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  • Howto Plot "Reverse" Cumulative Frequency Graph With ECDF

    - by neversaint
    I have no problem plotting the following cumulative frequency graph plot like this. library(Hmisc) pre.test <- rnorm(100,50,10) post.test <- rnorm(100,55,10) x <- c(pre.test, post.test) g <- c(rep('Pre',length(pre.test)),rep('Post',length(post.test))) Ecdf(x, group=g, what="f", xlab='Test Results', label.curves=list(keys=1:2)) But I want to show the graph in forms of the "reverse" cumulative frequency of values x ? (i.e. something equivalent to what="1-f"). Is there a way to do it? Other suggestions in R other than using Hmisc are also very much welcomed.

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  • sudo changes PATH - why?

    - by Michiel de Mare
    This is the PATH variable without sudo: $ echo 'echo $PATH' | sh /opt/local/ruby/bin:/usr/bin:/bin This is the PATH variable with sudo: $echo 'echo $PATH' | sudo sh /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/X11R6/bin As far as I can tell, sudo is supposed to leave PATH untouched. What's going on? How do I change this? (This is on Ubuntu 8.04). UPDATE: as far as I can see, none of the scripts started as root change PATH in any way. From man sudo: To prevent command spoofing, sudo checks ``.'' and ``'' (both denoting current directory) last when searching for a command in the user's PATH (if one or both are in the PATH). Note, however, that the actual PATH environment variable is not modified and is passed unchanged to the program that sudo executes.

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  • waiting for 2 different events in a single thread

    - by João Portela
    component A (in C++) - is blocked waiting for alarm signals (not relevant) and IO signals (1 udp socket). has one handler for each of these. component B (java) - has to receive the same information the component A udp socket receives. periodicaly gives instructions that should be sent through component A udp socket. How to join both components? it is strongly desirable that: the changes to attach component B to component A are minimal (its not my code and it is not very pleasent to mess with). the time taken by the new operations (usually communicating with component B) interfere very little with the usual processing time of component A - this means that if the operations are going to take a "some" time I would rather use a thread or something to do them. note: since component A receives udp packets more frequently that it has component B instructions to forward, if necessary, it can only forward the instructions (when available) from the IO handler. my initial ideia was to develop a component C (in C++) that would sit inside the component A code (is this called an adapter?) that when instanciated starts the java process and makes the necessary connections (that not so little overhead in the initialization is not a problem). It would have 2 stacks, one for the data to give component B (lets call it Bstack) and for the data to give component A (lets call it Astack). It would sit on its thread (lets call it new-thread) waiting for data to be available in Bstack to send it over udp, and listen on the udp socket to put data on the Astack. This means that the changes to component A are only: when it receives a new UDP packet put it on the Bstack, and if there is something on the Astack sent it over its UDP socket (I decided for this because this socket would only be used in the main thread). One of the problems is that I don't know how to wait for both of these events at the same time using only one thread. so my questions are: Do I really need to use the main thread to send the data over component A socket or can I do it from the new-thread? (I think the answer is no, but I'm not sure about race conditions on sockets) how to I wait for both events? boost::condition_variable or something similar seems the solution in the case of the stack and boost::asio::io_service io_service.run() seems like the thing to use for the socket. Is there any other alternative solution for this problem that I'm not aware of? Thanks for reading this long text but I really wanted you to understand the problem.

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  • Microbenchmark showing process-switching faster than thread-switching; what's wrong?

    - by Yang
    I have two simple microbenchmarks trying to measure thread- and process-switching overheads, but the process-switching overhead. The code is living here, and r1667 is pasted below: https://assorted.svn.sourceforge.net/svnroot/assorted/sandbox/trunk/src/c/process_switch_bench.c // on zs, ~2.1-2.4us/switch #include <stdlib.h> #include <fcntl.h> #include <stdint.h> #include <stdio.h> #include <semaphore.h> #include <unistd.h> #include <sys/wait.h> #include <sys/types.h> #include <sys/time.h> #include <pthread.h> uint32_t COUNTER; pthread_mutex_t LOCK; pthread_mutex_t START; sem_t *s0, *s1, *s2; void * threads ( void * unused ) { // Wait till we may fire away sem_wait(s2); for (;;) { pthread_mutex_lock(&LOCK); pthread_mutex_unlock(&LOCK); COUNTER++; sem_post(s0); sem_wait(s1); } return 0; } int64_t timeInMS () { struct timeval t; gettimeofday(&t, NULL); return ( (int64_t)t.tv_sec * 1000 + (int64_t)t.tv_usec / 1000 ); } int main ( int argc, char ** argv ) { int64_t start; pthread_t t1; pthread_mutex_init(&LOCK, NULL); COUNTER = 0; s0 = sem_open("/s0", O_CREAT, 0022, 0); if (s0 == 0) { perror("sem_open"); exit(1); } s1 = sem_open("/s1", O_CREAT, 0022, 0); if (s1 == 0) { perror("sem_open"); exit(1); } s2 = sem_open("/s2", O_CREAT, 0022, 0); if (s2 == 0) { perror("sem_open"); exit(1); } int x, y, z; sem_getvalue(s0, &x); sem_getvalue(s1, &y); sem_getvalue(s2, &z); printf("%d %d %d\n", x, y, z); pid_t pid = fork(); if (pid) { pthread_create(&t1, NULL, threads, NULL); pthread_detach(t1); // Get start time and fire away start = timeInMS(); sem_post(s2); sem_post(s2); // Wait for about a second sleep(1); // Stop thread pthread_mutex_lock(&LOCK); // Find out how much time has really passed. sleep won't guarantee me that // I sleep exactly one second, I might sleep longer since even after being // woken up, it can take some time before I gain back CPU time. Further // some more time might have passed before I obtained the lock! int64_t time = timeInMS() - start; // Correct the number of thread switches accordingly COUNTER = (uint32_t)(((uint64_t)COUNTER * 2 * 1000) / time); printf("Number of process switches in about one second was %u\n", COUNTER); printf("roughly %f microseconds per switch\n", 1000000.0 / COUNTER); // clean up kill(pid, 9); wait(0); sem_close(s0); sem_close(s1); sem_unlink("/s0"); sem_unlink("/s1"); sem_unlink("/s2"); } else { if (1) { sem_t *t = s0; s0 = s1; s1 = t; } threads(0); // never return } return 0; } https://assorted.svn.sourceforge.net/svnroot/assorted/sandbox/trunk/src/c/thread_switch_bench.c // From <http://stackoverflow.com/questions/304752/how-to-estimate-the-thread-context-switching-overhead> // on zs, ~4-5us/switch; tried making COUNTER updated only by one thread, but no difference #include <stdlib.h> #include <stdint.h> #include <stdio.h> #include <pthread.h> #include <unistd.h> #include <sys/time.h> uint32_t COUNTER; pthread_mutex_t LOCK; pthread_mutex_t START; pthread_cond_t CONDITION; void * threads ( void * unused ) { // Wait till we may fire away pthread_mutex_lock(&START); pthread_mutex_unlock(&START); int first=1; pthread_mutex_lock(&LOCK); // If I'm not the first thread, the other thread is already waiting on // the condition, thus Ihave to wake it up first, otherwise we'll deadlock if (COUNTER > 0) { pthread_cond_signal(&CONDITION); first=0; } for (;;) { if (first) COUNTER++; pthread_cond_wait(&CONDITION, &LOCK); // Always wake up the other thread before processing. The other // thread will not be able to do anything as long as I don't go // back to sleep first. pthread_cond_signal(&CONDITION); } pthread_mutex_unlock(&LOCK); return 0; } int64_t timeInMS () { struct timeval t; gettimeofday(&t, NULL); return ( (int64_t)t.tv_sec * 1000 + (int64_t)t.tv_usec / 1000 ); } int main ( int argc, char ** argv ) { int64_t start; pthread_t t1; pthread_t t2; pthread_mutex_init(&LOCK, NULL); pthread_mutex_init(&START, NULL); pthread_cond_init(&CONDITION, NULL); pthread_mutex_lock(&START); COUNTER = 0; pthread_create(&t1, NULL, threads, NULL); pthread_create(&t2, NULL, threads, NULL); pthread_detach(t1); pthread_detach(t2); // Get start time and fire away start = timeInMS(); pthread_mutex_unlock(&START); // Wait for about a second sleep(1); // Stop both threads pthread_mutex_lock(&LOCK); // Find out how much time has really passed. sleep won't guarantee me that // I sleep exactly one second, I might sleep longer since even after being // woken up, it can take some time before I gain back CPU time. Further // some more time might have passed before I obtained the lock! int64_t time = timeInMS() - start; // Correct the number of thread switches accordingly COUNTER = (uint32_t)(((uint64_t)COUNTER * 2 * 1000) / time); printf("Number of thread switches in about one second was %u\n", COUNTER); printf("roughly %f microseconds per switch\n", 1000000.0 / COUNTER); return 0; }

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  • overview/history of resident memory usage

    - by kapet
    I have a fairly complicated program (Python with SWIG'ed C++ code, long running server) that shows a constantly growing resident memory usage. I've been digging with the usual tools for the leak (valgrind, Pythons gc module, etc.) but to no avail so far. I'm a bit afraid that the actual problem is memory fragmentation within Python and/or libc managed memory. Anyway, my question is more specific right now: Is there a tool to visualize resident memory usage and ideally show how it develops over time? I think the raw data is in /proc/$PID/smaps but I was hoping there's some tool that shows me a nice graph of the amounts used by mmap'ed files vs. anonymous mmap'ed memory vs. heap over time so that it's easier to see (literally) what's changing. I couldn't find anything though. Does anybody know of a ready to use tool that graphs memory usage over space and time in an intuitive way?

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  • How can I get `find` to ignore .svn directories?

    - by John Kugelman
    I often use the find command to search through source code, delete files, whatever. Annoyingly, because Subversion stores duplicates of each file in its .svn/text-base/ directories my simple searches end up getting lots of duplicate results. For example, I want to recursively search for uint in multiple messages.h and messages.cpp files: # find -name 'messages.*' -exec grep -Iw uint {} + ./messages.cpp: Log::verbose << "Discarding out of date message: id " << uint(olderMessage.id) ./messages.cpp: Log::verbose << "Added to send queue: " << *message << ": id " << uint(preparedMessage->id) ./messages.cpp: Log::error << "Received message with invalid SHA-1 hash: id " << uint(incomingMessage.id) ./messages.cpp: Log::verbose << "Received " << *message << ": id " << uint(incomingMessage.id) ./messages.cpp: Log::verbose << "Sent message: id " << uint(preparedMessage->id) ./messages.cpp: Log::verbose << "Discarding unsent message: id " << uint(preparedMessage->id) ./messages.cpp: for (uint i = 0; i < 10 && !_stopThreads; ++i) { ./.svn/text-base/messages.cpp.svn-base: Log::verbose << "Discarding out of date message: id " << uint(olderMessage.id) ./.svn/text-base/messages.cpp.svn-base: Log::verbose << "Added to send queue: " << *message << ": id " << uint(preparedMessage->id) ./.svn/text-base/messages.cpp.svn-base: Log::error << "Received message with invalid SHA-1 hash: id " << uint(incomingMessage.id) ./.svn/text-base/messages.cpp.svn-base: Log::verbose << "Received " << *message << ": id " << uint(incomingMessage.id) ./.svn/text-base/messages.cpp.svn-base: Log::verbose << "Sent message: id " << uint(preparedMessage->id) ./.svn/text-base/messages.cpp.svn-base: Log::verbose << "Discarding unsent message: id " << uint(preparedMessage->id) ./.svn/text-base/messages.cpp.svn-base: for (uint i = 0; i < 10 && !_stopThreads; ++i) { ./virus/messages.cpp:void VsMessageProcessor::_progress(const string &fileName, uint scanCount) ./virus/messages.cpp:ProgressMessage::ProgressMessage(const string &fileName, uint scanCount) ./virus/messages.h: void _progress(const std::string &fileName, uint scanCount); ./virus/messages.h: ProgressMessage(const std::string &fileName, uint scanCount); ./virus/messages.h: uint _scanCount; ./virus/.svn/text-base/messages.cpp.svn-base:void VsMessageProcessor::_progress(const string &fileName, uint scanCount) ./virus/.svn/text-base/messages.cpp.svn-base:ProgressMessage::ProgressMessage(const string &fileName, uint scanCount) ./virus/.svn/text-base/messages.h.svn-base: void _progress(const std::string &fileName, uint scanCount); ./virus/.svn/text-base/messages.h.svn-base: ProgressMessage(const std::string &fileName, uint scanCount); ./virus/.svn/text-base/messages.h.svn-base: uint _scanCount; How can I tell find to ignore the .svn directories?

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  • file_operations Question, how do i know if a process that opened a file for writing has decided to c

    - by djTeller
    Hi Kernel Gurus, I'm currently writing a simple "multicaster" module. Only one process can open a proc filesystem file for writing, and the rest can open it for reading. To do so i use the inode_operation .permission callback, I check the operation and when i detect someone open a file for writing I set a flag ON. i need a way to detect if a process that opened a file for writing has decided to close the file so i can set the flag OFF, so someone else can open for writing. Currently in case someone is open for writing i save the current-pid of that process and when the .close callback is called I check if that process is the one I saved earlier. Is there a better way to do that? Without saving the pid, perhaps checking the files that the current process has opened and it's permission... Thanks!

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  • EXMPP Buillding Error

    - by pradeepchhetri
    I am trying to install exmpp but while building i am getting the following error: exmpp_tls_openssl.c: In function 'init_library': exmpp_tls_openssl.c:622: error: 'SSL_OP_NO_TICKET' undeclared (first use in this function) exmpp_tls_openssl.c:622: error: (Each undeclared identifier is reported only once exmpp_tls_openssl.c:622: error: for each function it appears in.) make[2]: *** [exmpp_tls_openssl_la-exmpp_tls_openssl.lo] Error 1 I have openssl-dev and openssl both installed. Can someone please tell me what is the problem.

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  • Tee a Pipe Asynchronously

    - by User1
    I would like to write the same information to two pipes, but I don't want to wait for the first pipe to read. Here's an example mkfifo one mkfifo two echo hi | tee one two & cat one & cat two & cat one does not start reading until cat two is run. Is there a way to make cat one run without waiting?

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  • Bash PATH: How long is too long?

    - by ajwood
    Hi, I'm currently designing a software quarantine pattern to use on Ubuntu. I'm not sure how standard "quarantine" is in this context, so here is what I hope to accomplish... Inside a particular quarantine is all of the stuff one needs to run an application (bin, share, lib, etc.). Ideally, the quarantine has no leaks, which means it's not relying on any code outside of itself on the system. A quarantine can be defined as a set of executables (and some environment settings needed to make them run). I think it will be beneficial to separate the built packages enough such that upgrading to a newer version of the quarantine won't require rebuilding the whole thing. I'll be able to update just a few packages, and then the new quarantine can use some of old parts and some of the new parts. One issue I'm wondering about is the environment variables I'll be setting up to use a particular quarantines. Is there a hard limit on how big PATH can be? (either in number of characters, or in the number of directories it contains) Might a path be so long that it affects performance? Thanks very much, Andrew p.s. Any other wisdom that might help my design would be greatly appreciated :)

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  • c, pass awk syntax as argument to execl

    - by Skuja
    I want to run following command in c to read systems cpu and memory usage: ps aux|awk 'NR > 0 { cpu +=$3; ram+=$4 }; END {print cpu,ram}' I am trying to pass it to execl command and after that read its output: execl("/bin/ps", "/bin/ps", "aux|awk", "'NR > 0 { cpu +=$3; ram+=$4 }; END {print cpu,ram}'",(char *) 0); but in terminal i am getting following error: ERROR: Unsupported option (BSD syntax) I would like to know how to properly pass awk as argument to execl?

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  • Question about using awk to print all columns great then nth

    - by Andy
    right now I have this line, and it worked until I had whitespace in the second field. svn status | grep '\!' | gawk '{print $2;}' > removedProjs is there a way to have awk print everything in $2 or greater? ($3, $4.. until we don't have anymore columns?) I suppose I should add that I'm doing this in a windows environment with cygwin.

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  • Convert HTML to RTF (HTML2RTF converter)

    - by Luca Matteis
    I'm looking for a simple HTML2RTF converter that I can use on my website which is using a *nix like Operating System. I haven't found anything on the internet, and was hoping the SO community would help me. PS: I don't want to implement this from scratch, and it doesn't really matter what language it's in, as long as I can run it on a *nix like system. If you guys have already some personalized implementation, the language preferred would be PHP.

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  • rsyncing - ignoring checksums

    - by paulj3000
    Trying to copy a bunch of data over and time, unfortunately, is of the essence. I'd like to do an rsync of all the data in one direction, pretty much rsync just clobbers what's over on the destination server. Is there a way to do an rsync and just say, "overwrite all files" Is there a better way of doing this? We're talking 500GB of data that only has to go in one direction.

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  • How to store and echo multiple lines elegantly in bash?

    - by EmpireJones
    I'm trying to capture a block of text into a variable, with newlines maintained, then echo it. However, the newlines don't seemed to be maintained when I am either capturing the text or displaying it. Any ideas regarding how I can accomplish this? Example: #!/bin/bash read -d '' my_var <<"BLOCK" this is a test BLOCK echo $my_var Output: this is a test Desired output: this is a test

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  • ldd output showing shared object file whose function is not called

    - by iamrohitbanga
    I ran ldd command on an executable created by Open MPI. It shows a reference to libpthread.so Using LD_PRELOAD variable I created my own implementation of pthread_create, but from the it output it seems that MPI implementation is not calling pthread_create as I had expected. Why does ldd show pthread so file in output if it is not being used? does Open MPI not use a separate MPI thread for every node to implement the functionality?

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  • Optimal directory structure for filesystem

    - by Pankaj
    We have large scale web application which has millions of customer. Each customer can have document based on document type. We may have 20-30 types of documents. We are planning to use GlusterFS for storing these documents. I'm trying to find out what are the limitations of Gluster as far as number of files/directories ? Do we need to have hierarchical directory structure ? What would be the optimal directory structure ? Does this make sense - CustmerId Documenttype File1 File2

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  • Socket left in TIME_WAIT after file transfer via netcat

    - by com
    Using Copying by NetCat I am trying to copy files throught network by NetCat. From console it work pretty well. First I run listening netcat on the destination machine and after I run sending on source machine. The problem is it's doen't work from script from the source machine: ssh -f user@$desthost 'nc -l 1234 | tar xvf - /dev/null &' #listening on destination host tar cv /tmp/file | nc $desthost 1234 #sending to destination host I saw that after running port 1234 is still was open and status of the socket was TIME_WAIT. If you know what's the problem, please, help me out. And by the way, after copying how can I validate that the content is identical? Thanks! Addendum: I found one very strange thing, the same implementation with screen on destination work works, but not stable, sometimes it doesn't copy a file. ssh user@$desthost screen -dm -S test 'nc -l 1234 | tar xvf - ' #listening on destination host Maybe there is an issue with timeout?

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  • Use the output of a command as input of the next command

    - by r2b2
    so i call this php script from the command line : /usr/bin/php /var/www/bims/index.php "projects/output" and it's output is : file1 file2 file3 What I would like to do is get this output and feed to the "rm" command but i think im not doing it right : /usr/bin/php /var/www/bims/index.php "projects/output" | rm My goal is to delete whatever file names the php script outputs. What should be the proper way to do this? Thanks!

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  • compare time using date command

    - by Andrei
    Say I want a certain block of bash script execute only if it is between 8 am (8:00) and 5 pm (17:00), and do nothing otherwise. The script is running continuously So far I am using date command. How to use it compare it current time within the range? Thanks

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  • Simple POSIX threads question

    - by Andy
    Hi, I have this POSIX thread: void subthread(void) { while(!quit_thread) { // do something ... // don't waste cpu cycles if(!quit_thread) usleep(500); } // free resources ... // tell main thread we're done quit_thread = FALSE; } Now I want to terminate subthread() from my main thread. I've tried the following: quit_thread = TRUE; // wait until subthread() has cleaned its resources while(quit_thread); But it does not work! The while() clause does never exit although my subthread clearly sets quit_thread to FALSE after having freed its resources! If I modify my shutdown code like this: quit_thread = TRUE; // wait until subthread() has cleaned its resources while(quit_thread) usleep(10); Then everything is working fine! Could someone explain to me why the first solution does not work and why the version with usleep(10) suddenly works? I know that this is not a pretty solution. I could use semaphores/signals for this but I'd like to learn something about multithreading, so I'd like to know why my first solution doesn't work. Thanks!

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