This is commonly caused by running out of file descriptors. 

There is the systems total file descriptor limit, what do you get from the command:

    sysctl fs.file-nr

This returns counts of file descriptors:

    &lt;in_use&gt; &lt;unused_but_allocated&gt; &lt;maximum&gt;

To find out what a users file descriptor limit is run the commands:

    sudo su - &lt;username&gt;
    ulimit -Hn

To find out how many file descriptors are in use by a user run the command:

    sudo lsof -u &lt;username&gt; 2&gt;/dev/null | wc -l

So now if you are having a system file descriptor limit issue you will need to edit your /etc/sysctl.conf file and add, or modify it it already exists, a line with fs.file-max and set it to a value large enough to deal with the number of file descriptors you need and reboot.

    fs.file-max = 204708

Another possibility is too many threads. We just ran into this error message when running a test harness against an app that uses a thread pool. We used

    watch -n 5 -d &quot;ps -eL &lt;java_pid&gt; | wc -l&quot;

to watch the ongoing count of Linux native threads running within the given Java process ID. After this hit about 1,000 (for us--YMMV), we started getting the error message you mention.


    myInterval = setInterval(function(){
         MyFunction();
    },50);

    function MyFunction()
    {
        //Can I call clearInterval(myInterval); in here?
    }

The interval&#39;s not stopping (not being cleared), if what I&#39;ve coded above is fine then it&#39;ll help me look elsewhere for what&#39;s causing the problem. Thanks.

EDIT: Let&#39;s assume it completes a few intervals before clearInterval is called which removes the need for setTimeout.

Javascript setInterval function to clear itself?

I&#39;m trying to understand how [`Flask-Login`][1] works.

I see in their documentation that they use a pre-populated list of users. I want to play with a database-stored users list.

However, I don&#39;t understand some things in this [`Flask-Login`][1] module.

&lt;!-- language: lang-py --&gt;

    @login_manager.user_loader
    def load_user(userid):
        #print &#39;this is executed&#39;,userid
        return user(userid, &#39;asdf&#39;)

This code will be called at every request? This is used to load all the details of my user object?

For now, I have this code:

&lt;!-- language: lang-py --&gt;

    @app.route(&#39;/make-login&#39;)
    def make_login():
        username = &#39;asdf&#39;
        password = &#39;asdf&#39;
        user_data = authenticate(username, password)
        user_obj = user(user_data[0], user_data[1])
        login_user(user_obj)
        return render_template(&#39;make-login.html&#39;)

When I access /make-login, I want to log in.

My user class:

&lt;!-- language: lang-py --&gt;

    class user(object):
        def __init__(self, id, username, active=True):
            self.username = username
            self.id = id
            #self.active = active
        def is_authenticated(self):
            return True  
                
        def is_active(self):
            return True
        
        def is_anonymous(self):
            return False
        
        def get_id(self):
            return 5

Also, I wrote another two functions for authenticate/register

&lt;!-- language: lang-py --&gt;

    def authenticate(username, password):
        
        cursor = db.cursor()
        password = md5.md5(password).hexdigest()
        try:
            query = &quot;SELECT * FROM `users` WHERE `username` = %s AND `password` = %s&quot;
            cursor.execute(query, (username, password))
            results = cursor.fetchall()
            #print results[0][0]
            #print &quot;here i am&quot;
            if not results:
                return False
            else:
                user_data = [results[0][0], results[0][1]]
                return user_data
                #self.authenticated = True
                #self.user_id = results[0][0]
                #session[&#39;username&#39;]  = results[&#39;username&#39;]
                #print type(results)
        except db.Error, e:
            return &#39;There was a mysql error&#39;    
    
    def register(username, password, email, *args):
        cursor = db.cursor()
        password = md5.md5(password).hexdigest()
        try:
            #query = &quot;INSERT INTO `users` (`username`, `password`, `email`) VALUES (&#39;%s&#39;, &#39;%s&#39;, &#39;%s&#39;)&quot; % (username, password, email)
            query = &quot;INSERT INTO `users` (`username`, `password`, `email`) VALUES (%s, %s, %s)&quot;
            cursor.execute(query, (username, password, email))
            db.commit()
            return True
        except db.Error, e:
            print &#39;An error has been passed. %s&#39; %e
            db.rollback()
            return False


I don&#39;t know how to make this [`Flask-Login`][1] work with MySQL. Also, I don&#39;t know if the user are logged-in. How can I get the user ID or the username?

Anyone can explain me in some rows how this [`Flask-Login`][1] works?


  [1]: https://flask-login.readthedocs.org/en/latest/

flask-login: can&#39;t understand how it works

I tried installing Intel MPI Benchmark on my computer and I got this error:

    fork: retry: Resource temporarily unavailable

Then I received this error again when I ran `ls` and `top` command.

What is causing this error?

Configuration of my machine:

    Dell precision T7500
    Scientific Linux release 6.2 (Carbon)


fork: retry: Resource temporarily unavailable

I tried installing Intel MPI Benchmark on my computer and I got this error:
<pre><code class="hljs language-makefile">fork: retry: Resource temporarily unavailable
</code></pre>
Then I received this error again when I ran <code>ls</code> and <code>top</code> command.
What is causing this error?
Configuration of my machine:
<pre><code class="hljs language-sql">Dell precision T7500
Scientific Linux release 6.2 (Carbon)
</code></pre>

In UNIX/LINUX, is there an easy way to track the time a command takes?


Track the time a command takes in UNIX/LINUX?

We are looking to upgrade the OS on our servers from Ubuntu 10.04 LTS to Ubuntu 12.04 LTS. Unfortunately, it seems that the latency to run a thread that has become runnable has significantly increased from the 2.6 kernel to the 3.2 kernel. In fact the latency numbers we are getting are hard to believe.

Let me be more specific about the test. We have a program that runs two threads. The first thread gets the current time (in ticks using RDTSC) and then signals a condition variable once a second. The second thread waits on the condition variable and wakes up when it is signaled. It then gets the current time (in ticks using RDTSC). The difference between the time in the second thread and the time in the first thread is computed and displayed on the console. After this the second thread waits on the condition variable once more. It will be signaled again by the first thread after about a second passes. 

So, in a nutshell we get a *thread to thread communication via condition variable* latency measurement once a second as a result.

In kernel 2.6.32, this latency is somewhere on the order of 2.8-3.5 us, which is reasonable. In kernel 3.2.0, this latency has increased to somewhere on the order of 40-100 us. I have excluded any differences in hardware between the two hosts. They run on identical hardware (dual socket X5687 {Westmere-EP} processors running at 3.6 GHz with hyperthreading, speedstep and all C states turned off). The test app changes the affinity of the threads to run them on independent physical cores of the same socket (i.e., the first thread is run on Core 0 and the second thread is run on Core 1), so there is no bouncing of threads on cores or bouncing/communication between sockets.

The only difference between the two hosts is that one is running Ubuntu 10.04 LTS with kernel 2.6.32-28 (the fast context switch box) and the other is running the latest Ubuntu 12.04 LTS with kernel 3.2.0-23 (the slow context switch box). All BIOS settings and hardware are identical.

Have there been any changes in the kernel that could account for this ridiculous slow down in how long it takes for a thread to be scheduled to run?

**Update:**
If you would like to run the test on your host and linux build, I have [posted the code to pastebin] for your perusal. Compile with:

    g++ -O3 -o test_latency test_latency.cpp -lpthread

Run with (assuming you have at least a dual-core box):

    ./test_latency 0 1 # Thread 1 on Core 0 and Thread 2 on Core 1

[posted the code to pastebin]: http://pastebin.com/3sx8Vhf1

**Update 2**:
After much searching through kernel parameters, posts on kernel changes and personal research, I have figured out what the problem is and have posted the solution as an answer to this question.


Context switches much slower in new linux kernels

It there a way to see what compiler and flags were used to create an executable file in *nix? I have an old version of my code compiled and I would like to see whether it was compiled with or without optimization. Google was not too helpful, but I&#39;m not sure I am using the correct keywords.

Get the compiler options from a compiled executable?

Please point out the point that I am missing:  

**openSUSE 11.3**

----------


    xx@linux-y3pi:~/Desktop/R&gt; sudo R CMD INSTALL rgdal_0.7-12.tar.gz 
    root&#39;s password:
    * installing to library ‘/usr/lib64/R/library’
    * installing *source* package ‘rgdal’ ...
    ** package ‘rgdal’ successfully unpacked and MD5 sums checked
    configure: gdal-config: gdal-config
    checking gdal-config usability... ./configure: line 1353: gdal-config: command not found
    no
    Error: gdal-config not found
    The gdal-config script distributed with GDAL could not be found.
    If you have not installed the GDAL libraries, you can
    download the source from  http://www.gdal.org/
    If you have installed the GDAL libraries, then make sure that
    gdal-config is in your path. Try typing gdal-config at a
    shell prompt and see if it runs. If not, use:
     --configure-args=&#39;--with-gdal-config=/usr/local/bin/gdal-config&#39;
    with appropriate values for your installation.
    
    ERROR: configuration failed for package ‘rgdal’
    * removing ‘/usr/lib64/R/library/rgdal’


----------

    xx@linux-y3pi:~/Desktop/R&gt; whereis gdal-config
    gdal-config: /usr/local/bin/gdal-config
    
    xx@linux-y3pi:~/Desktop/R&gt; gdal-config 
    Usage: gdal-config [OPTIONS]
    Options:
     [--prefix[=DIR]]
     [--libs]
     [--dep-libs]
     [--cflags]
     [--datadir]
     [--version]
     [--ogr-enabled]
     [--formats]
     xx@linux-y3pi:~/Desktop/R&gt;


----------


    &gt; sessionInfo()
    R version 2.15.1 (2012-06-22)
    Platform: x86_64-unknown-linux-gnu (64-bit)
    
    locale:
     [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
     [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
     [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
     [7] LC_PAPER=C                 LC_NAME=C                 
     [9] LC_ADDRESS=C               LC_TELEPHONE=C            
    [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
    
    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base     
    &gt; 


----------

    xx@linux-y3pi:~/Desktop/R&gt; gdal-config --version
    1.9.0

    xx@linux-y3pi:~/Desktop/R&gt; proj
    Rel. 4.8.0, 6 March 2012
    usage: proj [ -beEfiIlormsStTvVwW [args] ] [ +opts[=arg] ] [ files ]


----------

    linux-y3pi:~ # $PATH
    bash: /home/xx/qtsdk-2010.05/qt/bin/:/home/xx/qtsdk-2010.05/bin:/home/xx/qtsdk-2010.05/qt/bin:/home/xx/qtsdk-2010.05/qt/bin/:/home/xx/qtsdk-2010.05/bin:/usr/lib64/mpi/gcc/openmpi/bin:/home/xx/bin:/usr/local/bin:/usr/bin:/sbin:/usr/sbin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games: No such file or directory



Error: gdal-config not found while installing R dependent packages whereas gdal is installed

I have downloaded from a hardware vendor just a tarball of their Linux source tree (no Git repository metadata), is there a way to find out the version number of the kernel?

Is the version number usually stored in a file somewhere in the source tree?

I&#39;d like to be able to do this without compiling and running the kernel.



Where do I find the version of a Linux kernel source tree?

In fork child, if we modify a global variable, it will not get changed in the main program.

Is there a way to change a global variable in child fork?

    #include &lt;stdio.h&gt;
    #include &lt;stdlib.h&gt;
    #include &lt;unistd.h&gt;
    
    int glob_var;
    
    main (int ac, char **av)
    {
      int pid;
    
      glob_var = 1;
    
      if ((pid = fork()) == 0) {
        /* child */
        glob_var = 5;
      }
      else {
        /* Error */
        perror (&quot;fork&quot;);
        exit (1);
      }
    
      int status;
      while (wait(&amp;status) != pid) {
      }
       printf(&quot;%d\n&quot;,glob_var); // this will display 1 and not 5.
    }

How to share memory between processes created by fork()?

I have used threading before in my applications and know its concepts well, but recently in my operating system lecture I came across fork(). Which is something similar to threading.

I google searched difference between them and I came to know that:

 1. Fork is nothing but a new process that looks exactly like the old or the parent process but still it is a different process with different process ID and having  it’s own memory.
 2. Threads are light-weight process which have less overhead

But, there are still some questions in my mind.

 1. When should you prefer fork() over threading and vice-verse?
 2. If I want to call an external application as a child, then should I use fork() or threads to do it?
 3. While doing google search I found people saying it is bad thing to call a fork() inside a thread. why do people want to call a fork() inside a thread when they do similar things?
 4. Is it True that fork() cannot take advantage of multiprocessor system because parent and child process don&#39;t run simultaneously?


Forking vs Threading

I&#39;m hoping someone could shed some light on how to make the parent wait for _ALL_ child processes to finish before continuing after the fork. I have cleanup code which I want to run but the child processes need to have returned before this can happen.

    for (int id=0; id&lt;n; id++) {
      if (fork()==0) {
        // Child
        exit(0);      
      } else {
        // Parent
        ...
      }
      ...
    }

How to make parent wait for all child processes to finish?

A Zombie is created when a parent process does not use the wait system call after a child dies to read its exit status, and an orphan is child process that is reclaimed by init when the original parent process terminates before the child. 

In terms of memory management and the process table how are these processes handled differently, specifically in UNIX? 

What is an example or extreme case when the creation of zombies or orphans can be detrimental to the greater application or system?

Zombie process vs Orphan process

After few explorations, In my understanding, it is related to contribution.

Fork means to make a copy of the repository (the one being forked) into my own github account.
If I want to fork the official jQuery repository, then I would go to https://github.com/jquery/jquery and hit the &quot;Fork&quot; button and GitHub will copy the repository (jquery) to my account (http://github.com/sanjaykhadka). Then a copied version of that repository will be available to me at http://github.com/sanjaykhadka/jquery

Now I can make whatever the changes I wish to make to my repository and then send a pull request to the original repository (jQuery&#39;s repository), asking the jQuery team to merge my changes into their original repository.

Did I understand it properly, or does it mean something more or something else?

What does it mean to fork on GitHub?

As per my little knowledge `mpirun` and `mpiexec` both are launcher. Can anybody tell the exact difference between `mpiexec` and `mpirun`?

mpiexec vs mpirun

when I compile my script with only

    #include &lt;mpi.h&gt;

it tells me that there is no such file or directory.
But when i include the path to mpi.h as

    #include &quot;/usr/include/mpi/mpi.h&quot;

(the path is correct) it returns:
 

    In file included from /usr/include/mpi/mpi.h:2087:0,
                     from lbm.cc:7:
    /usr/include/mpi/openmpi/ompi/mpi/cxx/mpicxx.h:35:17: fatal error: mpi.h: No such file or directory
     #include &quot;mpi.h&quot;
                     ^
    compilation terminated.

Anyone know how to fix this?

fatal error: mpi.h: No such file or directory #include &lt;mpi.h&gt;

The `type map` is an important but confounding concept in MPI.  I would like a routine to display or print a type map for me. 

For example (taken from the MPI-3 standard),

     MPI_TYPE_CREATE_RESIZED(MPI_INT, -3, 9, type1) 

results in the typemap 

    {(lb_marker, -3), (int, 0), (ub_marker, 6)}.

Use that type again:

    MPI_TYPE_CONTIGUOUS(2, type1, type2) 

and the typemap is 

    {(lb_marker, -3), (int, 0), (int,9), (ub_marker, 15)}

I would like a way to display that typemap automatically. 

Certainly one could use `MPI_Type_get_contents` and `MPI_Type_get_envelope` and recursively descend until hitting the built-in types.  This is rather a giant pain and I would have thought 20 years on some tool would exist to do this for me. 

Some tools that are promising, but not quite working:

 * I had found MPImap from ~ 2001 [here][1].  First, it needs to be updated for modern Tcl/TK, patched to address some memory errors and after you do that; you get an unresponsive GUI.  Instead, I&#39;m looking for a library/routine I can call at run time. 

 * `MPIDU_Datatype_deubg` is an MPICH specific internal type-dumping routine.  It does not display the type map (it does display the dataloop representation, again close)

 * There once was a debugger called XMPI that lists among its features the ability to display a MPI type map.  This debugger appears to be LAM-MPI specific and does not make use of get_contents/ get_envelope.


  [1]: http://computation.llnl.gov/casc/mpimap/

Display a MPI typemap

I would like to know (in a few words) what are the main differences between OpenMP and MPI.

What are the differences between MPI and OpenMP?

I am trying to create a dumb version of a spin lock. Browsing the web, I came across a assembly instruction called &quot;PAUSE&quot; in x86 which is used to give hint to a processor that a spin-lock is currently running on this CPU. The intel manual and other information available state that 

&gt; The processor uses this hint to avoid the memory order violation in
&gt; most situations, which greatly improves processor performance. For
&gt; this reason, it is recommended that a PAUSE instruction be placed in
&gt; all spin-wait loops. The documentation also mentions that  &quot;wait(some
&gt; delay)&quot; is the pseudo implementation of the instruction.

The last line of the above paragraph is intuitive. If I am unsuccessful in grabbing the lock, I must wait for some time before grabbing the lock again.

However, what do we mean by memory order violation in case of a spin lock? 
Does &quot;memory order violation&quot; mean the incorrect *speculative* load/store of the instructions after spin-lock?

The spin-lock question has been asked on Stack overflow before but the memory order violation question remains unanswered (at-least for my understanding).

 

What is the purpose of the &quot;PAUSE&quot; instruction in x86?

I&#39;m confused on how many flops per cycle per core can be done with Sandy-Bridge and Haswell.
As I understand it with SSE it should be 4 flops per cycle per core for SSE and 8 flops per cycle per core for AVX/AVX2.  

This seems to be verified here,
https://stackoverflow.com/questions/8389648/how-to-achieve-4-flops-per-cycle
,and here,
https://stackoverflow.com/questions/12027922/sandy-bridge-cpu-specification.

However the link below seems to indicate that Sandy-bridge can do 16 flops per cycle per core and Haswell 32 flops per cycle per core
http://www.extremetech.com/computing/136219-intels-haswell-is-an-unprecedented-threat-to-nvidia-amd.

Can someone explain this to me?

Edit:
I understand now why I was confused.  I thought the term FLOP only referred  to single floating point (SP).  I see now that the test at https://stackoverflow.com/questions/8389648/how-to-achieve-4-flops-per-cycle are actually on double floating point (DP) so they achieve 4 DP FLOPs/cycle for SSE and 8 DP FLOPs/cycle for AVX.  It would be interesting to redo these test on SP.

FLOPS per cycle for sandy-bridge and haswell SSE2/AVX/AVX2

I have an issue with my HAXM installation. Here is the thing. I got this error every single time I tried to install HAXM for my computer:
![Installation error print-screen][1]

Problem is, that my computer supports Virtualization Technology (see pic below). Any idea how to fix this issue?
![enter image description here][2]


  [1]: http://i.stack.imgur.com/IRJU3.png
  [2]: http://i.stack.imgur.com/yW2H5.png

Intel HAXM installation error - This computer does not support Intel Virtualization Technology (VT-x)

I&#39;m trying to use the Intel HAX x86 emulator for Windows (8, if that matters).  I installed everything and created an AVD for the android version, and everything appears correct, but when I run it, I get this output:

    Starting emulator for AVD &#39;x86_QVGA_Level10&#39;
    emulator: device fd:1044
    HAX is working and emulator runs in fast virt mode
    emulator: Failed to sync vcpu reg
    emulator: Failed to sync HAX vcpu context

and the emulator won&#39;t run.  The significant part of this error `(Failed to sync vcpu reg)` is not mentioned ANYWHERE online, except in the [source code for the HAX itself](http://mirror.yongbok.net/pub/linux/android/repository/external/qemu/target-i386/hax-all.c), but I can&#39;t figure out how to make any sense of this.

Can anyone advise about how to get past this error?  I really need to get this working, because debugging on device and in the default emulators is painfully slow.

How do I fix &quot;Failed to sync vcpu reg&quot; error?

Just read this [fascinating article][1] about the 20x-200x slowdowns you can get on Intel CPUs with denormalized floats (floating point numbers very close to 0).

There is an option with SSE to round these off to 0, restoring performance when such floating point values are encountered. 

How do C# apps handle this? Is there an option to enable/disable `_MM_FLUSH_ZERO`?


  [1]: https://stackoverflow.com/a/9314926/1294758

Content Type	Original Author	Original Content on Stackoverflow
Question	user1260391	View Question on Stackoverflow
Solution 1 - Linux	Satish	View Answer on Stackoverflow
Solution 2 - Linux	user41871	View Answer on Stackoverflow

fork: retry: Resource temporarily unavailable

Linux Problem Overview

Linux Solutions

Solution 1 - Linux

Solution 2 - Linux

flask-login: can't understand how it works

Javascript setInterval function to clear itself?

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