideas.

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  • How can I do block-oriented disk I/O with Java? Or similar for a B+ tree

    - by Sanoj
    I would like to implement an B+ tree in Java and try to optimize it for disk based I/O. Is there an API for accessing individual disk blocks from Java? or is there an API that can do similar block-oriented access that fits my purpose? I would like to create something like Tokyo Cabinet in 100% Java. Is there anyone that knows what Java only databases like JavaDB is using in the back-end for this? I know that there are probably other languages than Java that can do this better, but I do this in a learning purpose only.

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  • Most efficient way to write over file after reading

    - by Ryan McClure
    I'm reading in some data from a file, manipulating it, and then overwriting it to the same file. Until now, I've been doing it like so: open (my $inFile, $file) or die "Could not open $file: $!"; $retString .= join ('', <$inFile>); ... close ($inFile); open (my $outFile, $file) or die "Could not open $file: $!"; print $outFile, $retString; close ($inFile); However I realized I can just use the truncate function and open the file for read/write: open (my $inFile, '+<', $file) or die "Could not open $file: $!"; $retString .= join ('', <$inFile>); ... truncate $inFile, 0; print $inFile $retString; close ($inFile); I don't see any examples of this anywhere. It seems to work well, but am I doing it correctly? Is there a better way to do this?

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  • Do we need seperate file path for window and linux in java

    - by Kishor Sharma
    I have a file on linux ubuntu server hosted with path name /home/kishor/project/detail/. When I made a web app in window to upload and download file from specified location i used path "c:\kishor\projects\detail\" for saving in window. For my surprise when i used window file path name in my server i am still able to get files and upload them, i.e, "c:\kishor\projects\detail\". Can anyone explain why it is working (as window and linux both use different file path pattern).

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  • Batch backup a harddrive without modifying access times C#

    - by johnathan-doena
    I'm trying to write a simple program that will backup my flash drive. I want it to work automatically and silently in the background, and I also want it to be as quick as possible. The thing is, resetting all the access times is useless to me, and something I want to avoid. I know I can read the access times and set them back, but I bet it will fail one day in the future. It would be much simpler to read the files without ever changing it. Also, what is the fastest way to do this? What differences would there be between, say, a flash drive and an external hard drive. I am writing this in C#, as it is the simplest way to do it and it will probably last more generations of Windows..

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  • Homemade fstat to get file size, always return 0 length.

    - by Fred
    Hello, I am trying to use my own function to get the file size from a file. I'll use this to allocate memory for a data structure to hold the information on the file. The file size function looks like this: long fileSize(FILE *fp){ long start; fflush(fp); rewind(fp); start = ftell(fp); return (fseek(fp, 0L, SEEK_END) - start); } Any ideas what I'm doing wrong here?

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  • Efficient file buffering & scanning methods for large files in python

    - by eblume
    The description of the problem I am having is a bit complicated, and I will err on the side of providing more complete information. For the impatient, here is the briefest way I can summarize it: What is the fastest (least execution time) way to split a text file in to ALL (overlapping) substrings of size N (bound N, eg 36) while throwing out newline characters. I am writing a module which parses files in the FASTA ascii-based genome format. These files comprise what is known as the 'hg18' human reference genome, which you can download from the UCSC genome browser (go slugs!) if you like. As you will notice, the genome files are composed of chr[1..22].fa and chr[XY].fa, as well as a set of other small files which are not used in this module. Several modules already exist for parsing FASTA files, such as BioPython's SeqIO. (Sorry, I'd post a link, but I don't have the points to do so yet.) Unfortunately, every module I've been able to find doesn't do the specific operation I am trying to do. My module needs to split the genome data ('CAGTACGTCAGACTATACGGAGCTA' could be a line, for instance) in to every single overlapping N-length substring. Let me give an example using a very small file (the actual chromosome files are between 355 and 20 million characters long) and N=8 import cStringIO example_file = cStringIO.StringIO("""\ header CAGTcag TFgcACF """) for read in parse(example_file): ... print read ... CAGTCAGTF AGTCAGTFG GTCAGTFGC TCAGTFGCA CAGTFGCAC AGTFGCACF The function that I found had the absolute best performance from the methods I could think of is this: def parse(file): size = 8 # of course in my code this is a function argument file.readline() # skip past the header buffer = '' for line in file: buffer += line.rstrip().upper() while len(buffer) = size: yield buffer[:size] buffer = buffer[1:] This works, but unfortunately it still takes about 1.5 hours (see note below) to parse the human genome this way. Perhaps this is the very best I am going to see with this method (a complete code refactor might be in order, but I'd like to avoid it as this approach has some very specific advantages in other areas of the code), but I thought I would turn this over to the community. Thanks! Note, this time includes a lot of extra calculation, such as computing the opposing strand read and doing hashtable lookups on a hash of approximately 5G in size. Post-answer conclusion: It turns out that using fileobj.read() and then manipulating the resulting string (string.replace(), etc.) took relatively little time and memory compared to the remainder of the program, and so I used that approach. Thanks everyone!

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  • Check whether a folder is a local or a network resource in .NET

    - by rwmnau
    Is there a quick way to check whether a path I have is on a local disk or somewhere on the network? I can't just check to see if it's a drive letter vs. UNC, because that would incorrectly identify mapped drives as local. I assumed it would be a boolean in the DirectoryInfo object, but it appears that it's not. I've found classic VB code to do this check (through an API), but nothing for .NET so far.

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  • unix shell, redirect output but keep on stdin

    - by Mike
    I'd like to have a shell script redirect stdout of a child process in the following manner Redirect stdout to a file Display the output of the process in real time I know I could do something like #!/bin/sh ./child > file cat file But that would not display stdout in real time. For instance, if the child was #!/bin/sh echo 1 sleep 1 echo 2 The user would see "1" and "2" printed at the same time

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  • best way to output a full precision double into a text file

    - by flevine100
    Hi, I need to use an existing text file to store some very precise values. When read back in, the numbers essentially need to be exactly equivalent to the ones that were originally written. Now, a normal person would use a binary file... for a number of reasons, that's not possible in this case. So... do any of you have a good way of encoding a double as a string of characters (aside from increasing the precision). My first thought was to cast the double to a char[] and write out the chars. I don't think that's going to work because some of the characters are not visible, produce sounds, and even terminate strings ('\0'... I'm talkin to you!) Thoughts?

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  • close file with fclose() but file still in use

    - by Marco
    Hi all, I've got a problem with deleting/overwriting a file using my program which is also being used(read) by my program. The problem seems to be that because of the fact my program is reading data from the file (output.txt) it puts the file in a 'in use' state which makes it impossible to delete or overwrite the file. I don't understand why the file stays 'in use' because I close the file after use with fclose(); this is my code: bool bBool = true while(bBool){ //Run myprogram.exe tot generate (a new) output.txt //Create file pointer and open file FILE* pInputFile = NULL; pInputFile = fopen("output.txt", "r"); // //then I do some reading using fscanf() // //And when I'm done reading I close the file using fclose() fclose(pInputFile); //The next step is deleting the output.txt if( remove( "output.txt" ) == -1 ){ //ERROR }else{ //Succesfull } } I use fclose() to close the file but the file remains in use by my program until my program is totally shut down. What is the solution to free the file so it can be deleted/overwrited? In reality my code isn't a loop without an end ; ) Thanks in advance! Marco Update Like ask a part of my code which also generates the file 'in use'. This is not a loop and this function is being called from the main(); Here is a piece of code: int iShapeNr = 0; void firstRun() { //Run program that generates output.txt runProgram(); //Open Shape data file FILE* pInputFile = NULL; int iNumber = 0; pInputFile = fopen("output.txt", "r"); //Put all orientations of al detected shapes in an array int iShapeNr = 0; int iRotationBuffer[1024];//1024 is maximum detectable shapes, can be changed in RoboRealm int iXMinBuffer[1024]; int iXMaxBuffer[1024]; int iYMinBuffer[1024]; int iYMaxBuffer[1024]; while(feof(pInputFile) == 0){ for(int i=0;i<9;i++){ fscanf(pInputFile, "%d", &iNumber); fscanf(pInputFile, ","); if(i == 1) { iRotationBuffer[iShapeNr] = iNumber; } if(i == 3){//xmin iXMinBuffer[iShapeNr] = iNumber; } if(i == 4){//xmax iXMaxBuffer[iShapeNr] = iNumber; } if(i == 5){//ymin iYMinBuffer[iShapeNr] = iNumber; } if(i == 6){//ymax iYMaxBuffer[iShapeNr] = iNumber; } } iShapeNr++; } fflush(pInputFile); fclose(pInputFile); } The while loop parses the file. The output.txt contains sets of 9 variables, the number of sets is unknown but always in sets of 9. output.txt could contain for example: 0,1,2,3,4,5,6,7,8,8,7,6,5,4,1,2,3,0

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  • How to open files in Java Swing without JFileChooser

    - by ron
    I'm using Java Swing (GUI) and I want to add a button to my project for opening files . I don't like the JFileChooser since it opens a small window for browsing through the files of the directories . Can I use something else , instead of the JFileChooser under Java Swing ? I've tried to use elements of SWT but it didn't work , meaning is the use of the button object and then use it inside the Jframe , but that failed , so I guess SWT and Swing don't mix together? Here is the example of Java Swing with JFileChooser and I'm looking for something like this to put in my JFrame.

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  • Can't access my files in ASP.NET web site

    - by jumbojs
    I'm having a very difficult time. I am running windows 2008 server, I have an Able Commerce site using ASP.NET with C#. I'm writing an automated task that will ftp some xml files down into a local directory on our web server and then the program parses the xml file and saves information to our database. The problem, once I save the files to our local directory, my program has no access to the files. The NETWORK SERVICE user permissions isn't being inherited by the xml files so my program can't do anything with them. I can manually change the permissions, but this wouldn't be automated and won't work. How can I get this to work? help please, it's very frustrating.

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