/usr/share/doc/quantum-espresso/html/node19.html

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">

<!--Converted with LaTeX2HTML 2008 (1.71)
original version by:  Nikos Drakos, CBLU, University of Leeds
* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan
* with significant contributions from:
  Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
<HTML>
<HEAD>
<TITLE>3.4 Tricks and problems</TITLE>
<META NAME="description" CONTENT="3.4 Tricks and problems">
<META NAME="keywords" CONTENT="user_guide">
<META NAME="resource-type" CONTENT="document">
<META NAME="distribution" CONTENT="global">

<META NAME="Generator" CONTENT="LaTeX2HTML v2008">
<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">

<LINK REL="STYLESHEET" HREF="user_guide.css">

<LINK REL="previous" HREF="node18.html">
<LINK REL="up" HREF="node15.html">
<LINK REL="next" HREF="node20.html">
</HEAD>

<BODY >
<!--Navigation Panel-->
<A NAME="tex2html381"
  HREF="node20.html">
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A> 
<A NAME="tex2html377"
  HREF="node15.html">
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A> 
<A NAME="tex2html373"
  HREF="node18.html">
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A> 
<A NAME="tex2html379"
  HREF="node1.html">
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="contents.png"></A>  
<BR>
<B> Next:</B> <A NAME="tex2html382"
  HREF="node20.html">About this document ...</A>
<B> Up:</B> <A NAME="tex2html378"
  HREF="node15.html">3 Parallelism</A>
<B> Previous:</B> <A NAME="tex2html374"
  HREF="node18.html">3.3 Parallelization levels</A>
 &nbsp; <B>  <A NAME="tex2html380"
  HREF="node1.html">Contents</A></B> 
<BR>
<BR>
<!--End of Navigation Panel-->
<!--Table of Child-Links-->
<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>

<UL>
<LI><UL>
<LI><A NAME="tex2html383"
  HREF="node19.html#SECTION00044010000000000000">3.4.0.1 Trouble with input files</A>
<LI><A NAME="tex2html384"
  HREF="node19.html#SECTION00044020000000000000">3.4.0.2 Trouble with MKL and MPI parallelization</A>
<LI><A NAME="tex2html385"
  HREF="node19.html#SECTION00044030000000000000">3.4.0.3 Trouble with compilers and MPI libraries</A>
</UL></UL>
<!--End of Table of Child-Links-->
<HR>

<H2><A NAME="SECTION00044000000000000000"></A>
<A NAME="SubSec:badpara"></A>
<BR>
3.4 Tricks and problems
</H2>

<P>
Many problems in parallel execution derive from the mixup of different
MPI libraries and runtime environments. There are two major MPI
implementations, OpenMPI and MPICH, coming in various versions,
not necessarily compatible; plus vendor-specific implementations
(e.g. Intel MPI). A parallel machine may have multiple parallel
compilers (typically, <TT>mpif90</TT> scripts calling different
serial compilers), multiple MPI libraries, multiple launchers
for parallel codes (different versions of <TT>mpirun</TT> and/or
<TT>mpiexec</TT>). You have to figure out the proper combination
of all of the above, which may require using command <TT>module</TT>
or manually setting environment variables and execution paths.
What exactly has to be done depends upon the configuration of your
machine. You should inquire with your system administrator or user
support (if available; if not, YOU are the system administrator
and user support and YOU have to solve your problems).

<P>
Always verify if your executable is actually compiled for
parallel execution or not: it is declared in the first lines
of output. Running several instances of a serial code with
<TT>mpirun</TT> or <TT>mpiexec</TT> produces strange crashes.

<P>

<H4><A NAME="SECTION00044010000000000000">
3.4.0.1 Trouble with input files</A>
</H4>
Some implementations of the MPI library have problems with input
redirection in parallel. This typically shows up under the form of
mysterious errors when reading data. If this happens, use the option
<TT>-i</TT> (or <TT>-in</TT>, <TT>-inp</TT>, <TT>-input</TT>),
followed by the input file name.
Example:
<PRE>
   pw.x -i inputfile -nk 4 &gt; outputfile
</PRE>
Of course the
input file must be accessible by the processor that must read it
(only one processor reads the input file and subsequently broadcasts
its contents to all other processors).

<P>
Apparently the LSF implementation of MPI libraries manages to ignore or to
confuse even the <TT>-i/in/inp/input</TT> mechanism that is present in all
Q<SMALL>UANTUM </SMALL>ESPRESSO codes. In this case, use the <TT>-i</TT> option of <TT>mpirun.lsf</TT>
to provide an input file.

<P>

<H4><A NAME="SECTION00044020000000000000">
3.4.0.2 Trouble with MKL and MPI parallelization</A>
</H4>
If you notice very bad parallel performances with MPI and MKL libraries,
it is very likely that the OpenMP parallelization performed by the latter
is colliding with MPI. Recent versions of MKL enable autoparallelization
by default on multicore machines.  You must set the environment variable
OMP_NUM_THREADS to 1 to disable it.
Note that if for some reason the correct setting  of variable
OMP_NUM_THREADS
does not propagate to all processors, you may equally run into trouble.
Lorenzo Paulatto (Nov. 2008) suggests to use the <TT>-x</TT> option to <TT>mpirun</TT> to
propagate OMP_NUM_THREADS to all processors.
Axel Kohlmeyer suggests the following (April 2008):
"(I've) found that Intel is now turning on multithreading without any
warning and that is for example why their FFT seems faster than
FFTW. For serial and OpenMP based runs this makes no difference (in
fact the multi-threaded FFT helps), but if you run MPI locally, you
actually lose performance. Also if you use the 'numactl' tool on linux
to bind a job to a specific cpu core, MKL will still try to use all
available cores (and slow down badly). The cleanest way of avoiding
this mess is to either link with
<BLOCKQUOTE>
<TT>-lmkl_intel_lp64 -lmkl_sequential -lmkl_core</TT> (on 64-bit:
x86_64, ia64)
<BR><TT>-lmkl_intel -lmkl_sequential -lmkl_core</TT> (on 32-bit, i.e. ia32 )

</BLOCKQUOTE>
or edit the <TT>libmkl_'platform'.a</TT> file. I'm using now a file
<TT>libmkl10.a</TT> with:
<PRE>
  GROUP (libmkl_intel_lp64.a libmkl_sequential.a libmkl_core.a)
</PRE>
It works like a charm". UPDATE: Since v.4.2, <TT>configure</TT> links by
default MKL without multithreaded support.

<P>

<H4><A NAME="SECTION00044030000000000000">
3.4.0.3 Trouble with compilers and MPI libraries</A>
</H4>
Many users of Q<SMALL>UANTUM </SMALL>ESPRESSO, in particular those working on PC clusters,
have to rely on themselves (or on less-than-adequate system managers) for
the correct configuration of software for parallel execution. Mysterious and
irreproducible crashes in parallel execution are sometimes due to bugs
in Q<SMALL>UANTUM </SMALL>ESPRESSO, but more often than not are a consequence of buggy
compilers or of buggy or miscompiled MPI libraries.

<P>
<HR>
<!--Navigation Panel-->
<A NAME="tex2html381"
  HREF="node20.html">
<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="next.png"></A> 
<A NAME="tex2html377"
  HREF="node15.html">
<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="up.png"></A> 
<A NAME="tex2html373"
  HREF="node18.html">
<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="prev.png"></A> 
<A NAME="tex2html379"
  HREF="node1.html">
<IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="contents.png"></A>  
<BR>
<B> Next:</B> <A NAME="tex2html382"
  HREF="node20.html">About this document ...</A>
<B> Up:</B> <A NAME="tex2html378"
  HREF="node15.html">3 Parallelism</A>
<B> Previous:</B> <A NAME="tex2html374"
  HREF="node18.html">3.3 Parallelization levels</A>
 &nbsp; <B>  <A NAME="tex2html380"
  HREF="node1.html">Contents</A></B> 
<!--End of Navigation Panel-->
<ADDRESS>
Filippo Spiga
2016-10-04
</ADDRESS>
</BODY>
</HTML>
quantum-espresso-data 6.0-3 / usr / share / doc / quantum-espresso / html / node19.html
