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• Converting FASTQ to FASTA with SED/AWK

  - by neversaint

  I have a data in that always comes in block of four in the following format (called FASTQ): @SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN +SRR018006.2016 GA2:6:1:20:650 length=36 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!+! @SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC +SRR018006.19405469 GA2:6:100:1793:611 length=36 7);;).;);;/;*.2>/@@7;@77<..;)58)5/>/ Is there a simple sed/awk/bash way to convert them into this format (called FASTA): >SRR018006.2016 GA2:6:1:20:650 length=36 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGN >SRR018006.19405469 GA2:6:100:1793:611 length=36 ACCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC In principle we want to extract the first two lines in each block-of-4 and replace @ with >.

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• How to convert dos/windows newline to unix newline in bash script?

  - by Koran Molovik

  I bash, how do I convert dos/windows newlines to unix? It must be non-interactive, not like starting vi and typing something in, but a command on the command line that can be put in a script file. The dos2unix and unix2dos commands are not available on the system. How do I do this with commands like sed/awk/tr?

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• How to declare a(n) vector/array of reducer objects in Cilk++?

  - by Jin

  Hi All, I had a problem when I am using Cilk++, an extension to C++ for parallel computing. I found that I can't declare a vector of reducer objects: typedef cilk::reducer_opadd<int> T_reducer; vector<T_reducer> bitmiss_vec; for (int i = 0; i < 24; ++i) { T_reducer r; bitmiss_vec.push_back(r); } However, when I compile the code with Cilk++, it complains at the push_back() line: cilk++ geneAttack.cilk -O1 -g -lcilkutil -o geneAttack /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h: In member function ‘void __gnu_cxx::new_allocator<_Tp>::construct(_Tp*, const _Tp&) [with _Tp = cilk::reducer_opadd<int>]’: /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_vector.h:601: instantiated from ‘void std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’ geneAttack.cilk:667: instantiated from here /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h:229: error: ‘cilk::reducer_opadd<Type>::reducer_opadd(const cilk::reducer_opadd<Type>&) [with Type = int]’ is private /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/ext/new_allocator.h:107: error: within this context /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h: In member function ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(__gnu_cxx::__normal_iterator<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type::pointer, std::vector<_Tp, _Alloc> >, const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’: /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_vector.h:605: instantiated from ‘void std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’ geneAttack.cilk:667: instantiated from here /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h:229: error: ‘cilk::reducer_opadd<Type>::reducer_opadd(const cilk::reducer_opadd<Type>&) [with Type = int]’ is private /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/vector.tcc:252: error: within this context /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_vector.h:605: instantiated from ‘void std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’ geneAttack.cilk:667: instantiated from here /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h:230: error: ‘cilk::reducer_opadd<Type>& cilk::reducer_opadd<Type>::operator=(const cilk::reducer_opadd<Type>&) [with Type = int]’ is private /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/vector.tcc:256: error: within this context /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h: In static member function ‘static _BI2 std::__copy_backward<_BoolType, std::random_access_iterator_tag>::__copy_b(_BI1, _BI1, _BI2) [with _BI1 = cilk::reducer_opadd<int>*, _BI2 = cilk::reducer_opadd<int>*, bool _BoolType = false]’: /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_algobase.h:465: instantiated from ‘_BI2 std::__copy_backward_aux(_BI1, _BI1, _BI2) [with _BI1 = cilk::reducer_opadd<int>*, _BI2 = cilk::reducer_opadd<int>*]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_algobase.h:474: instantiated from ‘static _BI2 std::__copy_backward_normal<<anonymous>, <anonymous> >::__copy_b_n(_BI1, _BI1, _BI2) [with _BI1 = cilk::reducer_opadd<int>*, _BI2 = cilk::reducer_opadd<int>*, bool <anonymous> = false, bool <anonymous> = false]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_algobase.h:540: instantiated from ‘_BI2 std::copy_backward(_BI1, _BI1, _BI2) [with _BI1 = cilk::reducer_opadd<int>*, _BI2 = cilk::reducer_opadd<int>*]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/vector.tcc:253: instantiated from ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(__gnu_cxx::__normal_iterator<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type::pointer, std::vector<_Tp, _Alloc> >, const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_vector.h:605: instantiated from ‘void std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’ geneAttack.cilk:667: instantiated from here /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h:230: error: ‘cilk::reducer_opadd<Type>& cilk::reducer_opadd<Type>::operator=(const cilk::reducer_opadd<Type>&) [with Type = int]’ is private /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_algobase.h:433: error: within this context /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h: In function ‘void std::_Construct(_T1*, const _T2&) [with _T1 = cilk::reducer_opadd<int>, _T2 = cilk::reducer_opadd<int>]’: /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_uninitialized.h:87: instantiated from ‘_ForwardIterator std::__uninitialized_copy_aux(_InputIterator, _InputIterator, _ForwardIterator, std::__false_type) [with _InputIterator = cilk::reducer_opadd<int>*, _ForwardIterator = cilk::reducer_opadd<int>*]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_uninitialized.h:114: instantiated from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = cilk::reducer_opadd<int>*, _ForwardIterator = cilk::reducer_opadd<int>*]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_uninitialized.h:254: instantiated from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>) [with _InputIterator = cilk::reducer_opadd<int>*, _ForwardIterator = cilk::reducer_opadd<int>*, _Tp = cilk::reducer_opadd<int>]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/vector.tcc:275: instantiated from ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(__gnu_cxx::__normal_iterator<typename std::_Vector_base<_Tp, _Alloc>::_Tp_alloc_type::pointer, std::vector<_Tp, _Alloc> >, const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’ /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_vector.h:605: instantiated from ‘void std::vector<_Tp, _Alloc>::push_back(const _Tp&) [with _Tp = cilk::reducer_opadd<int>, _Alloc = std::allocator<cilk::reducer_opadd<int> >]’ geneAttack.cilk:667: instantiated from here /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/cilk++/reducer_opadd.h:229: error: ‘cilk::reducer_opadd<Type>::reducer_opadd(const cilk::reducer_opadd<Type>&) [with Type = int]’ is private /usr/local/cilk/bin/../lib/gcc/x86_64-unknown-linux-gnu/4.2.4/../../../../include/c++/4.2.4/bits/stl_construct.h:81: error: within this context make: *** [geneAttack] Error 1 jinchen@galactica:~/workspace/biometrics/genAttack$ make cilk++ geneAttack.cilk -O1 -g -lcilkutil -o geneAttack geneAttack.cilk: In function ‘int cilk cilk_main(int, char**)’: geneAttack.cilk:670: error: expected primary-expression before ‘,’ token geneAttack.cilk:670: error: expected primary-expression before ‘}’ token geneAttack.cilk:674: error: ‘bitmiss_vec’ was not declared in this scope make: *** [geneAttack] Error 1 The Cilk++ manule says it supports array/vector of reducers, although there are performance issues to consider: "If you create a large number of reducers (for example, an array or vector of reducers) you must be aware that there is an overhead at steal and reduce that is proportional to the number of reducers in the program. " Anyone knows what is going on? How should I declare/use vector of reducers? Thank you

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• bash and flock (file lock) - Doesn't seem to be locking....

  - by Rory

  I am playing with using flock, a bash command for file locks to prevent 2 different instances of the code from running more than once. I am using this testing code: ( ( flock -x 200 ; sleep 10 ; echo "original finished" ; ) 200>./test.lock ) & ( sleep 2 ; ( flock -x -w 2 200 ; echo "a finished" ) 200>./test.lock ) & I am running 2 subshells (backgrounded). The (flock NUM; ...) NUM>FILE syntax is from flock's man page. I expect that the first subshell will get an exclusive lock on test.lock, then wait 10 seconds, then print "original finished", all the time holding the lock. The second subshell will start at more or less the same time, wait 2 seconds, then try to get a lock on test.lock, but timeout after 2 seconds. If it gets a lock, then it'll print "a finished". If it doesn't get the lock, that subshell should stop, and nothing should be printed. Since the first subshell is waiting longer, it will keep the lock for 10 seconds, so the second subshell should not get the lock, and shouldn't finish. i.e. one should see "original finished" printed and not both. What actually happens is that "a finished" is printed, then "original finished" is printed. This implies that that the second subshell is either (a) not using the same lock as the first subhsell or (b) that it fails to get the lock, but continues to execute or (c) something else. Why don't those locks work?

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• Supressing GUI?

  - by Legend

  I am trying to run a plugin designed for Vuze using Java. For this I am using a command like this: /home/x/jre1.6.0_14/bin/java -Dazureus.config.path=/home/x/plugin_directory -Dfile.encoding=ANSI_X3.4-1968 -classpath /home/x/P/lib/swtgraphics2d.jar:/home/x/P/lib/Azureus2.jar:/home/x/P/lib/swt.jar org.gudy.azureus2.ui.swt.Main The problem with this is that the launch is failing with an error: changeLocale: *Default Language* != English (United States). Searching without country.. changeLocale: Searching for language English in *any* country.. changeLocale: no message properties for Locale 'English (United States)' (en_US), using 'English (default)' Invoking main failed java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.aelitis.azureus.launcher.MainExecutor$1.run(MainExecutor.java:37) at java.lang.Thread.run(Unknown Source) Caused by: org.eclipse.swt.SWTError: No more handles [gtk_init_check() failed] at org.eclipse.swt.SWT.error(SWT.java:3910) at org.eclipse.swt.widgets.Display.createDisplay(Display.java:863) at org.eclipse.swt.widgets.Display.create(Display.java:851) at org.eclipse.swt.graphics.Device.<init>(Device.java:152) at org.eclipse.swt.widgets.Display.<init>(Display.java:479) at org.eclipse.swt.widgets.Display.<init>(Display.java:470) at org.gudy.azureus2.ui.swt.mainwindow.SWTThread.<init>(SWTThread.java:84) at org.gudy.azureus2.ui.swt.mainwindow.SWTThread.createInstance(SWTThread.java:59) at org.gudy.azureus2.ui.swt.mainwindow.Initializer.<init>(Initializer.java:110) at org.gudy.azureus2.ui.swt.Main.<init>(Main.java:88) at org.gudy.azureus2.ui.swt.Main.main(Main.java:255) ... 6 more Exception in thread "MainRunner" java.lang.SecurityException: VM exit operation prohibited at org.gudy.azureus2.core3.security.impl.SESecurityManagerImpl$2.checkExit(SESecurityManagerImpl.java:274) at java.lang.Runtime.exit(Unknown Source) at java.lang.System.exit(Unknown Source) at com.aelitis.azureus.launcher.MainExecutor$1.run(MainExecutor.java:42) at java.lang.Thread.run(Unknown Source) I am sure that this is happening because I am running the program on a terminal. Is there a way to supress the GUI or let the program think that the GUI was spawned successfully? Any suggestions?

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• How to define GPS module in Android?

  - by Osama Gamal

  I'm porting android to Devkit8000 which is a BeagleBoard clone. I have a GPS module connected on /dev/ttyS0. I could successfully get NMEA output when writing "cat /dev/ttyS0" in the terminal emulator. I want to know how to let android know that there is a GPS module on /dev/ttyS0 and it is outputting NMEA standard? To be able to use the android.location class with it! Is there something to edit in the android's source? adding driver for example, writing a code with android-ndk or what?

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• Update RHEL 5.1 to 5.4

  - by Rayne

  Hi all, I have a server currently running RHEL 5.1, and I would like to upgrade it to RHEL 5.4. The server is not connected to the Internet, so I don't think I can use "yum update". How would I be able to upgrade my server, and is it just a small-scale upgrade, like Windows patches, leaving everything on the server intact, or would it delete everything that was on the server? Thank you. Regards, Rayne

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• Need help again altering output of script

  - by Aaron

  wget --output-document=- http://runescape.com/title.ws 2>/dev/null \ | grep PlayerCount \ | head -1l \ | sed 's/^[^>]*>//' \ | sed "s/currently.*$/$(date '+%m\/%d\/%Y %H:%m:%S')/" \ | cut -d">" -f 3,4 \ | sed 's/<\/span>//' \ | awk '{print $3, $4, $1, $2}' Will output: 03/19/2012 18:03:58 123,822 people Would anyone be able to help me rewrite this so the output looks like: 03/19/2012 18:03:58,123822,people I need it this way because when I import it into googledocs, everything with a comma gets separated. Thanks if you help!

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• Possible to recover mysql root pass with sudo server access?

  - by jonathonmorgan

  I've inherited development for a website on vps hosting, and have login info for a user with sudo privileges, but don't have the password for the mysql root user. After digging around a little, it looks like the only way to fix this is to stop mysql (something like this: http://waoewaoe.wordpress.com/2010/02/03/recover-reset-mysql-root-password/). But because the website it's serving is currently in production, I'm hoping you guys can enlighten me to any potential consequences (or let me know if there's typically a file where the password would be accessible). a) during the time mysql is stopped, information in the database won't be accessible, right -- even by other users? b) will resetting the root password have any impact on other users after mysql has restarted? Will their username/passwords still be valid? The current application is using an account with limited privileges to read/write to the database, and while 5min downtime in the middle of the night would probably go unnoticed, half a day while I tie up loose ends/figure out what I screwed up will land in me hot water. Thanks in advance for your help!

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• Using pthread to perform matrix multiplication

  - by shadyabhi

  I have both matrices containing only ones and each array has 500 rows and columns. So, the resulting matrix should be a matrix of all elements having value 500. But, I am getting res_mat[0][0]=5000. Even other elements are also 5000. Why? #include<stdio.h> #include<pthread.h> #include<unistd.h> #include<stdlib.h> #define ROWS 500 #define COLUMNS 500 #define N_THREADS 10 int mat1[ROWS][COLUMNS],mat2[ROWS][COLUMNS],res_mat[ROWS][COLUMNS]; void *mult_thread(void *t) { /*This function calculates 50 ROWS of the matrix*/ int starting_row; starting_row = *((int *)t); starting_row = 50 * starting_row; int i,j,k; for (i = starting_row;i<starting_row+50;i++) for (j=0;j<COLUMNS;j++) for (k=0;k<ROWS;k++) res_mat[i][j] += (mat1[i][k] * mat2[k][j]); return; } void fill_matrix(int mat[ROWS][COLUMNS]) { int i,j; for(i=0;i<ROWS;i++) for(j=0;j<COLUMNS;j++) mat[i][j] = 1; } int main() { int n_threads = 10; //10 threads created bcos we have 500 rows and one thread calculates 50 rows int j=0; pthread_t p[n_threads]; fill_matrix(mat1); fill_matrix(mat2); for (j=0;j<10;j++) pthread_create(&p[j],NULL,mult_thread,&j); for (j=0;j<10;j++) pthread_join(p[j],NULL); printf("%d\n",res_mat[0][0]); return 0; }

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• Total stack sizes of threads in one process

  - by David

  I use pthreads_attr_getthreadsizes() to get default stack size of one thread, 8MB on my machine. But when I create 8 threads and allocate a very large stack size to them, say hundreds of MB, the program crash. So, I guess, shall ("Number of threads" x "stack size of per thread") shall less than a value(virtual memory size)?

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• Error in unzipping a file from a python script running as daemon

  - by Fedrick

  I am getting an error whenever i try to run following unzip command from a python script which is running as a daemon Command : unzip abcd.zip /dev/null Error End-of-central-directory signature not found$ a zip file, or it constitutes one disk of a multi-part archive. In the latter case the central directory and zipfile comment will be found on the last disk(s) of this archive unzip: cannot find zipfile directory in one of abcd.zip$ abcd.zip.zip, and cannot find abcd.zip.ZIP, period. Could anyone help me in this regard? Thanks in advance.

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• Can't import my module when start my twisted application under root

  - by kepkin

  Here is absolutely minimal application so you could try to reproduce it on your machine. Having two files for example in /home/aln/tmp/tw_test: server.tac MyLib.py MyLib.py class Solver(object): def solve(self): """ do extremely complex stuff here """ print "Hello from solve" server.tac #!/usr/bin/python import MyLib from twisted.application import internet, service from twisted.internet import protocol, reactor, defer, utils, threads from twisted.protocols import basic class MyProtocol(basic.LineReceiver): def lineReceived(self, line): if line=="new job": self.transport.write("started a job" + '\r\n') self.factory.run_defered() class MyFactory(protocol.ServerFactory, MyLib.Solver): protocol = MyProtocol def run_defered_helper(self): self.solve() def run_defered(self): d = threads.deferToThread(self.run_defered_helper) application = service.Application('MyApplication') factory = MyFactory() internet.TCPServer(1079, factory).setServiceParent(service.IServiceCollection(application)) Everything works fine when I start it under non-root user. aln@aln-laptop:tw_test$ twistd -ny server.tac 2010-03-03 22:42:55+0300 [-] Log opened. 2010-03-03 22:42:55+0300 [-] twistd 8.2.0 (/usr/bin/python 2.6.4) starting up. 2010-03-03 22:42:55+0300 [-] reactor class: twisted.internet.selectreactor.SelectReactor. 2010-03-03 22:42:55+0300 [-] <class 'MyFactory'> starting on 1079 2010-03-03 22:42:55+0300 [-] Starting factory <MyFactory object at 0x2d5ea50> 2010-03-03 22:42:59+0300 [MyProtocol,0,127.0.0.1] Hello from solve ^C2010-03-03 22:43:01+0300 [-] Received SIGINT, shutting down. 2010-03-03 22:43:01+0300 [-] (Port 1079 Closed) 2010-03-03 22:43:01+0300 [-] Stopping factory <MyFactory object at 0x2d5ea50> 2010-03-03 22:43:01+0300 [-] Main loop terminated. 2010-03-03 22:43:02+0300 [-] Server Shut Down. But if try to start it under root (which is going to happen in my real application) I receive the following exception: aln@aln-laptop:tw_test$ sudo twistd -ny server.tac [sudo] password for aln: Traceback (most recent call last): File "/usr/lib/python2.6/dist-packages/twisted/application/app.py", line 694, in run runApp(config) File "/usr/lib/python2.6/dist-packages/twisted/scripts/twistd.py", line 23, in runApp _SomeApplicationRunner(config).run() File "/usr/lib/python2.6/dist-packages/twisted/application/app.py", line 411, in run self.application = self.createOrGetApplication() File "/usr/lib/python2.6/dist-packages/twisted/application/app.py", line 494, in createOrGetApplication application = getApplication(self.config, passphrase) --- <exception caught here> --- File "/usr/lib/python2.6/dist-packages/twisted/application/app.py", line 505, in getApplication application = service.loadApplication(filename, style, passphrase) File "/usr/lib/python2.6/dist-packages/twisted/application/service.py", line 390, in loadApplication application = sob.loadValueFromFile(filename, 'application', passphrase) File "/usr/lib/python2.6/dist-packages/twisted/persisted/sob.py", line 215, in loadValueFromFile exec fileObj in d, d File "server.tac", line 2, in <module> import MyLib exceptions.ImportError: No module named MyLib Failed to load application: No module named MyLib If I try to load MyLib module in the python intepreter under root, it works fine: aln@aln-laptop:tw_test$ sudo python Python 2.6.4 (r264:75706, Dec 7 2009, 18:43:55) [GCC 4.4.1] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import MyLib >>> import sys >>> print(sys.path) ['', '/usr/lib/python2.6', '/usr/lib/python2.6/plat-linux2', '/usr/lib/python2.6/lib-tk', '/usr/lib/python2.6/lib-old', '/usr/lib/python2.6/lib-dynload', '/usr/lib/python2.6/dist-packages', '/usr/lib/python2.6/dist-packages/PIL', '/usr/lib/python2.6/dist-packages/gst-0.10', '/usr/lib/pymodules/python2.6', '/usr/lib/python2.6/dist-packages/gtk-2.0', '/usr/lib/pymodules/python2.6/gtk-2.0', '/usr/local/lib/python2.6/dist-packages'] >>> sys.path is absolutely the same for aln user. I tried sudo -E too. Any suggestions?

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• How can i install sun java to Fedora 8

  - by Tushar Ahirrao

  Hi I want to install java on my fedora 8 server but come to the step 9 that is mention in http://fedorasolved.org/browser-solutions/java-i386 but at the step 10 when i enter the command ln -s /opt/jre1.6.0_18/plugin/i386/ns7/libjavaplugin_oji.so /usr/lib/mozilla/plugins/libjavaplugin_oji.so it gives following error ln -s /opt/jre1.6.0_18/plugin/i386/ns7/libjavaplugin_oji.so /usr/lib/mozilla/plugins/libjavaplugin_oji.so ln: creating symbolic link `/usr/lib/mozilla/plugins/libjavaplugin_oji.so': No such file or directory can you help me please?

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• sed to insert on first match only

  - by SS.

  UPDATED: Using sed, how can I insert (NOT SUBSTITUTE) a new line on only the first match of keyword for each file. Currently I have the following but this inserts for every line containing Matched Keyword and I want it to only insert the New Inserted Line for only the first match found in the file: sed -ie '/Matched Keyword/ i\New Inserted Line' *.* For example: Myfile.txt: Line 1 Line 2 Line 3 This line contains the Matched Keyword and other stuff Line 4 This line contains the Matched Keyword and other stuff Line 6 changed to: Line 1 Line 2 Line 3 New Inserted Line This line contains the Matched Keyword and other stuff Line 4 This line contains the Matched Keyword and other stuff Line 6

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• Serial port : Read data problem, not reading complete data

  - by Anuj Mehta

  Hi I have an application where I am sending data via serial port from PC1 (Java App) and reading that data in PC2 (C++ App). The problem that I am facing is that my PC2 (C++ App) is not able to read complete data sent by PC1 i.e. from my PC1 I am sending 190 bytes but PC2 is able to read close to 140 bytes though I am trying to read in a loop. Below is code snippet of my C++ App Open the connection to serial port serialfd = open( serialPortName.c_str(), O_RDWR | O_NOCTTY | O_NDELAY); if (serialfd == -1) { /* * Could not open the port. */ TRACE << "Unable to open port: " << serialPortName << endl; } else { TRACE << "Connected to serial port: " << serialPortName << endl; fcntl(serialfd, F_SETFL, 0); } Configure the Serial Port parameters struct termios options; /* * Get the current options for the port... */ tcgetattr(serialfd, &options); /* * Set the baud rates to 9600... */ cfsetispeed(&options, B38400); cfsetospeed(&options, B38400); /* * 8N1 * Data bits - 8 * Parity - None * Stop bits - 1 */ options.c_cflag &= ~PARENB; options.c_cflag &= ~CSTOPB; options.c_cflag &= ~CSIZE; options.c_cflag |= CS8; /* * Enable hardware flow control */ options.c_cflag |= CRTSCTS; /* * Enable the receiver and set local mode... */ options.c_cflag |= (CLOCAL | CREAD); // Flush the earlier data tcflush(serialfd, TCIFLUSH); /* * Set the new options for the port... */ tcsetattr(serialfd, TCSANOW, &options); Now I am reading data const int MAXDATASIZE = 512; std::vector<char> m_vRequestBuf; char buffer[MAXDATASIZE]; int totalBytes = 0; fcntl(serialfd, F_SETFL, FNDELAY); while(1) { bytesRead = read(serialfd, &buffer, MAXDATASIZE); if(bytesRead == -1) { //Sleep for some time and read again usleep(900000); } else { totalBytes += bytesRead; //Add data read to vector for(int i =0; i < bytesRead; i++) { m_vRequestBuf.push_back(buffer[i]); } int newBytesRead = 0; //Now keep trying to read more data while(newBytesRead != -1) { //clear contents of buffer memset((void*)&buffer, 0, sizeof(char) * MAXDATASIZE); newBytesRead = read(serialfd, &buffer, MAXDATASIZE); totalBytes += newBytesRead; for(int j = 0; j < newBytesRead; j++) { m_vRequestBuf.push_back(buffer[j]); } }//inner while break; } //while

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• kill + ignore to kill proccess if not alive

  - by yael

  how to tell kill command to ignore to kill proccess if the proccess not alive? for example 3453 is alive proccess but 44534 not kill -9 3453 44534

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• Fail2Ban - Log to mysql

  - by user319660

  Hi! We have a few servers with SSH public (using sFTP). Obviously, the attacks ar too many. We want put the banned logs into a MySQL DB for make stats and etc. Have anyone tryied this? Thanks

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• Debian Package Control file Question.

  - by AJ

  Hello, I need to create a debian package for a java application. In my package there a .jar file which is executable , a script which will run this jar file and a .so file for fmod. I read the tutorial provided at http://tldp.org/HOWTO/html_single/Debian-Binary-Package-Building-HOWTO/ My question is in control file there is a Depends field which basically mentions the packages that need to installed in order to install my application. How do i find which packages are required for my application. I followed the instructions provided in the link for one of the .so and did ~/Desktop/PennTotalRecall/native/fmod/lib/linux64$ dpkg -S libfmodex64-4.28.09.so dpkg: libfmodex64-4.28.09.so not found. It gives above result. Also my application requires java 1.5 to be installed in order for it to run. How do I specify in my debian package. Thanks, AJ

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• How does fork() return for son process

  - by EpsilonVector

  I know htat fork() returns differently for the son and father processes, but I'm unable to find information on how this happens. How does the son process receives the return value 0 from fork? And what is the difference in regards to the call stack? As I understand it, for the father it goes something like this: father process--invokes fork--system_call--calls fork--fork executes--returns to--system_call--returns to--father process. What happens in the son side?

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• Alternatives to gprof

  - by Phenom

  What other programs do the same thing as gprof?

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• How to define an alias in fish shell?

  - by armandino

  I would like to define some aliases in fish. Apparently it should be possible to define them in ~/.config/fish/functions but they don't get auto loaded when I restart the shell. Any ideas? p.s. if anyone is using or has used fish in the past I'd be interested to hear your comments as to whether it offers anything that bash does not.

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• Uninstall Git completely on Ubuntu?

  - by Millisami

  I installed Git on Ubuntu Lucid (latest) manually as following. cd ~/tmp wget http://kernel.org/pub/software/scm/git/git-1.7.0.6.tar.gz tar -xzvf git-1.7.0.6.tar.gz cd git-1.7.0.6.tar.gz ./configure sudo make sudo make install Now, how can I completely uninstall it?

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• kill -9 + disable messages (standart output) from kill command

  - by yael

  hi all I write the following script this script enable timeout of 20 second if grep not find the relevant string in the file the script working well but the output from the script is like that: ./test: line 11: 30039: Killed how to disable this message from the kill command? how to tell kill command to ignore if process not exist? THX Yael !/bin/ksh ( sleep 20 ; [[ ! -z ps -ef | grep "qsRw -m1" | awk '{print $2}' ]] && kill -9 2/dev/null ps -ef | grep "qsRw -m1" | awk '{print $2}' ; sleep 1 ) & RESULT=$! print "the proccess:"$RESULT grep -qsRw -m1 "monitohhhhhhhr" /var if [[ $? -ne 0 ]] then print "kill "$RESULT kill -9 $RESULT fi print "ENDED" ./test the proccess:30038 ./test: line 11: 30039: Killed kill 3003

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• Bash script, read values from stdin pipe

  - by gmatt

  I'm trying to get bash to process data from stdin that gets piped it, but no luck, what I mean is none of the following work: echo "hello world" | test=($(< /dev/stdin)); echo test=$test test= echo "hello world" | read test; echo test=$test test= echo "hello world" | test=`cat`; echo test=$test test= where I want the output to be test=hello world. Note I've tried putting "" quotes around "$test" that doesn't work either.

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