mirror of https://gitlab.com/QEF/q-e.git
Documentation updated
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2761 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
giannozz
parent
31280c8de5
commit
313b6e9c69
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@ -44,16 +44,16 @@ The pseudopotential generation package "atomic" was written by
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Andrea Dal Corso and it is the result of many additions to
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the original code by Paolo Giannozzi.
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The input/output toolkit "iotk" was written by Giovanni Bussi
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(S3 Modena).
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The input/output toolkit "iotk" (http://www.s3.infm.it/iotk)
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was written by Giovanni Bussi (S3 Modena).
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A list of further contributors includes:
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Dario Alfe', Francesco Antoniella, Mauro Boero, Nicola Bonini,
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Claudia Bungaro, Paolo Cazzato, Davide Ceresoli, Gabriele Cipriani,
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Matteo Cococcioni, Cesar Da Silva, Alberto Debernardi, Gernot Deinzer,
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Oswaldo Dieguez, Andrea Ferretti, Ralph Gebauer, Martin Hilgeman,
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Eyvaz Isaev, Yosuke Kanai, Axel Kohlmeyer,
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Konstantin Kudin, Michele Lazzeri, Kurt Maeder, Francesco Mauri,
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Eyvaz Isaev, Yosuke Kanai, Axel Kohlmeyer, Konstantin Kudin,
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Michele Lazzeri, Sergey Lisenkov, Kurt Maeder, Francesco Mauri,
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Nicolas Mounet, Huy-Viet Nguyen, Pasquale Pavone, Mickael Profeta, Guido Roma,
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Manu Sharma, Alexander Smogunov, Kurt Stokbro, Pascal Thibaudeau,
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Antonio Tilocca, Paolo Umari, Renata Wentzcovitch, Malgorzata Wierzbowska,
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@ -1,6 +1,6 @@
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\documentclass[12pt,a4paper]{article}
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\def\version{3.0}
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\def\version{3.1}
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\def\stableversion{3.0} % last stable release
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\usepackage{epsfig}
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@ -183,8 +183,10 @@ Andrea Dal Corso and it is the result of many additions to the
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original code by Paolo Giannozzi.
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\hyphenation{mo-de-na}
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The input/output toolkit ``iotk'' was written by Giovanni Bussi (S3,
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Modena).
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The input/output toolkit ``iotk''
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(\htmladdnormallink{\texttt{http://www.s3.infm.it/iotk}}%
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{http://www.s3.infm.it/iotk/})
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was written by Giovanni Bussi (S3, Modena).
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\hyphenation{fran-ce-sco}
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\hyphenation{ce-re-so-li}
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@ -211,6 +213,7 @@ Yosuke Kanai,
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Axel Kohlmeyer,
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Konstantin Kudin,
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Michele Lazzeri,
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Sergey Lisenkov,
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Kurt Maeder,
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Francesco Mauri,
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Nicolas Mounet,
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@ -1060,7 +1063,7 @@ upgrade to a more recent version.
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If you get an error in the loading phase that looks like ``ld: file
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XYZ.o: unknown (unrecognized, invalid, wrong, missing, \dots) file
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type'', or ``While processing relocatable file XYZ.o, no relocatable
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objects were found'' (T3E), one of the following things have happened:
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objects were found'', one of the following things have happened:
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\begin{enumerate}
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\item you have leftover object files from a compilation with another
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@ -1159,7 +1162,7 @@ ifc)}
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\hfill\break
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If \texttt{configure} doesn't find the compiler, or if you get ``Error
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loading shared libraries...'' at run time, you have forgotten to
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loading shared libraries...'' at run time, you may have forgotten to
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execute the script that sets up the correct path and library path.
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Unless your system manager has done this for you, you should execute
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the appropriate script --- located in the directory containing the
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@ -1168,69 +1171,19 @@ Consult the documentation provided by Intel.
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Each major release of the Intel compiler differs a lot from
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the previous one. Do not mix compiled objects from different releases:
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they are incompatible. Intel compiler v.~7 and later use a different
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method to locate where modules are with respect to v.~$< 7$: if you
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are using the manual configuration, choose the appropriate line
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\texttt{MODULEFLAG=...} in \texttt{make.sys}.
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they are incompatible.
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Some releases of Intel compiler v.~7 and 8 yield ``Compiler Internal
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Error''.
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Update to the last version (presently 7.1.41, 8.0.046 or
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8.1.018, respectively), available via Intel Premier support
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(registration free of charge for Linux):
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In case of trouble, update your version with the most recent
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patches, available via Intel Premier support (registration free
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of charge for Linux):
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\htmladdnormallink%
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{\texttt{http://developer.intel.com/software/products/support/\#premier}}%
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{http://developer.intel.com/software/products/support/\#premier}.
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\hfill\break
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Intel v.~9 has a buggy preprocessing that either prevents compilation
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of \texttt{iotk}, or produces runtime errors in \texttt{cft3}. Workaround:
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modify \texttt{make.sys} to explicitly perform preprocessing using
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\texttt{/lib/cpp}, as in the following example (courtesy from Sergei
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Lysenkov):
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\begin{verbatim}
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.f90.o:
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$(CPP) $(CPPFLAGS) $< -o $*.F90
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$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
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CPP = /lib/cpp
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CPPFLAGS = -P -C -traditional $(DFLAGS) $(IFLAGS)
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\end{verbatim}
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Warnings ``size of symbol ... changed ...'' are produced by ifc 7.1 at
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the loading stage.
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These seem to be harmless, but they may cause the loader to stop,
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depending on your system configuration.
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If this happens and no executable is produced, add the following to
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\texttt{LDFLAGS}: \texttt{-Xlinker --noinhibit-exec}.
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On Intel CPUs, it is very convenient to use Intel MKL libraries.
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If \texttt{configure} doesn't find them, try
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\texttt{configure --enable-shared}.
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MKL also contains optimized FFT routines, but they are
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presently not supported: use FFTW instead. Note that Intel
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compiler v.~8 fails to load with MKL v.~5.2 or earlier versions,
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because some symbols that are referenced by MKL are missing. There
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is a fix for this (info from Konstantin Kudin): add libF90.a from
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ifc 7.1 at the linking stage, as the last library.
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Note that some combinations of not-so-recent versions of MKL
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and ifc may yield a lot of "undefined references" when statically
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loaded: use \texttt{configure --enable-shared},
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or remove the \texttt{-static} option in \texttt{make.sys}.
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Note that \texttt{pwcond.x} works only with recent versions
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(v.7 or later) of MKL.
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When using/testing/benchmarking MKL on SMP (multiprocessor)
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machines, one should set the environmental variable
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\texttt{OMP\_NUM\_THREADS} to 1, unless the OpenMP
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parallelization is desired. MKL by default sets the
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variable to the number of CPUs installed and thus gives
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the impression of a much better performance, as the CPUu time
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is only measured for the master thread (info from Axel Kohlmeyer).
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The I/O libraries used by older versions of the Intel compiler
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are incompatible
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with those called by most precompiled BLAS/LAPACK libraries
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(including ATLAS): you get error messages at linking stage.
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\paragraph{ifc v.~6 and earlier}
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The I/O libraries used by older versions of ifc are incompatible with
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those called by most precompiled BLAS/LAPACK libraries (including ATLAS):
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you get error messages at linking stage.
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A workaround is to recompile BLAS/LAPACK with ifc, or (better) to
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replace the BLAS routine \texttt{xerbla} and LAPACK routine
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\texttt{dlamch} (the only two containing I/O calls) with recompiled
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@ -1248,6 +1201,25 @@ in the following example:
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(assuming that the library and the two object files are in the same
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directory). See also Axel Kohlmeyer's web site.
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ifc 6 and earlier use a rather strange method to locate
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where modules are: you need to specify a ``catalog file''. Such a file
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should be created in each directory as \texttt{intel.pcl} either by the
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manual configuration script \texttt{configure.old} or by the newest
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\texttt{configure}. Starting with ifc 7, a more conventional method
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is used.
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\paragraph{ifc v.7}
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Some releases of ifc 7.0 and 7.1 yield ``Compiler Internal
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Error''. Update to the last version (should be 7.1.41).
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Warnings ``size of symbol ... changed ...'' are produced by ifc 7.1 at
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the loading stage.
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These seem to be harmless, but they may cause the loader to stop,
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depending on your system configuration.
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If this happens and no executable is produced, add the following to
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\texttt{LDFLAGS}: \texttt{-Xlinker --noinhibit-exec}.
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Linux distributions using glibc 2.3 or later (such as e.g. RedHat 9)
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may be incompatible with ifc 7.0 and 7.1.
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The incompatibility shows up in the form of messages ``undefined
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@ -1257,10 +1229,62 @@ A workaround is available: see
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{\texttt{http://newweb.ices.utexas.edu/misc/ctype.c}}%
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{http://newweb.ices.utexas.edu/misc/ctype.c}.
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There is a well known problem with version 8 of Intel compiler and
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pthreads (that are used both in Debian Woody and Sarge) that causes
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\paragraph{ifort v.8}
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Some releases of ifort 8 yield ``Compiler Internal Error''.
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Update to a more patched version: 8.0.046 for v.~8.0,
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8.1.018 for v.~8.1.
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There is a well known problem with ifort 8 and pthreads
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(that are used both in Debian Woody and Sarge) that causes
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"segmentation fault" errors (info from Lucas Fernandez Seivane).
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Version 7 does not have this problem.
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Version 7 did not have this problem.
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\paragraph{ifort v.9}
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At least some versions of ifort 9 have a buggy preprocessor that
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either prevents compilation of \texttt{iotk}, or produces runtime
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errors in \texttt{cft3}. Workaround: modify \texttt{make.sys} to
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explicitly perform preprocessing using \texttt{/lib/cpp}, as in
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the following example (courtesy from Sergei Lysenkov):
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\begin{verbatim}
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.f90.o:
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$(CPP) $(CPPFLAGS) $< -o $*.F90
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$(MPIF90) $(F90FLAGS) -c $*.F90 -o $*.o
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CPP = /lib/cpp
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CPPFLAGS = -P -C -traditional $(DFLAGS) $(IFLAGS)
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\end{verbatim}
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On some versions of RedHat Linux, you may get an obscure error:
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\texttt{IPO link: can not find "(" ... }, due to a bad system
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configuration. Add option \texttt{-no-ipo} to \texttt{LDFLAGS}
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in file \texttt{make.sys}.
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\paragraph{MKL}
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On Intel CPUs, it is very convenient to use Intel MKL libraries.
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If \texttt{configure} doesn't find them, try
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\texttt{configure --enable-shared}.
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MKL also contains optimized FFT routines, but they are
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presently not supported: use FFTW instead. Note that ifort 8 fails
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to load with MKL v.~5.2 or earlier versions,
|
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because some symbols that are referenced by MKL are missing. There
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is a fix for this (info from Konstantin Kudin): add libF90.a from
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ifc 7.1 at the linking stage, as the last library.
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Note that some combinations of not-so-recent versions of MKL
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and ifc may yield a lot of "undefined references" when statically
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loaded: use \texttt{configure --enable-shared},
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or remove the \texttt{-static} option in \texttt{make.sys}.
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Note that \texttt{pwcond.x} works only with recent versions
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(v.7 or later) of MKL.
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When using/testing/benchmarking MKL on SMP (multiprocessor)
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machines, one should set the environmental variable
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\texttt{OMP\_NUM\_THREADS} to 1, unless the OpenMP
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parallelization is desired. MKL by default sets the
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variable to the number of CPUs installed and thus gives
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the impression of a much better performance, as the CPUu time
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is only measured for the master thread (info from Axel Kohlmeyer).
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\paragraph{AMD CPUs, Intel Itanium}
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@ -1312,24 +1336,12 @@ configuration of MPI libraries: see section ``Running on parallel machines''.
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If you get weird errors with LAM-MPI, add \texttt{-D\_\_LAM} to preprocessing
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options and recompile. See also Axel Kohlmeyer's web site for more info.
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If you are dis satisfied with the performances in parallel
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If you are dissatisfied with the performances in parallel
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execution, read the ``Parallelization issues'' section.
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\paragraph{T3E}
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The following workaround is needed: in files \texttt{PW/bp\_zgefa.f}
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and \texttt{PW/bp\_zgedi.f}, replace all occurrences of
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\texttt{zscal}, \texttt{zaxpy}, \texttt{zswap}, \texttt{izamax} with
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\texttt{cscal}, \texttt{caxpy}, \texttt{cswap}, \texttt{icamax}.
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Also, in \texttt{PP/dist.f} you need to comment the call to
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\texttt{getarg} and uncomment the call to \texttt{pxfgetarg}.
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If you have a T3E with ``benchlib'' installed, you may want to use it
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by adding \texttt{-D\_\_BENCHLIB} to preprocessing flags.
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If you get errors at loading because symbols \texttt{LPUTP},
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\texttt{LGETV}, \texttt{LSETV} are undefined, you either need to link
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``benchlib'', or to remove \texttt{-D\_\_BENCHLIB} and recompile
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(after a \texttt{make clean}).
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T3D/T3E are no longer supported.
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\clearpage
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@ -2486,16 +2498,6 @@ warning messages and continues, pay attention to it but do not
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assume that something is necessarily wrong in your calculation:
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most warning messages signal harmless problems.
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Note for PC Linux clusters in parallel execution: in at least some
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versions of MPICH, the current directory is set to the directory where
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the \emph{executable code} resides, instead of being set to the
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directory where the code is executed.
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This MPICH weirdness may cause unexpected failures in some
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postprocessing codes that expect a data file
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in the current directory.
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Workaround: use symbolic links, or copy the executable to the current
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directory.
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Typical \texttt{pw.x} and/or \texttt{ph.x} (mis-)behavior:
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\paragraph{\texttt{pw.x} yields a message like ``error while loading
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@ -2675,6 +2677,13 @@ See info from Axel Kohlmeyer:\hfill\break
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{{\small\texttt{http://www.democritos.it/pipermail/pw\_forum/2005-April/002338.html}}}%
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{http://www.democritos.it/pipermail/pw_forum/2005-April/002338.html}
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Random crashes due to MPI errors have often been reported in Linux
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PC clusters. These are due either to hardware problems (defective
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RAM for instance) or to software bugs in MPI libraries or in the
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operating system. While we cannot guarantee with 100\% confidence
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that such problems are not due to Quantum-ESPRESSO, we think that
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this is at least 99.9999\% true.
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\paragraph{\texttt{pw.x} runs but nothing happens.}
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Possible reasons:
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@ -2989,6 +2998,18 @@ algorithm \\
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(\texttt{cell\_dynamics='damp-w'}) shouldn't break the symmetry.
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\end{itemize}
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\paragraph{Why are codes in PP/ complaining that they do not
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find some files?}
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For Linux PC clusters in parallel execution: in at least some
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versions of MPICH, the current directory is set to the directory where
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the \emph{executable code} resides, instead of being set to the
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directory where the code is executed.
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This MPICH weirdness may cause unexpected failures in some
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postprocessing codes that expect a data file in the current directory.
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Workaround: use symbolic links, or copy the executable to the current
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directory.
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\paragraph{\texttt{ph.x} stops with ``error reading file''.}
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The data file produced by \texttt{pw.x} is bad or incomplete or
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@ -2998,7 +3019,7 @@ the number of processors and pools for the phonon run should be the
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same as for the self-consistent run; all files must be visible to all
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processors.
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\paragraph{\texttt{ph.x} mumbles something like ``cannot recover'' or
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\paragraph{\texttt{ph.x} mumbles` something like ``cannot recover'' or
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``error reading recover file''.}
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You have a bad restart file from a preceding failed execution.
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@ -3101,6 +3122,52 @@ since v. 3.1).
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% low-symmetry lattice? should I use $E(v)$ curves, the stress,
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% variable-cell molecular dynamics?}
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\item {\em How is the charge density (the potential, etc.) stored?
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What position in real space corresponds to an array value? }
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The index of arrays used to store functions defined on 3D meshes is
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actually a shorthand for three indeces, following the FORTRAN
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convention ("leftmost index runs faster"). An example will explain
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this better. Suppose you have a 3D array of dimension \texttt{(nr1,nr2,nr3)},
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say \texttt{psi(nr1,nr2,nr3)}. FORTRAN compilers store this array
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sequentially in the computer RAM in the following way:
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\begin{quote}
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\texttt{psi(1,1,1)}\\
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\texttt{psi(2,1,1)}\\
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...\\
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\texttt{psi(nr1,1,1)}\\
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\texttt{psi(1,2,1)}\\
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\texttt{psi(2,2,1)}\\
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...\\
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\texttt{psi(nr1,2,1)}\\
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...\\
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\texttt{psi(nr1,nr2,1)}\\
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\texttt{psi(1,1,nr3)}
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\end{quote}
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etc
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Let \texttt{ind} be the position of the \texttt{(i,j,k)} element
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in the above list: the relation between \texttt{ind} and \texttt{(i,j,k)}
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is:
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\begin{equation}
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ind = i + (j-1)*nr1 + (k-1)*nr2*nr1
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\end{equation}
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This should clarify the relation between 1D and 3D indexing. In real
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space, the \texttt{(i,j,k)} point of the mesh is
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\begin{equation}
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{\bf r_{ijk}} = {i-1\over nr1}*\tau_1
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+ {j-1\over nr2}*\tau_2
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+ {k-1\over nr3}*\tau_3
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\end{equation}
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where the $\tau$'s are the basis vectors of the Bravais lattice. The
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latter are stored row-wise in the "AT" array:
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\begin{equation}
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\tau_1 = at(:,1), \tau_2 = at(:,2), \tau_3 = at(:,3)
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\end{equation}
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(info by Stefano Baroni)
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\item {\em Is there a simple way to determine the symmetry
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of a given phonon mode?}
|
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|
|
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Loading…
Reference in New Issue