Installation

CHARMM Release and Installation Welcome to the Fortran95 conversion of CHARMM, the result of about two years of intense effort by a core group of developers, and major contributions from many of the active development sites. Note that while all of the features included by default have been fully converted and verified via cross testing vs. different compilers and pre-conversion code, some optional features may not yet be functional; caveat emptor. Two new performance features available for the first time with this release are an implementation of the domain decomposition code of D.E. Shaw (chmdoc/domdec.doc) and an interface to the GPU based OpenMM code from Vijay Pandy (chmdoc/openmm.doc). Problems and questions related to the installation and post-installation testing of CHARMM may be posted in the "Installation and Performance" forum at www.charmm.org (registration required to post). This document contains a formal definition of the current CHARMM release followed by a detailed installation procedure. We describe here features and end-line-user-site installation. Issues regarding developer sites are documented in Develop: . * Contents / List of Contents of the current release * Machines / Machines supported * Install / Installation Procedure * Documentation / CHARMM Documentation via emacs INFO program * TOPPAR / Standard CHARMM Topology and Parameter Files * UserForm / CHARMM User Group support
Top CHARMM Release Package The CHARMM release package for CHARMM developers and user sites includes (1) complete source and include files, (2) updated documentation files, (3) some supporting data files, (4) testcases, (5) the PREFX preprocessor and tools needed to set up CHARMM development environments and (6) standard topology and parameter files. The files are organized in the followoing subdirectories. ~/ denotes the directory where you have unpacked (via tar) the CHARMM release package delivered to you. In ~/cnnXm, nn is the version number, X is the version trunk designator (a for alpha or developmental, b for beta release and c for gamma or general release) and m is the revision number. For example, c36b1 is CHARMM version 36 beta release revision 1. ~/cnnXm/ The main directory of CHARMM ~/cnnXm/source/ Contains all CHARMM source files ~/cnnXm/doc/ The most recent CHARMM documentation If 'info' is available on your host machine, you may 'soft' link this directory to the info directory to access the documentation via the info program. ~/cnnXm/support/ Supplementary programs and data files ~/cnnXm/test/ CHARMM testcases; post installation tests ~/cnnXm/tool/ Preprocessor, FLECS translator and other CHARMM installation utilities ~/cnnXm/toppar/ Standard topology/parameter files ~/cnnXm/build/ Contains Makefile, module makefiles and the log file of the install make command for each machine in the subdirectory named after the machine type. Created by the first use of install.com: ~/cnnXm/exec/ The CHARMM executable charmm will be stored here when installation is completed. ~/cnnXm/lib/ Contains library files
Top Supported Machine Platforms The current release version is available on the following platforms: altix SGI Itanium Altix series (64 bit) * em64t ifort compilers on x86_64 Linux * gnu Linux; GNU gfortran compiler by default ** gpu GPU using CUDA library g95 G95 compiler (Linux) hpitanium HP-UX Itaniums ibmaix IBM AIX not parallel ibmaixmp IBM AIX parallel ibmlnxmp IBM GNU/Linux parallel itanium INTEL Itanium 2 using ifort compiler nag Numerical Algorithms Group compiler (Linux) * osx Mac OSX machines xt4 Cray XT4/XT5 using compute node Linux * confirmed to work; others may work, but are unconfirmed (no reports) ** developmental versions only The new code relies on the full Fortran95 feature set, and some common Fortran2003 extensions implemented by most modern Fortran compilers. The suggested compiler release versions are: GCC gfortran 4.4.x or later, except 4.5.1 Intel ifort 11.1 or later PGI pgf95 11.1 or later The above lists are expected to change as usage of the Fortran95 conversion becomes more widespread. The older Fortran77 version of CHARMM was historically available on these types of machines: Alliant Apollo Convex Cray X-MP, Cray Y-MP, Cray-2, and Cray T3E DEC Stations running Ultrix DEC Alpha Stations running OSF Hewlett-Packard Apollo 700 Series IBM-3090 running AIX IBM-RS/6000 Intel iPSC Hypercube Silicon Graphics (SGI) Sun, Hal See parallel.doc for details on historical parallel versions.
Top User Site CHARMM Installation The installation is carried out by the shell script ~/cnnXm/install.com. Change your working directory to ~/cnnXm and run install.com. install.com expects one or more arguments. Without arguments, the following listing is produced: N.B.: This is the new Fortran95 revision of CHARMM; read install.doc Usage: install.com host-machine-type [charmm-size] [Sw] [1] host-machine-type is one of the following. altix SGI Itanium Altix series (64 bit) em64t ifort compilers on x86_64 Linux gnu Linux; GNU compiler by default gpu GPU using CUDA library g95 G95 compiler hpitanium HP-UX Itaniums ibmaix IBM AIX not parallel ibmaixmp IBM AIX parallel ibmlnxmp IBM GNU/Linux parallel itanium INTEL Itanium 2 using ifort compiler nag Numerical Algorithms Group compiler osx Mac OSX machines xt4 Cray XT4/XT5 using compute node Linux [3] [Sw] are install switches, which must be specified after the host-machine-type argument. You may specify any of the following. Optional args clean or distclean can be used and are recommended prior to re-installation with changed options MPIF90, MPICH, SCALI, and MPISPECIAL are mutually exclusive additional options to be used with M; MPIF90 is the default. X include Xlib graphics, along with .ps .pov .fdat files M links to MPI 1 to halt after setting up installation directory. 2 to halt after making installation utilities. Q replace QUANTUM with GAMESS. U replace QUANTUM with GAMESS-UK. C replace QUANTUM with CADPAC. T replace QUANTUM with SCCDFTB. QC replace QUANTUM with Q-CHEM. QT replace QUANTUM with Turbomole. SQ replace QUANTUM with SQUANTUM, only with altix/gnu/ibmaix. W replace QUANTUM with MNDO97, only with altix/gnu/ibmaix/sgi. QS replace QUANTUM with QMMMSEMI (AMBER Semi-empirical QMMM). G09 replace QUANTUM with Gaussian09. APBS compile with APBS support. FFTW compile with FFTW support (only effective with COLFFT keyword). MKL compile with MKL support (only effective with COLFFT keyword). OPENMM add support for OpenMM (see chmdoc/openmm.doc) PIPF add support for Polarizable Intermolecular Potential Function POLYR add support for POLYRATE interface GAMUS add support for GAMUS (requires LAPACK installation) S Uses TCP/IP SOCKET library for parallel. FULL For FULL featured version (default). LITE For a version with reduced functional features. IFORT Uses Intel Fortran ifort/Linux for gnu (default is gfortran). G95 Uses g95/Linux for gnu (default is gfortran). PGF95 Uses PGI pgf95/Linux for gnu (default is gfortran). PS Uses PathScale Linux compiler for gnu (default is gfortran). NIH Uses extra keywords for NIH. TSRI Uses extra keywords for TSRI. MPIF90 Relies entirely on mpif90 wrapper for MPI compiling/linking. NERSC Relies entirely on ftn wrapper for NERSC compiling/linking. MPICH adds special library options for standard MPICH. SCALI adds special library options for standard SCALI MPI Connect. MPISPECIAL prompts for special MPI library options for load. GA Use GA tools version of GAMESS-UK D link dynamically (ifc/ifort) MODPREF add/remove keywords from pref.dat (w/ addtl. parameter) e.g. +CGENFF to add, -MMFF to remove keepf Will keep the preprocessed .f90 files in build/mach. DEBUG/debug Compile with debugging options to compiler (FCD) big_e/lit_e Use big/little_endian binary I/O if supported by compiler The switch '2' can be used to stop installation and modify the pref.dat file to further customize CHARMM features. When install switches other than the machine type are changed for subsequent builds with different features, it is very important to first delete any existing build/machine-type and lib/machine-type subdirectories. Simple Examples: ./install.com gnu 1. installs the preprocessor PREFX in ~/cnnXm/tool (prefx_gnu), 2. generates the proper ~/cnnXm/build/gnu/pref.dat file (PREFX data file) with the FULL feature set, 3. generates makefile suitable for computers running under Linux (~/cnnXm/build/gnu/Makefile), 4. processes FORTRAN and C source files, compiles and builds module libraries in ~/cnnXm/lib/gnu, and 5. links them to produce the executable ~/cnnXm/exec/gnu/charmm. ./install.com em64t M 1. As above, but using ifort compiler 2. The M option adds parallel support via an MPI implementation 3. Creates lib/em64t_M, build/em64t_M, etc. 4. See the MPI information in Additional Notes (below) Note that it is assumed the PATH variable has been set to point to the locations of the compiler and optional MPI wrapper, and that these are properly installed and working on your systems. Adding features: ./install.com gnu M +CORSOL 1. As above, but adds the CORSOL feature (chmdoc/corsol.doc) ./install.com gnu M +ENSEMBLE 1. Adds ENSEMBLE replica exchange code (chmdoc/ensemble.doc) ./install.com gnu M +REPDSTR +GENCOMM +ASYNC_PME ./install.com em64t M +REPDSTR +GENCOMM +ASYNC_PME +CMPI 1. Adds REPDSTR replica exchange code (chmdoc/repdstr.doc) 2. Not compatible with ENSEMBLE; they are mutually exclusive 3. By default, gnu includes the CMPI feature, em64t does not Additional Notes: For MPI usage, the distribution of choice (OpenMPI, MPICH, MPICH2, etc.) **MUST** have the mpi.mod file created from mpi.f90 using the same compiler release version that will be used to compile CHARMM. In some cases, it may also be useful to set the environment variables MPI_HOME or else MPI_INCLUDE and MPI_LIB To speed compilation, one can use multiple threads with make via export MAKE_COMMAND="make -j4" # bash setenv MAKE_COMMAND "make -j4" # tcsh The command tool/NewCharmmTree creates a subdir with links to source, etc., allowing for compile variations w/o having to copy the entire distribution.
Top CHARMM Documentation The CHARMM documentation set is being updated and improved. The up-to-the-date documentation set is included in the current release. The documentation is an integral part of CHARMM. The INFO format files can be converted to static HTML files via support/htmldoc, or the doc2html package available in the Script Archive forum at www.charmm.org The files can also be made accessible through the info program or GNU emacs. If either is available on your system, you may incorporate the documentation into the info-tree structure. The following is the info-building procedure. (1) Locate the info directory. On tammy.harvard.edu, it is /usr/lib/gemacs/info. It may differ on your machine. (2) Find the file, dir, in the info directory. You should have a write access of the directory. If the info directory is protected, contact your system manager and let him do the job. Edit the dir file and insert the following one line under "* Menu". CHARMM / CHARMM Documentation It should appear exactly as shown; asterisk (*) in the first column, etc. The the part of dir file may look like this. File: dir Node: Top This is the top of the INFO tree Quick Key Reference d return here q exit ? list INFO commands h help mCHARMM<return> go into CHARMM documentation 1 go into CHARMM documentation (works for 1..5) u go up =========================================================================== CHARMM / CHARMM Documentation * Emacs: (emacs). Yours truly * Info: (info). This documentation browsing system. (3) Save the file and exit the editor. You now have to link the CHARMM documentation directory as in the following. ln -s ~/cnnXm/doc chmdoc Remember that ~/ is the parent directory that holds the charmm directory.
Top CHARMM Topology and Parameter Files The current distribution has topology files: top_all22_prot.rtf top_all35_ethers.rtf top_all36_carb.rtf top_all36_cgenff.rtf top_all36_lipid.rtf top_all36_na.rtf top_all36_prot.rtf and matching parameter files: par_all22_prot.prm par_all35_ethers.prm par_all36_carb.prm par_all36_cgenff.prm par_all36_lipid.prm par_all36_na.prm par_all36_prot.prm These are now all in FLEX format, and have been modularized such that there are no conflicts of chemical type names or integer code numbers used in the MASS statements. As a consequence, there is no longer any need for pre-combined files such as the previous "prot_na" or "prot_lipid" files. Water and ion residues and parameters are now in toppar_water_ions.str which should be read via STREAM after the other RTF and PARAM files. The toppar/stream subdir has many additional molecules, along with many of the model compounds used in the parameter development. There are number of other special purpose subdirs, such as gbsw, drude, and non_charmm. However, new developments and updates, along with a wealth of other material concerning CHARMM parameter sets can be found at URL http://mackerell.umaryland.edu/MacKerell_Lab.html The extended (united) atom parameters for proteins are the same as those included with CHARMM20, which are based on Wally Reiher's thesis. For the extended atom nucleic acid parameters, those of Nilsson and Karplus, J. Comp. Chem. 7:591-616, 1986 are used. These were also included in the CHARMM20 release and are the only set to include explicit hydrogen bonding terms. Some alterations of the extended atom nucleic acid topology and parameter files have been made in order to maintain compatibility with the multiple dihedral scheme in CHARMM22. Comments, questions, and problems related to the distributed topology and parameter files should be posted in the Parameter Set forum at www.charmm.org
Top CHARMM User Support Users are encouraged to register for the CHARMM forums hosted at www.charmm.org, an active web based bulletin board with specific forums for usage, and for questions and problems involving installation and testing. The forms, problem.form and bugfix.form in the support/form directory may be useful in reporting problems and bugfixes. If you have questions/comments/suggestions about CHARMM management, send your remark to chmgr@tammy.harvard.edu.