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User's Guide for Quantum ESPRESSO

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1. DFT using a Plane Wave PW basis set and pseu dopotentials It also includes other packages for more specialized calculations PWneb energy barriers and reaction pathways through the Nudged Elastic Band NEB method PHonon vibrational properties with Density Functional Perturbation Theory PostProc codes and utilities for data postprocessing PWcond ballistic conductance XSPECTRA K edge X ray adsorption spectra TD DFPT spectra from Time Dependent Density Functional Perturbation Theory The following auxiliary packages are included as well PWgui a Graphical User Interface producing input data files for PWscf and some PostProc codes atomic atomic calculations and pseudopotential generation QHA utilities for the calculation of projected density of states PDOS and of the free energy in the Quasi Harmonic Approximation to be used in conjunction with PHonon PlotPhon phonon dispersion plotting utility to be used in conjunction with PHonon A copy of required external libraries is also included Finally several additional packages that exploit data produced by QUANTUM ESPRESSO or patch some QUANTUM ESPRESSO routines can be installed as plug ins Wannier90 maximally localized Wannier functions WanT quantum transport properties with Wannier functions YAMBO electronic excitations within Many Body Perturbation Theory GW and Bethe Salpeter equation PLUMED calculation of free energy surface through met
2. PW orbitals in the PW basis set as well as charges and density in either reciprocal or real space are distributed across processors This is usually referred to as PW paralleliza tion Al linear algebra operations on array of PW real space grids are automatically and effectively parallelized 3D FFT is used to transform electronic wave functions from reciprocal to real space and vice versa The 3D FFT is parallelized by distributing planes of the 3D grid in real space to processors in reciprocal space it is columns of G vectors that are distributed to processors tasks In order to allow good parallelization of the 3D FFT when the number of processors exceeds the number of FFT planes FFTs on Kohn Sham states are redistributed to task groups so that each group can process several wavefunctions at the same time linear algebra group A further level of parallelization independent on PW or k point parallelization is the parallelization of subspace diagonalization iterative orthonormal ization Both operations required the diagonalization of arrays whose dimension is the number of Kohn Sham states or a small multiple of it All such arrays are distributed block like across the linear algebra group a subgroup of the pool of processors orga nized in a square 2D grid As a consequence the number of processors in the linear algebra group is given by n where n is an integer n must be smaller than the number of proces s
3. 0 91 and later versions http www g95 org work The exe cutables that produce are however slower let us say 20 or so that those produced by gfortran which in turn are slower by another 20 or so than those produced by ifort Linux PCs with Sun Studio compiler The Sun Studio compiler sunf95 is free web site http developers sun com sunstudio and comes with a set of algebra libraries that can be used in place of the slow built in libraries It also supports OpenMP which g95 does not On the other hand it is a pain to compile MPI with it Furthermore the most recent version has a terrible bug that totally miscompiles the iotk input output library you ll have to compile it with reduced optimization info by Lorenzo Paulatto March 2010 Linux PCs with AMD Open64 suite The AMD Open64 compiler suite openf95 web site http developer amd com cpu open64 pages default aspx can be freely downloaded from the AMD site It is recognized by configure but little tested It sort of works but it fails to pass several tests info by Paolo Giannozzi March 2010 I have configured for Pathscale then switched to the Open64 compiler by editing make sys make pw succeeded and pw x did process my file but with make all I get an internal compiler error in CPV wf f90 info by Cezary Sliwa April 2011 Linux PCs with Intel compiler ifort The Intel compiler ifort is available for free for personal usage http software
4. Choose a meaningful subject Do not use reply to start a new thread it will confuse the ordering of messages into threads that most mailers can do In particular do not use reply to a Digest e Be short no need to send 128 copies of the same error message just because you this is what came out of your 128 processor run No need to send the entire compilation log for a single error appearing at the end e Avoid excessive or irrelevant quoting of previous messages Your message must be imme diately visible and easily readable not hidden into a sea of quoted text e Remember that even experts cannot guess where a problem lies in the absence of sufficient information One piece of information that must always be provided is the version number of QUANTUM ESPRESSO e Remember that the mailing list is a voluntary endeavor nobody is entitled to an answer even less to an immediate answer e Finally please note that the mailing list is not a replacement for your own work nor is it a replacement for your thesis director s work 1 4 Terms of use QUANTUM ESPRESSO is free software released under the GNU General Public License See http www gnu org licenses old licenses gp1 2 0 txt or the file License in the distribution We shall greatly appreciate if scientific work done using QUANTUM ESPRESSO distribu tion will contain an explicit acknowledgment and the following reference P Giannozzi S Baroni N Bonini M Calan
5. Ouro DEMOCRITOS DEmocritos MOdeling Center for Y Research In aTOmistic Simulation IOM User s Guide for QUANTUM ESPRESSO version 5 1 Contents 1 Introduction LL People E IEA LAO e rt RO O O O A ea e E A a 1 3 Guidelines for posting to the mailing list 0 o 1 4 Terms of use 2 Installation 2 1 Download AAA bas de de a at Re a e eee e 2 3 1 Manual configuration lt 2 ici 2 A A 2 4 Libraries eee A ee bee ee ae eee eee bees Bad bee e goatee amp die es amp Gee Be Gee as eae om ee ee be ee Se ee 2 7 1 All architectures 2 a a narra a a es ce es 21 3 MINI rear E Be ee Se a Go bn ale doe Ss 2 7 4 IBM BlueGene 0 0 0000000000000 ee Skee eae Se Be a ee ee ee eee ee 2 7 6 Linux PC clusters with MPI oaa 2C MacOS sus sins ass aoe ee bee a e i Pas oo ee NA A be Be Seog ea oe HAP en a Oe eee ee eee 3 3 Parallelization levels 3 3 1 Understanding parallel I QO ic 5 lt by dace be a Ge eae ee oe eS Paty ae es e a A eee ee 1 Introduction This guide gives a general overview of the contents and of the installation of QUANTUM ESPRESSO opEn Source Package for Research in Electronic Structure Simulation and Op timization version 5 1 The QUANTUM ESPRESSO distribution contains the core packages PWscf Plane Wave Self Consistent Field and CP Car Parrinello for the calculation of electronic structure prop erties within Density Functional Theory
6. for moderator approval are automatically deleted with no further processing sorry too much spam In case of trouble carefully check that your return e mail is the correct one i e the one you used to subscribe Since pw_forum has a sizable traffic an alternative low traffic list pw_users pwscf org is provided for those interested only in QUANTUM ESPRESSO related news such as e g announcements of new versions tutorials etc You can subscribe but not post to this list from the web site Contacts section If you need to contact the developers for specific questions about coding proposals offers of help etc please send a message to the developers mailing list q e developers qe forge org Do not post general questions they will be ignored 1 3 Guidelines for posting to the mailing list Life for subscribers of pw_forum will be easier if everybody complies with the following guide lines e Before posting please browse or search the archives links are available in the Contacts section of the web site Most questions are asked over and over again Also make an attempt to search the available documentation notably the FAQs and the User Guide s The answer to most questions is already there e Reply to both the mailing list and the author or the post using Reply to all not Reply the Reply To field no longer points to the mailing list e Sign your post with your name and affiliation e
7. info by Lorenzo Paulatto Nov 2010 Release 12 0 2 seems to work and to produce faster executables than previous versions on 64 bit CPUs info by P Giannozzi March 2011 ifort v 11 Segmentation faults were reported for the combination ifort 11 0 081 MKL 10 1 1 019 OpenMP 1 3 3 The problem disappeared with ifort 11 1 056 and MKL 10 2 2 025 Carlo Nervi Oct 2009 Linux PCs with MKL libraries On Intel CPUs it is very convenient to use Intel MKL libraries They can be also used for AMD CPU selecting the appropriate machine optimized libraries and also together with non Intel compilers Note however that recent versions of MKL 10 2 and following do not perform well on AMD machines configure should recognize properly installed MKL libraries By default the non threaded version of MKL is linked unless option configure with openmp is specified In case of trouble refer to the following web page to find the correct way to link MKL http software intel com en us articles intel mkl link line advisor Recent MKL versions also contain optimized FFT routines and a FFTW interface For parallel MPI execution on multiprocessor SMP machines set the environmental variable OMP_NUM_THREADS to 1 unless you know what you are doing See Sec 3 for more info on this and on the difference between MPI and OpenMP parallelization Linux PCs with ACML libraries For AMD CPUs especially recent ones you may find convenient to link AMD acml librarie
8. intel com It produces fast executables at least on Intel CPUs but not all versions work as expected ifort versions lt 9 1 are not recommended due to the presence of subtle and insidious bugs In case of trouble update your version with the most recent patches available via Intel Premier support registration free of charge for Linux http software intel com en us articles intel software developer support Since each major release of ifort differs a lot from the previous one compiled objects from different releases may be incompatible and should not be mixed If configure doesn t find the compiler or if you get Error loading shared libraries at run time you may have forgotten to execute the script that sets up the correct PATH and library path Unless your system manager has done this for you you should execute the appropriate script located in the directory containing the compiler executable in your initialization files Consult the documentation provided by Intel The warning feupdateenv is not implemented and will always fail showing up in recent versions can be safely ignored Warnings on bad preprocessing option when compiling iotk and complains about recommanded formats should also be ignored 17 ifort v 12 release 12 0 0 miscompiles iotk leading to mysterious errors when reading data files Workaround increase the parameter BLOCKSIZE to e g 131072 1024 when opening files in iotk src iotk_files 90
9. performance i e don t use an NFS mounted directory NOTA BENE do not use a directory containing other data the examples will clean it If you have compiled the parallel version of QUANTUM ESPRESSO this is the default if parallel libraries are detected you will usually have to specify a launcher program such as mpirun or mpiexec and the number of processors see Sec 3 for details In order to do that edit again the environment_variables file and set the PARA_PREFIX and PARA_POSTFIX variables as needed Parallel executables will be run by a command like this PARA_PREFIX pw x PARA_POSTFIX i file in gt file out For example if the command line is like this as for an IBM SP poe pw x procs 4 i file in gt file out you should set PARA_PREFIX poe PARA_POSTFIX procs 4 Furthermore if your machine does not support interactive use you must run the commands specified above through the batch queuing system installed on that machine Ask your system administrator for in structions For execution using OpenMP on N threads you should set PARA_PREFIX to env OMP_NUM_THREADS N Notice that most tests and examples are devised to be run serially or on a small number of processors do not use tests and examples to benchmark parallelism do not try to run on too many processors To run an example go to the corresponding directory e g PW examples example01 and execute run_example This will create a subdirecto
10. 1 are no longer supported 2 7 3 IBM AIX v 4 3 1 of the CP code Wannier function dynamics crashes with segmentation violation on some AIX v 6 machines Workaround compile it with mpx1f95 instead of mpx1f90 Info by Roberto Scipioni June 2011 On IBM machines with ESSL libraries installed there is a potential conflict between a few LAPACK routines that are also part of ESSL but with a different calling sequence The appearance of run time errors like ON ENTRY TO ZHPEV PARAMETER NUMBER 1 HAD AN ILLEGAL VALUE is a signal that you are calling the bad routine If you have defined D__ESSL you should load ESSL before LAPACK see variable LAPACK_LIBS in make sys 2 7 4 IBM BlueGene The current configure is tested and works on the machines at CINECA and at J lich For other sites you may need something like configure ARCH ppc64 bg BLAS_LIBS LAPACK_LIBS SCALAPACK_DIR BLACS_DIR where the various _LIBS and _DIR suggest where the various libraries are located 2 7 5 Linux PC Both AMD and Intel CPUs 32 bit and 64 bit are supported and work either in 32 bit emu lation and in 64 bit mode 64 bit executables can address a much larger memory space than 32 bit executable but there is no gain in speed Beware the default integer type for 64 bit machine is typically 32 bit long You should be able to use 64 bit integers as well but it is not guaranteed to work and will not give any advantage anyway Curre
11. MPI OpenMP The idea is to have one or more MPI process es per multicore node with OpenMP parallelization inside a same node This option is activated by configure with openmp which adds preprocessing flag D_OPENMP and one of the following compiler options ifort openmp xlf gsmp omp PGI mp fta mp nonuma OpenMP parallelization is currently implemented and tested for the following combinations of FFTs and libraries internal FFTW copy requires D__FFTW ESSL requires D__ESSL or D__LINUX_ESSL link with lesslsmp Currently ESSL when available are faster than internal FFTW 23 3 3 1 Understanding parallel I O In parallel execution each processor has its own slice of data Kohn Sham orbitals charge density etc that have to be written to temporary files during the calculation or to data files at the end of the calculation This can be done in two different ways e distributed each processor writes its own slice to disk in its internal format to a different file e collected all slices are collected by the code to a single processor that writes them to disk in a single file using a format that doesn t depend upon the number of processors or their distribution The distributed format is fast and simple but the data so produced is readable only by a job running on the same number of processors with the same type of parallelization as the job who wrote the data and if all files are on a file s
12. NTUM ESPRESSO has an internal copy of an old FFTW version and it can use the following vendor specific FFT libraries IBM ESSL SGI SCSL SUN sunperf NEC ASL configure will first search for vendor specific FFT libraries if none is found it will search for an external FFTW v 3 library if none is found it will fall back to the internal copy of FFTW If you have recent versions v 10 or later of MKL installed you may use the FFTW3 interface provided with MKL This can be directly linked in MKL distributed with v 12 of the Intel compiler In earlier versions only sources are distributed you have to compile them and to modify file make sys accordingly MKL must be linked after the FFTW MKL interface 10 MPI libraries MPI libraries are usually needed for parallel execution unless you are happy with OpenMP multicore parallelization In well configured machines configure should find the appropriate parallel compiler for you and this should find the appropriate libraries Since often this doesn t happen especially on PC clusters see Sec 2 7 6 Other libraries QUANTUM ESPRESSO can use the MASS vector math library from IBM if available only on AIX If optimized libraries are not found The configure script attempts to find optimized libraries but may fail if they have been installed in non standard places You should exam ine the final value of BLAS_LIBS LAPACK LIBS FFT_LIBS MPI_LIBS if needed MASS _LIBS IBM only either in
13. adynamics GIPAW Gauge Independent Projector Augmented Waves NMR chemical shifts and EPR g tensor GWL electronic excitations within GW Approximation Documentation on single packages can be found in the Doc or doc directory of each package A detailed description of input data is available for most packages in files INPUT_ txt and INPUT_ html The QUANTUM ESPRESSO codes work on many different types of Unix machines in cluding parallel machines using both OpenMP and MPI Message Passing Interface and GPU accelerated machines QUANTUM ESPRESSO also runs on Mac OS X and MS Windows machines see section A GPU enabled version of most important codes is available on GitHub https github com fspiga QE GPU Further documentation beyond what is provided in this guide can be found in e the Doc directory of the QUANTUM ESPRESSO distribution e the QUANTUM ESPRESSO web site www quantum espresso org e the archives of the mailing list See section Contacts for more info People who want to contribute to QUANTUM ESPRESSO should read the Developer Manual Doc developer_man pdf This guide does not explain the basic Unix concepts shell execution path directories etc and utilities needed to run QUANTUM ESPRESSO it does not explain either solid state physics and its computational methods If you want to learn the latter you should first read a good textbook such as e g the book by Richard Martin Electronic Structure Basi
14. ame as the general version number If you are using the SVN sources see the GUI README file instead If make refuses for some reason to download additional packages manually download them into subdirectory archive not unpacking or or uncompressing them and try make again Also see Sec 2 1 2 6 Running tests and examples As a final check that compilation was successful you may want to run some or all of the examples There are two different types of examples e automated tests Quick and exhaustive but not meant to be realistic implemented only for PWscf and CP e examples Cover many more programs and features of the QUANTUM ESPRESSO distribution but they require manual inspection of the results Instructions for the impatient cd PW tests check_pw x j for PWscf PW tests README contains a list of what is tested For CP 12 cd CPV tests check_cp x j Instructions for all others edit file environment_variables setting the following variables as needed BIN_DIR directory where executables reside PSEUDO_DIR directory where pseudopotential files reside TMP_DIR directory to be used as temporary storage area The default values of BIN_DIR and PSEUDO DIR should be fine unless you have installed things in nonstandard places TMP DIR must be a directory where you have read and write access to with enough available space to host the temporary files produced by the example runs and possibly offering high I O
15. c Theory and Practical Methods Cambridge University Press 2004 or Density functional theory a practical introduction D S Sholl J A Steckel Wiley 2009 or Electronic Structure Calcula tions for Solids and Molecules Theory and Computational Methods J Kohanoff Cambridge University Press 2006 Then you should consult the documentation of the package you want to use for more specific references All trademarks mentioned in this guide belong to their respective owners 1 1 People The maintenance and further development of the QUANTUM ESPRESSO distribution is pro moted by the DEMOCRITOS National Simulation Center of IOM CNR under the coordination of Paolo Giannozzi Univ Udine Italy and Layla Martin Samos Univ Nova Gorica with the strong support of the CINECA National Supercomputing Center in Bologna under the respon sibility of Carlo Cavazzoni Main contributors to QUANTUM ESPRESSO in addition to the authors of the paper mentioned in Sect 1 4 are acknowledged in the documentation of each package An alphabetic list of further contributors who answered questions on the mailing list found bugs helped in porting to new architectures wrote some code contributed in some way or another at some stage follows Ake Sandgren Audrius Alkauskas Alain Allouche Francesco Antoniella Uli As chauer Francesca Baletto Gerardo Ballabio Mauro Boero Pietro Bonf Claudia Bungaro Paolo Cazzato Gabriele Cipriani Ismaila Dabo Jiay
16. ce v 4 2 configure links by default MKL without multithreaded support Trouble with compilers and MPI libraries Many users of QUANTUM 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 Mysteri ous and irreproducible crashes in parallel execution are sometimes due to bugs in QUANTUM ESPRESSO but more often than not are a consequence of buggy compilers or of buggy or miscompiled MPI libraries 25
17. ded by fortran and C source files clib external libraries written in C flib external libraries written in Fortran install installation scripts and utilities pseudo pseudopotential files used by examples upftools converters to unified pseudopotential format UPF Doc general documentation archive contains plug ins in tar gz form while others are specific to a single package PW PWscf package NEB PWneb package PP PostProc package PHonon PHonon package PWCOND PWcond package CPV CP package atomic atomic package GUI PWGui package Finally directory COUPLE contains code and documentation that is useful to call QUANTUM ESPRESSO programs from external codes 2 2 Prerequisites To install QUANTUM ESPRESSO from source you need first of all a minimal Unix envi ronment basically a command shell e g bash or tcsh and the utilities make awk sed MS Windows users need to have Cygwin a UNIX environment which runs under Windows installed see http www cygwin com Note that the scripts contained in the distribution assume that the local language is set to the standard i e C other settings may break them Use export LC_ALL C sh bash or setenv LC_ALL C csh tcsh to prevent any problem when running scripts including installation scripts Second you need C and Fortran 95 compilers For parallel execution you will also need MPI libraries and a parallel i e MPl aware compiler For massively parallel machi
18. dra R Car C Cavazzoni D Ceresoli G L Chiarotti M Cococcioni I Dabo A Dal Corso S Fabris G Fratesi S de Gironcoli R Gebauer U Gerstmann C Gougoussis A Kokalj M Lazzeri L Martin Samos N Marzari F Mauri R Mazzarello S Paolini A Pasquarello L Paulatto C Sbraccia S Scandolo G Sclauzero A P Seitsonen A Smo gunov P Umari R M Wentzcovitch J Phys Condens Matter 21 395502 2009 http arxiv org abs 0906 2569 Note the form QUANTUM ESPRESSO for textual citations of the code Please also see package specific documentation for further recommended citations Pseudopotentials should be cited as for instance We used the pseudopotentials C pbe rrjkus UPF and O pbe vbc UPF from http www quantum espresso org 2 Installation For machines with GPU acceleration see the page qe forge org gf project q e gpu and the file README GPU in the GPU enabled distribution for more specific information 2 1 Download Presently QUANTUM ESPRESSO is distributed in source form some precompiled executa bles binary files are provided for PWgui Packages for the Debian Linux distribution are how ever made available by debichem developers Stable releases of the QUANTUM ESPRESSO source package current version is 5 1 can be downloaded from the Download section of www quantum espresso org If you plan to run on GPU machines download the GPU enabled version also reachable from the same link Uncompres
19. e than one thread fixed in v 10 2 4 21 4 other QUANTUM ESPRESSO specific parallelization options to be read and interpreted by the running code Items 1 and 2 are machine and installation dependent and may be different for interactive and batch execution Note that large parallel machines are often configured so as to disallow interactive execution if in doubt ask your system administrator Item 3 also depend on your specific configuration shell execution path etc Item 4 is optional but it is very important for good performances We refer to the next section for a description of the various possibilities 3 3 Parallelization levels In QUANTUM ESPRESSO several MPI parallelization levels are implemented in which both calculations and data structures are distributed across processors Processors are organized in a hierarchy of groups which are identified by different MPI communicators level The groups hierarchy is as follow world is the group of all processors MPLCOMM_WORLD images Processors can then be divided into different images each corresponding to a different self consistent or linear response calculation loosely coupled to others pools each image can be subpartitioned into pools each taking care of a group of k points bands each pool is subpartitioned into band groups each taking care of a group of Kohn Sham orbitals also called bands or wavefunctions still experimental
20. e that has problems If it doesn t work or if you experience weird problems at run time try to install patches for your version of the compiler most vendors release at least a few patches for free or to upgrade to a more recent compiler version e If you get error messages at the loading phase that look like file XYZ o unknown not recognized invalid wrong file type file format module version one of the following things have happened 1 you have leftover object files from a compilation with another compiler run make clean and recompile 2 make did not stop at the first compilation error it may happen in some software configurations Remove the file o that triggers the error message recompile look for a compilation error If many symbols are missing in the loading phase you did not specify the location of all needed libraries LAPACK BLAS FFTW machine specific optimized libraries in the needed order If only symbols from clib are missing verify that you have the correct C to Fortran bindings defined in include c_defs h Note that QUANTUM ESPRESSO is self contained with the exception of MPI libraries for parallel compilation if system libraries are missing the problem is in your compiler library combination or in their usage not in QUANTUM ESPRESSO e If you get an error like Can t open module file global_version mod your machine doesn t like the script that produces file version 90 with the correct ver
21. ests and it is much safer to use internal libraries The minimum recommended configuration line is presuming the environment is set correctly configure CC gcc mp 4 3 CXX g mp 4 3 F77 g95 F90 g95 FC g95 CPP cpp mp 4 3 with internal blas with internal lapack Compilation with Intel compilers Newer versions of Intel compiler 11 1 067 support Mac OS X 10 6 and furthermore they are bundled with intel MKL 32 bit binaries obtained using 11 1 088 are tested and no problems have been encountered so far Sadly as of 11 1 088 the 64 bit binary misbehave under some tests Any attempt to compile 64 bit binary using v lt 11 1 088 will result in very strange compilation errors Like the previous section I would recommend installing macports compiler suite First make sure that you are using the 32 bit version of the compilers i e opt intel Compiler 11 1 088 bin ifortvars sh ia32 opt intel Compiler 11 1 088 bin iccvars sh ia32 will set the environment for 32 bit compilation in my case Then the MPI environment has to be set up for Intel compilers similar to previous section The recommended configuration line for QUANTUM ESPRESSO is configure CC icc CXX icpc F77 ifort F90 ifort FC ifort CPP cpp mp 4 3 MKL libraries will be detected automatically if they are in their default locations Otherwise mklvars32 has to be sourced before the configuration script Security issues MacOs 10 6 comes with a disabled firewall Prepari
22. flicts and without missing symbols If they aren t and the compilation fails configure will revert to serial compilation 18 Apart from such problems QUANTUM ESPRESSO compiles and works on all non buggy properly configured hardware and software combinations In some cases you may have to recompile MPI libraries not all MPI installations contain support for the fortran 90 compiler of your choice or for any fortran 90 compiler at all If QUANTUM ESPRESSO does not work for some reason on a PC cluster try first if it works in serial execution A frequent problem with parallel execution is that QUANTUM ESPRESSO does not read from standard input due to the configuration of MPI libraries see Sec 3 4 If you are dissatisfied with the performances in parallel execution see Sec 3 and in particular Sec 3 4 2 7 7 Mac OS Newer Mac OS X machines 10 4 and later with Intel CPUs are supported by configure with gcc4 g95 gfortran and the Intel compiler ifort with MKL libraries Parallel compilation with OpenMPI also works Mysterious crashes occurring when zdotc is called are due to the same incompatibility of complex functions with some optimized BLAS as reported in the Linux PCs with gfortran paragraph Workaround add preprocessing option Dzdotc zdotc_wrapper to DFLAGS Detailed installation instructions for Mac OS X 10 6 Instructions for 10 6 3 by Osman Baris Malcioglu tested as of May 2010 Summary for the hasty e GNU f
23. ke pp compiles the postprocessing package PostProc e make pwcond downloads the balistic conductance package PWcond from qe forge unpacks it and compiles it All executables are linked in main bin directory 11 e make pwall produces all of the above e make 1d1 downloads the pseudopotential generator package atomic from qe forge un packs it and compiles it All executables are linked in main bin directory e make xspectra downloads the package XSpectra from qe forge unpacks it and compiles it All executables are linked in main bin directory e make upf produces utilities for pseudopotential conversion in directory upftools e make all produces all of the above e make plumed unpacks PLUMED patches several routines in PW CPV and clib recom piles PWscf and CP with PLUMED support e make w90 downloads wannier90 unpacks it copies an appropriate make sys file pro duces all executables in W90 wannier90 x and in bin e make want downloads WanT from qe forge unpacks it runs its configure produces all executables for WanT in WANT bin e make yambo downloads yambo from qe forge unpacks it runs its configure produces all yambo executables in YAMBO bin e make gipaw downloads GIPAW from qe forge unpacks it runs its configure produces all GIPAW executables in GIPAW bin and in main bin directory For the setup of the GUI refer to the PWgui X Y Z INSTALL file where X Y Z stands for the version number of the GUI should be the s
24. lation flags after a previous successful or failed compilation you must run make clean before recompiling unless you know exactly which routines are affected by the changed settings and how to force their recompilation 2 4 Libraries QUANTUM ESPRESSO makes use of the following external libraries e BLAS http www netlib org blas and e LAPACK http www netlib org lapack for linear algebra e FETW http www fftw org for Fast Fourier Transforms A copy of the needed routines is provided with the distribution However when available optimized vendor specific libraries should be used this often yields huge performance gains BLAS and LAPACK QUANTUM ESPRESSO can use the following architecture specific replacements for BLAS and LAPACK MKL for Intel Linux PCs ACML for AMD Linux PCs ESSL for IBM machines SCSL for SGI Altix SUNperf for Sun If none of these is available we suggest that you use the optimized ATLAS library see http math atlas sourceforge net Note that ATLAS is not a complete replacement for LAPACK it contains all of the BLAS plus the LU code plus the full storage Cholesky code Follow the instructions in the ATLAS distributions to produce a full LAPACK replacement Sergei Lisenkov reported success and good performances with optimized BLAS by Kazushige Goto The library is now available under an open source license see the GotoBLAS2 page at http www tacc utexas edu tacc software gotoblas2 FFT QUA
25. nes or for simple multicore parallelization an OpenMP aware compiler and libraries are also required Big machines with specialized hardware e g IBM SP CRAY etc typically have a Fortran 95 compiler with MPI and OpenMP libraries bundled with the software Workstations or commodity machines using PC hardware may or may not have the needed software If not you need either to buy a commercial product e g Portland or to install an open source compiler like gfortran or g95 Note that several commercial compilers are available free of charge under some license for academic or personal usage e g Intel Sun 2 3 configure To install the QUANTUM ESPRESSO source package run the configure script This is actually a wrapper to the true configure located in the install subdirectory configure will try to detect compilers and libraries available on your machine and set up things ac cordingly Presently it is expected to work on most Linux 32 and 64 bit PCs all Intel and AMD CPUs and PC clusters SGI Altix IBM SP and BlueGene machines NEC SX Cray XT machines Mac OS X MS Windows PCs and for experts on several GPU accelerated hardware Detailed installation instructions for some specific HPC machines can be found in files instal1 README sys where sys is the machine name Instructions for the impatient cd espresso X Y Z configure make all Symlinks to executable programs will be placed in the bin subdirectory Note tha
26. ng a ipfw based firewall is recommended Open source and free GUIs such as WaterRoof and NoobProof are available that may help you in the process 20 3 Parallelism 3 1 Understanding Parallelism Two different parallelization paradigms are currently implemented in QUANTUM ESPRESSO 1 Message Passing MPI A copy of the executable runs on each CPU each copy lives in a different world with its own private set of data and communicates with other executables only via calls to MPI libraries MPI parallelization requires compilation for parallel execution linking with MPI libraries execution using a launcher program depending upon the specific machine The number of CPUs used is specified at run time either as an option to the launcher or by the batch queue system 2 OpenMP A single executable spawn subprocesses threads that perform in parallel spe cific tasks OpenMP can be implemented via compiler directives explicit OpenMP or via multithreading libraries library OpenMP Explicit OpenMP require compilation for OpenMP execution library OpenMP requires only linking to a multithreading version of mathematical libraries e g ESSLSMP ACML_MP MKL the latter is natively multi threading The number of threads is specified at run time in the environment variable OMP_NUM_THREADS MPI is the well established general purpose parallelization In QUANTUM ESPRESSO several parallelization levels specified at run time via c
27. nment of those machines In some cases cross compilation requires to specify the target machine with the host option This feature has not been extensively tested but we had at least one successful report compilation for NEC SX6 on a PC Currently supported architectures are ia32 Intel 32 bit machines x86 running Linux ia64 Intel 64 bit Itanium running Linux x86_64 Intel and AMD 64 bit running Linux see note below aix IBM AIX machines solaris PC s running SUN Solaris sparc Sun SPARC machines crayxt4 Cray XT4 XT5 XE machines mac686 Apple Intel machines running Mac OS X cygwin MS Windows PCs with Cygwin mingw32 Cross compilation for MS Windows using mingw 32 bits mingw64 As above 64 bits necsx NEC SX 6 and SX 8 machines ppc64 Linux PowerPC machines 64 bits ppc64 mn as above with IBM xlf compiler ppc64 bg IBM BlueGene arm ARM machines with gfortran Note x86_64 replaces amd64 since v 4 1 Cray Unicos machines SGI machines with MIPS architecture HP Compaq Alphas are no longer supported since v 4 2 PowerPC Macs are no longer supported since v 5 0 Finally configure recognizes the following command line op tions enable parallel compile for parallel MPI execution if possible default yes enable openmp compile for OpenMP execution if possible default no enable shared use shared libraries if available default yes no is implemented untested in only a few cases enable debug compile wi
28. ntly the following compilers are supported by configure Intel ifort Portland pgf90 gfortran g95 Pathscale pathf95 Sun Studio sunf95 AMD Open64 openf95 The ordering approximately reflects the quality of support Both Intel MKL and AMD acml mathematical libraries are supported Some combinations of compilers and of libraries may however require manual editing of make sys 15 It is usually convenient to create semi statically linked executables with only libc libm libpthread dynamically linked If you want to produce a binary that runs on different machines compile it on the oldest machine you have i e the one with the oldest version of the operating system If you get errors like IPO Error unresolved _ suml_cos2 at the linking stage your compiler is optimized to use the SSE version of sine cosine etc contained in the SVML library Append 1svml to the list of libraries in your make sys file info by Axel Kohlmeyer oct 2007 Linux PCs with Portland compiler pgf90 QUANTUM ESPRESSO does not work reliably or not at all with many old versions lt 6 1 of the Portland Group compiler pgf90 Use the latest version of each release of the compiler with patches if available see the Portland Group web site http www pgroup com Linux PCs with Pathscale compiler Version 3 1 and version 4 open source of the Pathscale EKO compiler work info by Cezary Sliwa April 2011 and Carlo Nervi June 2011 In case of m
29. ommand line options to the executable are implemented with MPI This is your first choice for execution on a parallel machine Library OpenMP is a low effort parallelization suitable for multicore CPUs Its effectiveness relies