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1. BLAS 0 should always work and means that the MOLPRO Fortran BLAS routines are used On some platforms IBM SGI SUN BLAS 4 will give better performance in this case some 32 bit BLAS routines are used from the system library these are then called from wrapper routines which convert 64 to 32 bit integer arguments Note that this might cause problems if more than 2 GB of memory is used For good performance it is important to use appropriate BLAS libraries in particular a fast implementation of the matrix multiplication dgemm is very important for MOLPRO Therefore you should use a system tuned BLAS library whenever available MOLPRO will automatically detect the most appropriate BLAS library in many cases In certain cases in particular when the BLAS library is installed in a non default location configure should be directed to the appropriate directory with configure blaspath path to lib dir Specification of BLAS libraries can be simplified by placing any relevant downloaded libraries in the directory blaslibs configure searches this directory and then with lower priority some potential system directories for libraries relevant to the hardware For Intel and AMD Linux systems we recommend the following BLAS libraries MKL The Intel Math Kernel Library MKL ATLAS The Automatically Tuned Linear Algebra Software ATLAS library You must use the atlas library specific to your proces sor Pentium III Linux_PIIISSE12. Pentium 4 Xeon Linux_P4SSE2 AMD Athlon Linux_ATHLON AMD Opteron Linux_HAMMER64SSE2_2 64 bit When using atlas MOLPRO will automatically compile in the extra lapack subroutines which do not come by default with the package and so the liblapack a which comes with Atlas is sufficient ACML For Opteron systems then AMD Core Math Library ACML is the preferred blas library SGI Altix can use the scs1 library is preferred HP platforms can use the mlib math library IBM Power platforms can use the ess1 package 3 INSTALLATION FROM SOURCE FILES vi 5 configure prompts for the optional bin directory INST BIN for linking MOLPRO This directory should be one normally in the PATH of all users who will access MOLPRO and its specification will depend on whether the installation is private or public 6 configure prompts for the Molpro installation directory PREFIX 7 configure prompts for the destination directory for documentation This should nor mally be a directory that is mounted on a worldwide web server This is only relevant if the documentation is also going to be installed from this directory see below The full list of command line options recognized by configure are a f90 use Absoft Pro Fortran compiler uto ga hpmpi auto build GA with MPI and HP MPI uto ga mpich auto build GA with MPI and MPICH uto ga openmpi auto build GA with MPI and Open MPI gae f f f f f J J g
3. for all users of the installed version 3 9 Installation of documentation The documentation is available on the web at http www molpro net info users It is also in cluded with the source code The PDF user s manual is found in the directory Molpro doc manual pdf with the HTML version in the directory Molpro doc manual index html After make install the documentation is installed in the doc subdirectory of PREFIX specified in CONFIG file generated by the configure command Numerous example input files are in cluded in the manual and can alternatively be seen in the directory Molpro examples 3 10 Simple building for single workstations Linux or Mac OS X The following instructions are quick instructions for installing MOLPRO on a single workstation Linux or Mac OS X system The instructions assume GNU compilers have been installed de tails of getting GNU compilers for common Linux distributions are contained in the prerequi sites section but these can be substituted with alternative compilers For serial MOLPRO configur batch gcc gfortran make 3 INSTALLATION FROM SOURCE FILES x For parallel MOLPRO one can use configur batch gcc gfortran mpp mppbase path to ga build make if Global Arrays has already been built There is a simpler option providing the curl utility is installed and the machine is connected to the internet configur batch gcc gfortran mpp auto ga mpich make which will
4. 0 use Sun Fortran compiler x86_64 use settings for 64 bit x86 machine xle use IBM compiler xlf use IBM Fortran compiler 3 4 Compilation and linking After configuration the remainder of the installation is accomplished using the GNU make command Remember that the default make on many systems will not work and that it is essential to use GNU make cf section 3 2 Everything needed to make a functioning program together with all ancillary files is carried out by default simply by issuing the command make in the MOLPRO base directory Most of the standard options for GNU make can be used safely in particular j can be used to speed up compilation on a parallel machine The program can then be accessed by making sure the bin directory is included in the PATH and issuing the command molpro If MPI library is used for building Global Arrays or building MOLPRO directly please be aware that some MPI libraries use mpd daemons to launch parallel jobs In this case mpd daemons must already be running before make 3 5 Adjusting the default environment for MOLPRO The default running options for MOLPRO are stored in the script bin molpro After program installation either using binary or from source files this file should be reviewed and adjusted if necessary to make system wide changes 3 6 Tuning MOLPRO can be tuned for a particular system by running in the root directory the command make tuning This job automatically determi
5. MOLPRO Installation Guide Version 2012 1 Pfaffenwaldring 55 D 70569 Stuttgart Federal Republic of Germany P J Knowles School of Chemistry Cardiff University Main Building Park Place Cardiff CF10 3AT United Kingdom SHAI c4678cObfb1 0df7al36fe8d2f70bbc43d96eab90 Copyright 2012 University College Cardiff Consultants Limited 1 OBTAINING THE DISTRIBUTION MATERIALS i 1 Obtaining the distribution materials MOLPRO is distributed to licensees on a self service basis using the world wide web Those enti tled to the code should obtain it from https www molpro net download supplying the username and password given to them The web pages contain both source code and binaries although not everyone is entitled to source code and binaries are not available for every platform Execution of MOLPRO whether a supplied binary or built from source requires a valid licence key Note that the key consists of two components namely a list of comma separated key value pairs and a password string and these are separated by amp In most cases the licence key will be automatically downloaded from the website when building or installing the software 2 Installation of pre built binaries Binaries are given as self extracting tar archives which are installed by running them on the command line There are binaries tuned for several architectures These also support parallel execution The parallel binaries are built using GA with
6. MPI There is a generic serial binary which should run on all A32 architectures The tar archives are fully relocatable the location can be changed when running the script interactively the default is usr local If the script finds a licence key which has been cached in SHOME molpro token from a previous install then that key will be installed with the software If the script cannot find a key or automatically download it from the molpro website then the script will prompt that this part of the install has failed All files of Molpro are installed but the user must then manually install the key with the library files in a file named token e g usr local lib molpro mpptype arch lib t Other configuration options as described in section 3 5 may also be specified in the script file usr local bin molpro 3 Installation from source files 3 1 Overview There are usually four distinct stages in installing MOLPRO from source files Configuration A shell script that allows specification of configuration options is run and creates a configuration file that drives subsequent installa tion steps Compilation The program is compiled and linked and other miscellaneous utilities and files including the default options file are built The essential resulting components are 1 The molpro shell script which launches thge main executable In serial case one can directly run the main executable 2 The molpro exe executable w
7. automatically download and install MPICH and Global Arrays 3 11 Installation on a Cygwin system On a Windows machine Cygwin should be installed In addition to the default package list one should also install the packages listed in table I If undertaking development work table 2 Package Package Group Reason gcc core Devel compiling C files gcc fortran Devel compiling Fortran files gcc g Devel compiling C files make Devel need GNU make ca certificates Net download boost curl Net token download libgmp3 Libs bug needed by make exe libltdl7 Devel bug needed by make exe Table 1 Cygwin requirments for user install contains a list of potentially useful packages Package Package Group Reason bison Devel bison gdb Devel gdb git Devel git libxslt Libs xsltproc openssh Net ssh vim Editors vi Table 2 Cygwin packages for developers With the above steps configure can be run and the Molpro built in the normal way
8. brary which will be used instead of compiling the equivalent MOLPRO routines Set up password less ssh by running the following commands and not entering a password when prompted ssh keygen t rsa cat ssh id_rsa pub gt gt ssh authorized_keys This must be done for each user account which will be running MOLPRO 3 INSTALLATION FROM SOURCE FILES iv 3 3 Configuration Once the distribution has been unpacked change to the Mol pro directory that has been created Having changed to the Molpro directory you should check that the directory containing the Fortran compiler you want to use is in your PATH Then run the command configure batch which creates the file CONFIG This file contains machine dependent parameters such as com piler options Normally CONFIG will not need changing but you should at the least examine it and change any configuration parameters which you deem necessary Any changes made to CONFIG will be lost next time configure is invoked so it is best to supply as many of these as possible via the command line The configure procedure may be given command line options and if run without batch additionally prompts for a number of parameters 1 On certain machines it is possible to compile the program to use either 32 or 64 bit in tegers and in this case configure may be given a command line option i4 or i8 respectively to override the default behaviour Generally the 64 bit choice allows larger
9. cal mpich2 install include and the mppbase directory should contain file mpi h Please ensure the built in or freshly built MPI 2 library fully supports MPI 2 standard and works properly For desktop or single node installations there are a series of options prefixed with auto which build any prerequisites and can be used in place of mppbase eg configure mpp auto ga mpich 3 INSTALLATION FROM SOURCE FILES v 3 If any system libraries are in unusual places it may be necessary to specify them explicitly as the arguments to a L command line option 4 configure asks whether you wish to use system BLAS subroutine libraries MOLPRO has its own optimised Fortran version of these libraries and this can safely be used On most machines however it will be advantageous to use a system tuned version instead On the command line one can specify the level of BLAS to be used from the system e g blas2 For example if you specify 2 the system libraries will be used for level 2 and level 1 BLAS but MOLPRO s internal routines will be used for level 3 i e matrix matrix multiplication Normally however one would choose either 0 or 3 which are the defaults depending upon whether a BLAS library is found A special situation arises if 64 bit integers are in use i8 since on many platforms the system BLAS libraries only supports 32 bit integer arguments In such cases e g IBM SGI SUN either 0 or 4 can be given for the BLAS level
10. calculations files larger than 2Gb more than 16 active orbitals but can be slower if the underlying hardware does not support 64 bit integers Note that if i 4 is used then large files greater than 2Gb are supported on most systems but even then the sizes of MOL PRO records are restricted to 16 Gb since the internal addressing in MOLPRO uses 32 bit integers If i8 is used the record and file sizes are effectively unlimited Normally we recommend using the default determined by configure 2 In the case of building for parallel execution the option mpp must be given on the com mand line This enables both mpp and mppx parallelism for the distinction between these two parallelism modes please refer to the user manual section 2 The option mppbase must also be given followed by the location of the Global Arrays build directory or the MPI 2 library include directory For the case of using the Global Arrays toolkit one example can be configur mpp mppbase usr local ga version If using a Global Arrays build with an MPI library the appropriate MPI executable should appear first in PATH when more than one is available Queries regarding Global Arrays installations should be sent directly to the Global Arrays team any Molpro related queries will assume a fully functional Global Arrays suite with all internal tests run successfully For the case of using the MPI 2 library one example can be configur mpp mppbase usr lo
11. duce parallel Molpro mppbase specify mpp base path for includes and libraries nagfor use NAG Fortran compiler natom max number of atoms nbasis max number of basis functions noaims do not compile aims code noblas Don t use external BLAS library noboost Do not use binary part of Boost library nocuda don t compile CUDA code nOCxx do not compile C code nolapack don t use external LAPACK library nolargefiles Do not use largefiles noneci do not compile neci code noopenmp compile without openmp noxml2 do not use libxml2 nprim max number of primitives nrec max number of records nstate max number of states per symmetry nsymm max number of state symmetries nvalence max number of valence orbitals nvcc use NVIDIA CUDA C compiler opencc use Open64 C compiler openf90 use Open64 Fortran compiler openmp compile with openmp openmp mismatch Override exit with mismatched compilers openmpi Use settings for standard openmpi openmpi sg Use settings for openmpi compiled with SGE pathcc use Pathscale C compiler pathf90 use Pathscale Fortran compiler pgcc use Portland C compiler pgf90 use Portland Fortran compiler prefix Specify top level installation directory 3 INSTALLATION FROM SOURCE FILES Vili slater compile slater code sm 13 Use settings for sm_13 architecture for CUDA compilation sm 20 Use settings for sm_20 architecture for CUDA compilation sunce use Sun C compiler sunf9
12. g i mE ST Si uto ga mvapich2ib auto build GA with MPI and MVAPICHZ2 over Infiniband uto ga openmpi sge auto build GA with MPI and Open MPI with SGE support uto mpich auto build MPICH uto mvapich2ib auto build MVAPICH2 over Infiniband uto openmpi auto build Open MPI uto openmpi sge auto build Open MPI with SGE support atch run script non interactively las use external BLAS library laspath specify blas library path lock compile Block code c use C compiler named cc lang use Clang C compiler uda try to get settings for compiling CUDA code 90 use f90 Fortran compiler CG use Fujitsu C compiler orce link Force linking of main executable ort use fort Fortran compiler E use frt Fortran compiler 95 use G95 Fortran compiler cc use GNU Compiler Collection C compiler forker Use settings for mpich2 configured with gforker option fortran use gfortran Fortran compiler 386 use settings for i386 machine 4 Makes default integer variables 4 bytes long 686 use settings for i686 machine 8 Makes default integer variables 8 bytes long Ec use Intel C compiler 3 INSTALLATION FROM SOURCE FILES vii ifort use Intel Fortran compiler inst pl append PL to PREFIX when running make install intel mpi lsf Use settings for Intel MPI with LSF j number of make threads for building prerequisites lapack use external LAPACK library lapackpath specify LAPACK library path letter specify letter latex paper size mpp pro
13. hich is the main program For parallel computation multiple copies of molpro exe are started by a single instance of molpro shell script using the appropri ate system utility e g moirun parallel etc 3 INSTALLATION FROM SOURCE FILES il 3 Machine ready basis set and other utility libraries Validation A suite of self checking test jobs is run to provide assurance that the code as built will run correctly Installation The program can be run directly from the source tree in which it is built but it is usually recommended to run the procedure that installs the essential components in standard system directories 3 2 Prerequisites The following are required or strongly recommended for installation from source code 1 A Fortran 90 compiler Fortran77 only compilers will not suffice On HPC systems the latest vendor supplied compiler should be used The program is regularly tested with recent versions of GNU and Intel Fortran compilers 2 GNU make freely available from http www fsf org and mirrors GNU make must be used most system standard makes do not work In order to avoid the use of a wrong make it may be useful to set an alias e g alias make gmake s A recent version of GNU make is required 3 80 or above 3 About 10GB disk space strongly system dependent more with large blocksize file sys tems and where binary files are large during compilation Typically 100Mb is needed for the finally installed p
14. nes a number of tuning parameters and appends these to the file bin molpro Using these parameters MOLPRO will select the best BLAS routines depending on the problem size This job should run on an empty system It may typically take 10 minutes depending on the processor speed and you should wait for completion of this run before doing the next steps 3 7 Testing At this stage it is essential to check that the program has compiled correctly The makefile target test i e command make test will do this using the full suite of test jobs and although this takes a significantly long time it should always be done when porting for the first time A much faster test which checks the main routes through the program can be done using make 3 INSTALLATION FROM SOURCE FILES ix quicktest For parallel installation it is highly desirable to perform this validation with more than one running process This can be done conveniently through the make command line as for example make MOLPRO_OPTIONS n2 test If any test jobs fail the cause must be investigated If after due efforts to fix problems of a local origin the problem cannot be resolved the developers of MOLPRO would appreciate receiving a report There is a web based mechanism at https www molpro net bugzilla at which as many details as possible should be filled in It may also be helpful to attach a copy of the CONFIG file along with the failing output Please note that the purpose of
15. rogram Large calculations will require larger amounts of disk space 4 One or more large scratch file systems each containing a directory that users may write on There are parts of the program in which demanding I O is performed simultane ously on two different files and it is therefore helpful to provide at least two filesystems on different physical disks if other solutions such as striping are not available The directory names should be stored in the environment variables STMPDIR STMPDIR2 STMPDIR3 These variables should be set before the program is installed preferably in profile or cshrc since at some stages the installation procedures will check for them cf section 3 5 5 If the program is to be built for parallel execution then the Global Arrays toolkit or the MPI 2 library is needed For building MOLPRO with the Global Arrays toolkit we rec ommend the latest stable version although earlier versions may also work This is avail able from and should be installed prior to compil ing MOLPRO For building MOLPRO with the MPI 2 library we recommend to use the built in MPI 2 library which may have advantages of optimization on some platforms If there is no built in one on the platform a fresh MPI 2 library e g MPICH2 see http http www mpich org should be installed prior to compiling MOLPRO Many MPI 2 libraries including Intel MPI Bull MPI MPICH2 and Open MPI have been tested and others untested co
16. such bug reports is to help the developers improve the code and not for providing advice on installation or running 3 8 Installing the program for production Although the program can be used in situ it is usually convenient to copy only those files needed at run time into appropriate installation directories as specified at configuration time see section 3 3 and stored in the file CONFIG To install the program in this way do make install The complete source tree can then be archived and deleted The overall effect of this is to create a shell script in the INSTBIN directory The name should relate to the architecture type of build integer etc Symbolic links relating to the type of build are then made and finally providing that INSTBIN molpro is not a file a symbolic link is created to the new script In some cases it is preferable to create a localized script in INSTBIN molpro which will not be over written The overall effect of this cascade of links is to provide in the normal case the commands molpro and one or both of molpros serial and molprop parallel for normal use with the long names remaining available for explicit selection of particular variants For normal single variant installations none of the above has to be worried about and the molpro command will be available from directory INSTBIN During the install process the key from HOME molpro token is copied to PREFIX token so that the key will work
17. uld also work 6 The source distribution of MOLPRO which consists of a compressed tar archive with a file name of the form molpro 2012 1 tar gz The archive can be unpacked using gunzip and tar 3 INSTALLATION FROM SOURCE FILES lil 3 2 1 Fedora packages To build using GNU compilers one should ensure the following packages are installed via yum gcc c provides GNU C and C compiler gcc gfortran provides GNU Fortran compiler Optionally one can choose to install blas devel provides a BLAS library lapack devel provides a LAPACK library which will be used instead of compiling the equivalent MOLPRO routines 3 2 2 openSUSE packages To build using GNU compilers one should ensure the following packages are installed via YaST gcc c provides GNU C and C compiler gcc fortran provides GNU Fortran compiler make provides GNU make Optionally one can choose to install blas provides a BLAS library lapack provides a LAPACK library which will be used instead of compiling the equivalent MOLPRO routines 3 2 3 Ubuntu packages To build using GNU compilers one should ensure the following packages are installed via apt get build essential provides GNU C compiler gfortran provides GNU Fortran compiler curl provides curl for downloading patches openssh server provides ssh access to localhost Optionally one can choose to install libblas dev provides a BLAS library liblapack dev provides a LAPACK li
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