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automatically be expanded to include useful information about the checkin (including the file's revision number). With the switch over to SVN this was lost because SVN only does this expansion if you explicitly ask for it (for every single file). I have added a script to the contrib directory that sets the appropriate property to get SVN to do this expansion. This script will make it easy to do this every time new source files are added. It is called svn_expand_Id, the script contains some comments that explain the issue and how it addresses this. This checkin sets this property for a subset of the relevant files (trying to commit all files at once failed with svn crashing). In future the script will only affect those files for which the property was not set before.
856 lines
34 KiB
Text
856 lines
34 KiB
Text
====================================================
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$Id$
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----------------------------------------------------
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GUIDE TO INSTALLING NWChem
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---------------------------
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This Guide gives general directions for compiling and installing
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NWChem. Please read through all sections pertaining to your
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installation before beginning. The sections for this guide are
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Soure Code Protection - required reading for everyone
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Basic Build Instructions - required reading for everyone
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Alternative One-Time Build - only for one-time build, NOT
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recommended for site installations
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General Site Installation - tips to make NWChem useful for
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many users
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Building with MPI - alternative to the default TCGMSG build
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Building with Python - tips for including Python in your build
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Optimization Tips - how to compile NWChem to get better
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performance
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Point of Contact Users - required reading for the site's point of
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contact (usually the one doing the build)
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GA Related Issues - only for people that want to try out the
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latest version of GA or are having problems
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with GA on their platform
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ARMCI-related installation - ARMCI installation on high
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issues performance networks
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Running on Fujitsu machines - some notes on the Fujitsu system
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Building and Running NWChem - system information for clusters
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on Myrinet clusters using Myrinet interconnect
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Building and Running NWChem - system information for clusters
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on Giganet clusters using Giganet interconnect
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Building and Running NWChem - system information for clusters
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on Infiniband clusters using Infiniband interconnect
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Building for Windows - brief instructions for compiling under
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Windows NT or Windows 98
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Memory Script - information about a script that can help
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you set the default memory for your system
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Troubleshooting - if you have build problems
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BASIC BUILD INSTRUCTIONS:
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-------------------------
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DO THESE STEPS IN ORDER OR THE BUILD WILL FAIL
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----
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1) You must use GNU make with a version of at least 3.71. You can
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check this by seeing if make understands the "-v" flag. Type
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% make -v
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If you get version information, you are using GNU make. If you
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get anything else, you will need to figure out where the GNU make
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is on your system (it may possibly be call gmake or gnumake) or
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you will need to install it yourself (See the web site
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http://prep.ai.mit.edu/software/make/make.html. It doesn't matter
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what the GNU make is called (i.e., gmake, gnumake, etc., are
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all OK), just use this name instead of make in the instructions
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below.
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2) You can set a few OPTIONAL environment variables to let NWChem know
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more about your system. If you don't set the variables listed below,
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NWChem will pick "reasonable" defaults:
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LARGE_FILES needed to circumvent the 2 GB limit
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where possible
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(note that your system administrator must also
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enable large files in the file system), e.g.
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setenv LARGE_FILES TRUE
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LIB_DEFINES additional defines for the C preprocessor
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(for both Fortran and C), e.g.
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setenv LIB_DEFINES -DDFLT_TOT_MEM=16777216
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This sets the dynamic memory available for NWChem to run,
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where the units are in doubles. Check out the Section for
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MEMORY SCRIPT below.
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TCGRSH alternate path for rsh, it is intended to
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allow usage of ssh in TCGMSG (default
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communication protocol for workstation builds).
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setenv TCGRSH /usr/local/bin/ssh
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IMPORTANT: ssh should not ask for a password. In order to do that:
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1) On the master node, run "ssh-keygen"
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2) For each slave node, slave_node,
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% scp ~/.ssh/identity.pub username@slave_node:.ssh/authorized_keys
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Note: For general installations, it is often useful to add the
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environment variables described in this Guide to your shell script
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(eg. your .cshrc file) so that you have a "record" of the environment
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that you built in and so you can perform the build again in the same
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manner. You can either do this now and type "source .cshrc" or you
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can wait until you have decided the options that you will always use.
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3) Set the environment variable, NWCHEM_TOP, to the top directory
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of the NWChem tree (where *this* file lives), e.g.
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% setenv NWCHEM_TOP /home/adrian/nwchem
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For release versions the directory name must include the release tag.
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A suitable name would be e.g.
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% setenv NWCHEM_TOP /home/adrian/nwchem-<release tag>
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All the following directions assume that the current working
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directory is $NWCHEM_TOP/src so issue the command
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"cd $NWCHEM_TOP/src"
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4) The currently supported platforms are:
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NWCHEM_TARGET Platform OS/Version compilers LARGE_FILES
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----------------------------------------------------------------------
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SOLARIS Sun Solaris 2.X y
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SOLARIS64 Sun Solaris 2.X Sun,Fujitsu y
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IBM IBM RS/6000 AIX 4.X,5.X y
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IBM64 IBM RS/6000 AIX 4.X,5.X y
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DECOSF DEC AXP Tru64 4.0-5.0 y
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SGI_N32 SGI 64 bit os IRIX 6.5
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using 32 ints
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SGITFP SGI 64 bit os IRIX 6.5 y
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cray-sv2 Cray X1 UNICOS/mp Cray y
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LAPI IBM SP AIX/LAPI y
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LAPI64 IBM SP AIX/LAPI y
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LINUX x86 RH,MDK,SLES GNU,Intel,PGI y
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ppc YD2.1,SLES GNU,xlf y
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LINUX64 Alpha RedHat 6.2 Compaq y
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ia64 RedHat 7.2 Intel y
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x86_64 SLES, RH PGI,PathScale,Intel y
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ppc64 SLES, RH xlf y
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HPUX hppa HPUX 11.0 y
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HPUX64 hppa HPUX 11.0 y
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ia64 HPUX 11.0 y
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WIN32 Intel x86 Windows98/NT Compaq
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MACX Apple MacOSX Darwin GNU,xlf,Intel
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BGL Bluegene/L SLES blrts_xlf y
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BGP Bluegene/P SLES bgxlf y
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Cray XT4 Cray XT4 SLES/CNL ftn y
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----------------------------------------------------------------------
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Set the environment variable, NWCHEM_TARGET, to the symbolic name
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that matches your target platform, e.g.
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% setenv NWCHEM_TARGET LAPI
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Some systems also allow you to set NWCHEM_TARGET_CPU
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NWCHEM_TARGET CPU type NWCHEM_TARGET_CPU
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----------------------------------------------------------
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SGITFP R8000 R8000
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R10000 R10000
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R12000 R12000
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SGI_N32 R8000 R8000
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R10000 R10000
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R12000 R12000
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5) Configure to build the modules you need. As a first shot you might
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want to build everything (i.e. "all"), and if you start running out of
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memory you can exclude modules. You can choose one or more from
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Module Description
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---------------------------------------------------------
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all Everything useful
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pnnl Everything useful including python
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qm All quantum mechanics modules
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md MD only build
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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If you are familiar with building NWChem you
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can be more selective with the modules you
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really need. If you are a novice at this then
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use only one of the four module names listed above!
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Note that not all of the possible builds have been
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tested using the individual modules listed below.
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- - - - - - - - - - - - - - - - - - - - - - - - -
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ddscf RHF and UHF SCF energies
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nwdft DFT energies
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gradients SCF gradients
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dftgrad DFT gradients
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stepper Geometry optimization with stepper
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driver Geometry optimization with driver
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moints 4-index
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rimp2 RI-MP2
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ccsd CCSD & CCSD(T)
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property Properties analysis
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nwpw Build the plane wave pseudo-potential code
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python Build python interface to NWChem
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---------------------------------------------------------
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To configure to build everything use the command
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% cd $NWCHEM_TOP/src
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% make nwchem_config NWCHEM_MODULES=all
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OR
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% cd $NWCHEM_TOP/src
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% setenv NWCHEM_MODULES all
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% make nwchem_config
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Combinations of these tags are allowed. For example,
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% setenv NWCHEM_MODULES "all python"
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will build the union of these three module identifiers.
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6) If your NWCHEM_TARGET is CRAY-T3E or cray-sv2, perform the
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precision conversion:
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% cd $NWCHEM_TOP/src
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% make dbl_to_sngl
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This is necessary only on machines where 64 bit is single
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precision in order to match BLAS routine names to vendor-supplied
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libraries (or if converting back from such source into the
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standard of 64 bit is double precision).
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7) Finally, compile and link:
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% make >& make.log
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This should install the executables and libraries into
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platform-specific subdirectories in the directory tree. For
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example, if the target platform equals LAPI then the following
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subdirectories are created:
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$NWCHEM_TOP/bin/LAPI (executables)
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$NWCHEM_TOP/lib/LAPI (libraries)
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8) If you will be installing NWChem for general site use please also
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build the version info to help us determine exactly which version
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and patched version of NWChem you are using. To do this you do the
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following:
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cd $NWCHEM_TOP/src/util
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make version
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make
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cd $NWCHEM_TOP/src
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make link
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Note: Some compilers cannot build the full version file due to a
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lack of memory available to the compiler. If the make in
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$NWCHEM_TOP/src/util fails try instead:
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cd $NWCHEM_TOP/src/util
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make smallversion
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make
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cd $NWCHEM_TOP/src
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make link
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USE OF NON DEFAULT COMPILERS:
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-----------------------------
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Use of compilers different from the default ones is possible by
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supplying the following options to the make command:
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make FC="fortran compiler" and/or CC="C compiler"
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E.g:
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make FC=ifort
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(Intel Fortran compiler replacing GNU g77 on x86 platforms)
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Possible choices
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NWCHEM_TARGET uname -m FC CC
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---------------------------------------
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LINUX i386 ifort icc Intel compilers for IA32
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LINUX i386 pgf77 Portland Group f77 compiler
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LINUX64 ppc xlf xlc IBM compilers
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LINUX64 ia64 ifort Intel C compiler for IA64
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LINUX64 x86_64 pathf90 PathScale f90 compiler
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LINUX64 x86_64 ifort Intel EM64T Fortran compiler
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LINUX64 x86_64 pgf90 PGI Fortran90 compiler
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LINUX64 ppc64 xlf xlc IBM compilers
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MACX xlf xlc IBM compilers
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SOLARIS64 frt fcc Fujitsu Compilers
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Notes:
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1) On Pentium4/Xeon machine, use of the Intel compiler is strongly
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recommended since performance gains of 30-40% with respect to g77 are
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not unusual. On PentiumIII and AMD computers perfomance
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improvements of 10-20% have been observed.
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2) using the Portland Group Compiler, pgf77, is available.
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However, NWChem development is under the GNU and Intel suite of
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compilers and so the pgf77 version is far from being optimal.
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3) use of the GNU fortran compiler (g77) on 64-bit architecture
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(e.g. x86_64) is not encouraged because of the NWChem default use
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of 64-bit integers on 64-bit architectures.
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ALTERNATIVE ONE-TIME BUILD:
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---------------------------
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An alternative to steps 3 thru 7 is to specify all variables
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on the make command line. This is recommended only for one
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time builds. For instance, to build just the quantum mechanical
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codes on an IBM workstation
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make NWCHEM_TOP=/home/nwchem NWCHEM_TARGET=IBM NWCHEM_MODULES=qm
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Sometimes but infrequently the GNU make program fails with a single
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line specification. If this happens try
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make NWCHEM_TOP=/home/nwchem NWCHEM_MODULES=qm nwchem_config
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make NWCHEM_TOP=/home/nwchem NWCHEM_TARGET=IBM
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GENERAL SITE INSTALLATION:
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--------------------------
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The build procedures outlined above will allow use of NWChem within
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the NWChem directory structure. The code will look for the basis set
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library file in a default place within that directory structure. To
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install the code in a general, public place (e.g., /usr/local/NWChem)
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you need to do the following:
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A) determine the local storage path for the install files. (e.g.,
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/usr/local/NWChem).
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B) make directories
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mkdir /usr/local/NWChem
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mkdir /usr/local/NWChem/bin
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mkdir /usr/local/NWChem/data
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C) cp $NWCHEM_TOP/bin/${NWCHEM_TARGET}/nwchem /usr/local/NWChem/bin
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* cp $NWCHEM_TOP/bin/${NWCHEM_TARGET}/parallel /usr/local/NWChem/bin
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cd /usr/local/NWChem/bin
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chmod 755 nwchem
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chmod 755 parallel
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*Note: parallel does not exist for all builds. To learn how to use
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parallel consult the on-line documentation at:
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http://www.emsl.pnl.gov/pub/docs/nwchem/doc/user/index.html
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or read the README files in $NWCHEM_TOP/src/tcgmsg
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For SPs:
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** cp $NWCHEM_TOP/bin/${NWCHEM_TARGET}/jobtime usr/local/NWChem/bin
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cp $NWCHEM_TOP/bin/${NWCHEM_TARGET}/jobtime.pl usr/local/NWChem/bin
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**Note: These scripts use perl to get information from LoadLeveller
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to get time information. jobtime may need to be modified
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to find perl on your system. If you can't get these to
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work, timing information will not be available for your
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system. However, jobs will still run.
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D) cd $NWCHEM_TOP/src/basis
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cp -r libraries /usr/local/NWChem/data
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cd $NWCHEM_TOP/src/
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cp -r data /usr/local/NWChem
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cd $NWCHEM_TOP/src/nwpw
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cp -r libraryps /usr/local/NWChem/data
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E) Each user will need a .nwchemrc file to point to these default data
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files. A global one could be put in /usr/local/NWChem/data and a
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symbolic link made in each users $HOME directory which is probably
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the best plan for new installs. Users would have to issue the
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following command prior to using NWChem:
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ln -s /usr/local/NWChem/data/default.nwchemrc $HOME/.nwchemrc
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F) Contents of the default.nwchemrc file based on the above
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information should be:
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nwchem_basis_library /usr/local/NWChem/data/libraries/
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nwchem_nwpw_library /usr/local/NWChem/data/libraryps/
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ffield amber
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amber_1 /usr/local/NWChem/data/amber_s/
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amber_2 /usr/local/NWChem/data/amber_q/
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amber_3 /usr/local/NWChem/data/amber_x/
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amber_4 /usr/local/NWChem/data/amber_u/
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spce /usr/local/NWChem/data/solvents/spce.rst
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charmm_s /usr/local/NWChem/data/charmm_s/
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charmm_x /usr/local/NWChem/data/charmm_x/
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Of course users can copy this file instead of making the symbolic
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link described above and change these defaults at their discretion.
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It is can also be useful to use the NWCHEM_BASIS_LIBRARY environment variable
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when testing a new installation when an old one exists. This will allow you to
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overwrite the value of nwchem_basis_library in your .nwchemrc file and point to
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the new basis library. For example:
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setenv NWCHEM_BASIS_LIBRARY "$NWCHEM/data-5.0/libraries/"
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Do not forget the trailing "/".
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BUILDING WITH MPI:
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------------------
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NWChem can be compiled to use MPI instead of TCGMSG for message
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passing on many systems. Several environment variables need to be
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set to compile with NWChem. These are:
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USE_MPI - set to "y" if you want to compile with MPI
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USE_MPIF - set to "y" if you want to the NWPW module to use fortran-bindings of MPI
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LIBMPI - name of the library with -l (eg. -lmpich)
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MPI_LIB - directory where the MPI library resides
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MPI_INCLUDE - directory where the MPI include files reside
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Below are some implementation specific settings:
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MPICH
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setenv MPI_LOC /usr/local #location of mpich
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setenv MPI_LIB $MPI_LOC/lib
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setenv MPI_INCLUDE $MPI_LOC/include
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setenv LIBMPI "-lfmpich -lmpich -lpmpich"
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MPIPro:
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setenv LIBMPI "-lmpipro -lpthread"
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LAM version 6.5, 7.0.x
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setenv MPI_LIB /usr/lib
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setenv LIBMPI "-llamf77mpi -lmpi -llam -lpthread"
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setenv MPI_INCLUDE /usr/include/
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MPICH/GM
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same as for MPICH, plus
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setenv GM_HOME /usr/local/gm-1.2/binary #location of GM software
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setenv GM_INCLUDE $GM_HOME/include
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setenv GM_LIB $GM_HOME/lib
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setenv ARMCI_NETWORK GM
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setenv GMPI_SHMEM_FILE /tmp/$USER.gm
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HP SC Alpha serie
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setenv LIBMPI "-lfmpi -lmpi -lelan"
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setenv ARMCI_NETWORK QUADRICS
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HPUX
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setenv MPI_INCLUDE /opt/mpi/include
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setenv MPI_LIB /opt/mpi/lib/pa1.1/
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setenv LIBMPI -lmpi
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HPUX64
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setenv MPI_INCLUDE /opt/mpi/include
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setenv MPI_LIB /opt/mpi/lib/pa20_64/
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setenv LIBMPI -lmpi
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SGI_N32
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setenv LIBMPI -lmpi
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WIN32/NT-MPICH
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set MPI_INCLUDE=c:\PROGRA~1\ARGONN~1\MPICHN~1.4\SDK\INCLUDE
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set MPI_LIB=c:\PROGRA~1\ARGONN~1\MPICHN~1.4\SDK\lib
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set NWCHEM_EXTRA_LIBS=%MPI_LIB%\mpich.lib
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WIN32/WMPI1.3
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set MPI_INCLUDE=c:\WMPI1.3\INCLUDE
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set MPI_LIB=c:\WMPI1.3\LIB\CONSOLE
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set NWCHEM_EXTRA_LIBS=%MPI_LIB%\cvwmpi.lib
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IBM
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setenv MPI_INCLUDE /usr/lpp/ppe.poe/include
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setenv MPI_LIB /usr/lpp/ppe.poe/lib/
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setenv LIBMPI "-binitfini:poe_remote_main -lmpi_r -lvtd_r \
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-I/usr/lpp/ssp/css/include -llapi_r -lpthreads \
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-L/usr/lpp/ppe.poe/lib/threads -L/usr/lpp/ppe.poe/lib \
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-L/usr/lpp/ppe.poe/lib/ip "
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To run with MPI, "parallel" should not be used. The way
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we usually run nwchem under MPI are the following:
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1) using mpirun:
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mpirun -np 8 $NWCHEM_TOP/bin/${NWCHEM_TARGET}}/nwchem h2o.nw
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NOTE: In some MPI implementation, NWChem fails to read the input
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file argument (h2o.nw in the previous example). If this is the
|
|
case, you have to copy your input file in the working directory
|
|
as nwchem.nw.
|
|
|
|
2) If you have all nodes connected via shared memory
|
|
and you have installed the ch_shmem version of MPICH,
|
|
you can do
|
|
|
|
$NWCHEM_TOP/bin/${NWCHEM_TARGET}/nwchem -np 8 h2o.nw
|
|
|
|
The previous NOTE about the input file argument applies to
|
|
this case, too.
|
|
|
|
BUILDING WITH PYTHON:
|
|
---------------------
|
|
|
|
Python programs may be embedded into the NWChem input and
|
|
used to control the execution of NWChem. The following are
|
|
the instructions for building NWChem with the Python interface
|
|
and for running jobs which include Python.
|
|
|
|
1) To build with Python, you first need to have Python
|
|
available on your machine. If you don't have it, you can
|
|
download it at http://www.python.org, following their
|
|
instructions for installation and testing. We have tested
|
|
NWChem with Python versions 1.5.1, 1.5.2, 1.6 and 2.0.
|
|
|
|
2) Make sure that "python" is part of the definition of
|
|
NWCHEM_MODULES before starting the build. For example,
|
|
|
|
% setenv NWCHEM_MODULES "all python"
|
|
|
|
3) Set the environment variables PYTHONHOME and PYTHONVERSION.
|
|
For example,
|
|
|
|
% setenv PYTHONHOME /usr/local/Python-1.5.1
|
|
% setenv PYTHONVERSION 1.5
|
|
% setenv USE_PYTHON64 y
|
|
|
|
(Note that the third number in the version should not be kept:
|
|
2.2.3 should be set as 2.2 )
|
|
|
|
4) Proceed with the rest of the build as described in the
|
|
Basic Build Instructions.
|
|
|
|
To run with Python, make sure that PYTHONHOME is set as
|
|
mentioned above. You will also need to set PYTHONPATH to
|
|
include any modules that you are using in your input. Then,
|
|
run NWChem as usual. Examples of Python within NWChem are
|
|
in the $NWCHEM_TOP/QA/tests/pyqa and $NWCHEM_TOP/contrib/python
|
|
directories.
|
|
|
|
|
|
OPTIMIZATION TIPS:
|
|
------------------
|
|
|
|
The basic build tries to optimize NWChem for most systems and
|
|
most operating systems. Therefore, possible optimizations have
|
|
been excluded. IF you want to further optimize NWChem, first be
|
|
warned that we will NOT be able to provide support for this
|
|
activity. Also, if you have problems with your optimized code,
|
|
we will not be able to support you since we, in general, cannot
|
|
reproduce your environment. That being said, here are some tips
|
|
for optimizing the code.
|
|
|
|
In general, NWChem uses its own basic linear algebra subroutines
|
|
(BLAS). These are generally not as fast as vendor supplied BLAS
|
|
or other fast BLAS libraries. For instance, we have found the
|
|
Automatically Tuned Linear Algebra Software (ATLAS) to be faster
|
|
on several platforms (http://math-atlas.sf.net/). To include
|
|
faster BLAS routines, set the environment variable BLASOPT before
|
|
building the code. For example, with ATLAS
|
|
|
|
% setenv BLASOPT "-L/usr/local/ATLAS -lf77blas -latlas"
|
|
|
|
Other good choices of optimized BLAS libraries on Intel hardware
|
|
include:
|
|
1) Goto/Flame
|
|
http://www.cs.utexas.edu/users/flame/goto/
|
|
2) Intel MKL
|
|
http://www.intel.com/software/products/mkl/mkl60/
|
|
|
|
|
|
If you are using HP computers (either PA-RISC or IA-64), you might
|
|
want to try the MLIB library
|
|
http://www.hp.com/go/mlib
|
|
|
|
If you are using SGI computers (either MIPS or IA-64), you might
|
|
want to try the SCSL library
|
|
http://www.sgi.com/software/scsl.html
|
|
|
|
If you are using IBM RS6000 computers, you might
|
|
want to try the ESSL library
|
|
http://www-1.ibm.com/servers/eserver/pseries/library/sp_books/essl.html
|
|
|
|
WARNING: In the case of 64-bit platforms, most vendors optimized BLAS
|
|
libraries cannot be used. This is due to the fact that while
|
|
nwchem uses 64-bit integers (i.e. integer*8) on 64-bit platforms,
|
|
most of the vendors optimized BLAS libraries used 32-bit integers.
|
|
BLAS libraries not supporting 64-bit integers:
|
|
CXML (DECOSF), ESSL (LAPI64), MKL (LINUX64/ia64), ACML(LINUX64/x86_64),
|
|
Goto/Flame(LINUX64).
|
|
A methods is now available to link against the libraries mentioned above;
|
|
please do the following:
|
|
1) cd $NWCHEM_TOP/src
|
|
2) make clean
|
|
3) make 64_to_32
|
|
4) make USE_64TO32=y HAS_BLAS=yes BLASOPT=" optimized BLAS"
|
|
e.g. for IBM64: make USE_64TO32=y HAS_BLAS=yes BLASOPT="-lessl -lmass"
|
|
|
|
If you are interested in "tweaking" compile options, the
|
|
appropriate place to do this is the $NWCHEM_TOP/config/makefile.h
|
|
file. First find the appropriate section for your $NWCHEM_TARGET
|
|
and then edit the appropriate options. Again, please note that
|
|
changes to the makefile are NOT supported and you are on your own
|
|
in this endeavor!
|
|
|
|
If you are running on an IBM SP, you might want to consider
|
|
optimizing the value of -bmaxdata in the makefile.h file. This
|
|
option specifies the maximum amount of space to reserve for the
|
|
program stack segment.
|
|
|
|
On Apple MacOSX, setting USE_VECLIB=y links against the vecLib
|
|
library, available at
|
|
http://developer.apple.com/hardware/ve/vector_libraries.html
|
|
|
|
|
|
SUPPORT:
|
|
-----------------------
|
|
All distribution issues (such as how do I get the code
|
|
or how do I get the latest version) should be directed to the
|
|
ms3distribution@emsl.pnl.gov support queue. All other issues should go
|
|
to the nwchem-users mailing list (nwchem-users@emsl.pnl.gov, a public
|
|
mailing list archived at
|
|
http://www.emsl.pnl.gov/docs/nwchem/nwchem-support/).
|
|
|
|
|
|
GA RELATED ISSUES:
|
|
-------------------
|
|
Occasionally, bugs in NWChem are associated with the Global Array tools
|
|
(http://www.emsl.pnl.gov/docs/global/ga.html). Check out the URL
|
|
http://www.emsl.pnl.gov/docs/global/support.html for GA installation
|
|
related issues. NOTE: some installations do not even work without some of
|
|
the system related issues being resolved that are listed in that URL.
|
|
|
|
To compile the latest version of GA for NWChem, following these steps:
|
|
|
|
1) Get a new version of GA at the above URL.
|
|
|
|
2) Untar it into a temporary directory (for this example, lets call it
|
|
/tmp) using the instructions on the GA download web page.
|
|
|
|
3) % cd $NWCHEM_TOP/src/tools
|
|
|
|
4) % mv GNUmakefile ../GNUmakefile.tools
|
|
|
|
5) % rm -r * (Make sure you are in the tools directory before doing this!)
|
|
|
|
6) Copy the new GA files into the tools directory. For example,
|
|
% cp -R /tmp/g/* .
|
|
|
|
7) % mv ../GNUmakefile.tools GNUmakefile
|
|
|
|
8) If all of your environmental variables are set, start with step 5 of
|
|
the Basic Build Instructions. If they are not set, start with step 2.
|
|
|
|
|
|
ARMCI-RELATED INSTALLATION ISSUES
|
|
---------------------------------------------------------------
|
|
|
|
The ARMCI_NETWORK environmental variable must be defined in order to
|
|
achieve best performance on high performance networks. The following
|
|
table summarize supported combinations of ARMCI_NETWORK and NWCHEM_TARGET.
|
|
|
|
ARMCI_NETWORK NWCHEM_TARGET Network Protocol
|
|
---------------------------------------------------------
|
|
GM LINUX Myrinet GM
|
|
LINUX64
|
|
VIA LINUX Giganet/CLAN VIA
|
|
MELLANOX LINUX InfiniBand VAPI
|
|
LINUX64
|
|
OPENIB LINUX InfiniBand OpenIB
|
|
LINUX64
|
|
ELAN3 or LINUX Quadrics/QsNet Elan3/Shmem
|
|
QUADRICS DECOSF
|
|
LINUX64
|
|
ELAN4 LINUX64 Quadrics/QsNetII Elan4
|
|
|
|
BGMLMPI BGL IBM BlueGene Torus/ BGLMPI
|
|
DCMFMPI BGP Global Tree/Interrupt DCMF,MPI
|
|
|
|
PORTALS LINUX64 Cray SeaStar/HyperTransport PORTALS
|
|
MPI-SPAWN LINUX64 Myrinet MX or Infiniband MPI2
|
|
|
|
For more information/support, you are referred to the ARMCI support page at
|
|
section 2.1.2 of the following URL
|
|
http://www.emsl.pnl.gov/docs/global/um/build.html
|
|
|
|
|
|
BUILDING AND RUNNING NWCHEM ON INFINIBAND CLUSTERS WITH OPENIB
|
|
(or MELLANOX) NETWORK :
|
|
------------------------------------------------
|
|
Before starting the NWChem compilation, the following environmental
|
|
variables need be defined (a sample for OpenIB network with mavpich):
|
|
|
|
USE_MPI=y
|
|
IB_HOME="location of OpenIB software"
|
|
IB_INCLUDE=$IB_HOME/include
|
|
IB_LIB=$IB_HOME/lib64
|
|
IB_LIB_NAME="-libumad -lpthread"
|
|
ARMCI_NETWORK=OPENIB
|
|
MPI_LOC="location of MPI libs"
|
|
MPI_LIB=$MPI_LOC/lib
|
|
MPI_INCLUDE=$MPI_LOC/include
|
|
LIBMPI=-lmpich
|
|
|
|
|
|
BUILDING FOR WINDOWS:
|
|
---------------------
|
|
The right target is WIN32. Before starting the compilation, you must have
|
|
installed the Compaq Visual Fortran compiler (version 6.0 and 6.1 have been
|
|
successfully tested) and the NT.MPICH library
|
|
(http://www-unix.mcs.anl.gov/~ashton/mpich.nt/ ). Then, you need to have
|
|
defined this series of variables (that you can set in autoexec.bat):
|
|
|
|
set NWCHEM_TOP=c:\nwchem
|
|
set NWCHEM_TARGET=WIN32
|
|
|
|
set MPI_INCLUDE=c:\PROGRA~1\ARGONN~1\MPICH.NT.1.2.3\SDK\INCLUDE
|
|
set MPI_LIB=c:\PROGRA~1\ARGONN~1\MPICH.NT.1.2.3\SDK\lib
|
|
set NWCHEM_EXTRA_LIBS=c:\PROGRA~1\ARGONN~1\MPICH.NT.1.2.3\SDK\lib\mpich.lib
|
|
|
|
You'll first need to create the util_version.F file in the util directory
|
|
cd $NWCHEM_TOP\src\util
|
|
cp util_v_stub.F util_version.F
|
|
|
|
For nwchem-5.0 you will also need to modify the matmul.c file in the tools/global/src
|
|
directory
|
|
cd $NWCHEM_TOP\src\tools\src
|
|
edit matmul.c and change all instances of "ga_error_" to "ga_error"
|
|
|
|
To start the compilation, start the Microsoft makefile utility from the
|
|
top level source directory by typing
|
|
|
|
nmake
|
|
|
|
The name of the executable is nw32.exe.
|
|
|
|
Note: This build has only been tested using Compac visual fortran (version 6.6) and Microsoft
|
|
C/C++ (Version 12.00) on windows XP and windows 2000.
|
|
|
|
Reminder: For Compaq visual fortran don't forget to execute the "dfvars" script.
|
|
|
|
|
|
BUILDING NWCHEM on BLUEGENE/L:
|
|
------------------------------------------
|
|
Set up the following environmental variables:
|
|
|
|
setenv NWCHEM_TARGET BGL
|
|
setenv ARMCI_NETWORK BGMLMPI
|
|
setenv BGLSYS_DRIVER /bgl/BlueLight/ppcfloor
|
|
setenv BGLSYS_ROOT ${BGLSYS_DRIVER}/bglsys
|
|
setenv BLRTS_GNU_ROOT ${BGLSYS_DRIVER}/blrts-gnu
|
|
setenv BGDRIVER ${BGLSYS_DRIVER}
|
|
setenv BGCOMPILERS ${BLRTS_GNU_ROOT}/bin
|
|
setenv USE_MPI y
|
|
setenv LARGE_FILES TRUE
|
|
setenv MPI_LIB ${BGLSYS_ROOT}/lib
|
|
setenv MPI_INCLUDE ${BGLSYS_ROOT}/include
|
|
setenv LIBMPI "-lfmpich_.rts -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts"setenv BGMLMPI_INCLUDE /bgl/BlueLight/ppcfloor/bglsys/include
|
|
setenv BGMLLIBS /bgl/BlueLight/ppcfloor/bglsys/lib
|
|
|
|
to compile:
|
|
make FC=blrts_xlf
|
|
|
|
BUILDING NWCHEM on BLUEGENE/P:
|
|
------------------------------------------
|
|
Set up the following environmental variables:
|
|
setenv NWCHEM_TARGET BGP
|
|
setenv ARMCI_NETWORK DCMFMPI
|
|
setenv MSG_COMMS DCMFMPI
|
|
setenv USE_MPI y
|
|
setenv LARGE_FILES TRUE
|
|
setenv BGP_INSTALLDIR /bgsys/drivers/ppcfloor
|
|
setenv BGCOMPILERS /bgsys/drivers/ppcfloor/gnu-linux/bin
|
|
setenv BGP_RUNTIMEPATH /bgsys/drivers/ppcfloor/runtime
|
|
setenv ARMCIDRV ${BGP_INSTALLDIR}
|
|
setenv BGDRIVER ${ARMCIDRV}
|
|
setenv MPI_LIB ${BGDRIVER}/comm/lib
|
|
setenv MPI_INCLUDE ${BGDRIVER}/comm/include
|
|
setenv LIBMPI "-L${MPI_LIB} -lfmpich_.cnk -lmpich.cnk -ldcmfcoll.cnk -ldcmf.cnk -lpthread -lrt -L${BGP_RUNTIMEPATH}/SPI -lSPI.cna"
|
|
setenv BGMLMPI_INCLUDE ${MPI_INCLUDE}
|
|
|
|
to compile:
|
|
make FC=bgxlf
|
|
|
|
|
|
BUILDING NWCHEM FOR CRAY XT3/XT4 (OS: Compute Node Linux (CNL))
|
|
---------------------------------------------------------------
|
|
Environmental variables for building and running:
|
|
|
|
setenv NWCHEM_TARGET LINUX64
|
|
setenv USE_MPI y
|
|
setenv ARMCI_NETWORK PORTALS
|
|
setenv MA_USE_ARMCI_MEM 1
|
|
setenv LIBMPI " "
|
|
setenv MPI_INCLUDE "$MPICH_DIR/include -I/opt/xt-pe/default/include -I/opt/xt-catamount/default/catamount/linux/include"
|
|
|
|
to compile:
|
|
make FC=ftn
|
|
|
|
|
|
MEMORY SCRIPT:
|
|
--------------
|
|
In the $NWCHEM_TOP/contrib directory there is a script named "getmem.nwchem".
|
|
This script should be run after you have followed the Basic Build
|
|
instructions. This script will try to figure out the amount of
|
|
memory on the machine, the number of processors, make an educated guess on
|
|
the amount of memory that can be used per processor, recompile the appropriate
|
|
files and then relink the executable. Be sure to watch the values that are
|
|
printed at the beginning of the script to make sure that it has used
|
|
reasonable values.
|
|
|
|
|
|
TROUBLESHOOTING:
|
|
----------------
|
|
|
|
Here are some tips for "common" problems when compiling NWChem. If you have
|
|
read through the installation guide and followed the directions carefully
|
|
and you are still having problems, please send your make.log file to
|
|
nwchem-users@emsl.pnl.gov along with information about your machine and
|
|
the environment variables that you have set. If you have modified any of
|
|
the files in the NWChem source tree, we need to know this, but do not
|
|
expect that we will be able to help you.
|
|
|
|
1) Check the "Known Bugs" and "FAQ" page at our web site
|
|
http://www.emsl.pnl.gov/pub/docs/nwchem
|
|
|
|
2) "make nwchem_config" gives an error message like
|
|
"Not a recognized command".
|
|
|
|
You probably don't have GNU make. Go back to step 1 in the Basic
|
|
Build Instructions.
|
|
|
|
3) I get an error about clock skew and some directories are not compiled.
|
|
|
|
Some platforms have problems where the parallel make sees time lags.
|
|
This can be solved by several different methods:
|
|
|
|
A) Perform multiple make commands at the $NWCHEM_TOP/src level.
|
|
|
|
B) If you know which directories need to be compiled, just type
|
|
"make" in those directories. Then type "make link" in the
|
|
$NWCHEM_TOP/src directory.
|
|
|
|
C) Another solution is to edit the $NWCHEM_TOP/src/config/makefile.h
|
|
file, find the section relating to your $NWCHEM_TARGET, and edit
|
|
the MAKEFLAGS line so that the number after -j is a "1".
|
|
|
|
i.e. MAKEFLAGS = -j 1 --no-print-directory
|
|
|
|
4) I accidently performed the "make dbl_to_sngl" command and now
|
|
the code won't compile.
|
|
|
|
You will need to run "make sngl_to_dbl" in the $NWCHEM_TOP/src
|
|
directory. You will also need to type "make realclean" and start
|
|
over at step 5 in the Basic Build Instructions.
|
|
|
|
5) I accidently built for the wrong $NWCHEM_TARGET and need to start
|
|
over.
|
|
|
|
You will need to clean up all of the files associated with the
|
|
previous build. So, type "make realclean" in the $NWCHEM_TOP/src
|
|
directory. Then start at step 4 in the Basic Build Instructions,
|
|
setting the environment variables with the values that you want.
|
|
|
|
6) I am getting "Word too long" errors when compiling.
|
|
|
|
This sometimes happens when the system shell being used is ksh.
|
|
The solution is to
|
|
|
|
A) Edit the $NWCHEM_TOP/src/config/makelib.h file, and take out
|
|
the lines that have LOCKFILE in them.
|
|
|
|
B) Then, edit the $NWCHEM_TOP/src/config/makefile.h file, find the
|
|
section relating to your $NWCHEM_TARGET, and edit
|
|
the MAKEFILES line so that the number after -j is a "1".
|
|
|
|
i.e. MAKEFLAGS = -j 1 --no-print-directory
|
|
|
|
7) I have a compile problem in $NWCHEM_TOP/src/nwpw/libraryps/nwpw_libfile.F
|
|
with a missing ' in the line.
|
|
|
|
This happens when the path that you are compiling in gets long. We will
|
|
be fixing this in the next release. But in the meantime, there
|
|
are at least two ways to fix this:
|
|
|
|
A) Compile in a directory with a short path.
|
|
|
|
B) Edit the $NWCHEM_TOP/src/nwpw/libraryps/GNUmakefile and change
|
|
$(SRCDIR) to a shorter path. It is useful if this is where
|
|
you will be putting the pseudopotential libraries.
|