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Bump all packages that use perl, or depend on a p5-* package, or are called p5-*. I hope that's all of them.
2012-10-03 23:53:53 +02:00
# $NetBSD: Makefile,v 1.11 2012/10/03 21:53:59 wiz Exp $
Import GROMACS 4.0.7 as biology/gromacs. From pkgsrc-wip, packaged originally by Peter Ibsen Hansen. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
2010-03-15 15:08:49 +01:00
#
Update to Gromacs 4.5.5 Notable changes in Gromacs 4.5.5: * Improved pdb2gmx -chainsep option and reintroduced the -merge option. * Fixed mdrun file appending truncating files to 0 bytes when continuation runs stopped before writing new output. * Fixed COM pulling with multiple constraints checking the convergence of one constraint instead of all. * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms. * AmberGS force field is now based on Amber94 instead of Amber96. * Moved hydrogens in Charmm27 protein termini to separate charge groups and added ACE and CT3 residue types. * Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. * Many small updates to the manual pages of programs.
2012-01-14 01:38:18 +01:00
DISTNAME= gromacs-4.5.5
Bump all packages that use perl, or depend on a p5-* package, or are called p5-*. I hope that's all of them.
2012-10-03 23:53:53 +02:00
PKGREVISION= 2
Import GROMACS 4.0.7 as biology/gromacs. From pkgsrc-wip, packaged originally by Peter Ibsen Hansen. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
2010-03-15 15:08:49 +01:00
CATEGORIES= biology
MASTER_SITES= ftp://ftp.gromacs.org/pub/gromacs/
MAINTAINER= pkgsrc-users@NetBSD.org
HOMEPAGE= http://www.gromacs.org/
COMMENT= Molecular dynamics package
LICENSE= gnu-gpl-v2
# Official recommendation is not to use the gcc 4.1.x set of compilers.
GNU_CONFIGURE= yes
USE_LIBTOOL= yes
USE_PKGLOCALEDIR= yes
Update to GROMACS 4.5.1 GROMACS 4.5.1 is bug fix release. Release notes for 4.5 New features * Pencil decomposition of the reciprocal space PME grid to improve scaling. This reduces the amount of communication for high parallelization and improves load balancing with up to 40% overall performance improvement for large systems. * Memory usage is improved for very large systems, allowing simulations of >100 million atoms. * Running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build. MPI is now only required for parallelization over the network. * Domain decomposition can now also be used without periodic boundary conditions * GPU acceleration support on NVIDIA cards. This first release with GPU support based on OpenMM provides up to an order of magnitude faster performance for implicit solvent simulations, but PME simulations are about as fast as on a high-end CPU. * Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default. * Increased tolerance for networked file system failures and cluster node crashes: checkpoint handling is safer and mdrun forces file system cache flushes during checkpoints. * Full CMake support. After the 4.5 release we will be switching the default build tool from autoconf to cmake, and possibly deprecate autoconf in the future. * Full support for seven AMBER force fields in the standard distribution, with default Amber names. We also include the recent Amber99sb-ildn in the distribution. * Support for CHARMM27, including cmap for dihedrals * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines in both single and double precision. * Highly efficient all-vs-all assembly kernels for both vanilla and generalized born interactions, in both single and double precision. * Much better support for nucleic acid simulations, including automatic handling by pdb2gmx. * Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains. * Symplectic Trotter Leap-Frog integrator for twin-range non-bonded interactions. * Support for Bennet acceptance ratio calculations through direct calculation of Hamiltonian differences during the simulation. * File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD libraries are required). * pdb2gmx now retains the residue numbers from the input, mdrun and all tools use these original numbers. New tools * g_bar: Bennett acceptance ratio (BAR) free energy calculations, including automatic error estimates and phase space overlap measures. * g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table * g_select: Library support for "dynamic index groups" based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. * g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. * g_membed: a very convenient utility for rapidly embedding membrane proteins into equilibrated lipid bilayers * g_pme_error: estimates the error of the electrostatic forces if using the SPME algorithm. TO be incorporated in g_tune_pme Changes that might affect your results * grompp by default sets the new nstcalcenergy parameter equal to nstlist, this has no effect on the integration, only on the energy averages stored in ener.edr * grompp by default sets the new nsttcouple parameter equal to nstlist, this means T-coupling is done less frequently; grompp checks if tau_t is large enough * grompp by default sets the new nstpcouple parameter equal to nstlist, this means P-coupling is done less frequently; grompp checks if tau_p is large enough * mdrun results with old tpr files with twin-range non-bonded interactions will be different, because of the new symplectic integrator * for free-energy calculations sc-sigma now also sets the minimum soft-core sigma (old tpr files retain the old behavior, which can be enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)
2010-09-03 22:52:39 +02:00
USE_TOOLS+= pkg-config
Import GROMACS 4.0.7 as biology/gromacs. From pkgsrc-wip, packaged originally by Peter Ibsen Hansen. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
2010-03-15 15:08:49 +01:00
CONFIGURE_ARGS+= --enable-shared
CONFIGURE_ARGS+= --enable-double --program-suffix=
CONFIGURE_ARGS+= --with-gsl
Update to GROMACS 4.5.1 GROMACS 4.5.1 is bug fix release. Release notes for 4.5 New features * Pencil decomposition of the reciprocal space PME grid to improve scaling. This reduces the amount of communication for high parallelization and improves load balancing with up to 40% overall performance improvement for large systems. * Memory usage is improved for very large systems, allowing simulations of >100 million atoms. * Running on a multi-core node now uses thread-based parallelization to automatically spawn the optimum number of threads in the default build. MPI is now only required for parallelization over the network. * Domain decomposition can now also be used without periodic boundary conditions * GPU acceleration support on NVIDIA cards. This first release with GPU support based on OpenMM provides up to an order of magnitude faster performance for implicit solvent simulations, but PME simulations are about as fast as on a high-end CPU. * Check-pointing is made more secure:MD5sum are used to verify that all files are correctly in-place before a simulation is appended. Output file appending at continuation is turned on by default. * Increased tolerance for networked file system failures and cluster node crashes: checkpoint handling is safer and mdrun forces file system cache flushes during checkpoints. * Full CMake support. After the 4.5 release we will be switching the default build tool from autoconf to cmake, and possibly deprecate autoconf in the future. * Full support for seven AMBER force fields in the standard distribution, with default Amber names. We also include the recent Amber99sb-ildn in the distribution. * Support for CHARMM27, including cmap for dihedrals * Efficient Generalized-Born implicit solvent support including the Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating the generalized Born-interaction formula for greater speed, and optimized SSE-routines in both single and double precision. * Highly efficient all-vs-all assembly kernels for both vanilla and generalized born interactions, in both single and double precision. * Much better support for nucleic acid simulations, including automatic handling by pdb2gmx. * Support for Velocity-Verlet integrators for reversible T- and P-coupling; MTTK pressure control integrators; Nose-Hoover chains. * Symplectic Trotter Leap-Frog integrator for twin-range non-bonded interactions. * Support for Bennet acceptance ratio calculations through direct calculation of Hamiltonian differences during the simulation. * File formats: All GROMACS tools can now read any VMD supported trajectory format, without converting trajectory first. (VMD libraries are required). * pdb2gmx now retains the residue numbers from the input, mdrun and all tools use these original numbers. New tools * g_bar: Bennett acceptance ratio (BAR) free energy calculations, including automatic error estimates and phase space overlap measures. * g_rdf was a little bit enhanced that structure factors can be calculated for any system, by supplying the necessary data via sfactor.dat. Most of the common atomtypes are already contained, but everybody who needs more freedom can enhance the table * g_select: Library support for "dynamic index groups" based on textual selections (experimental feature). See the tool g_select, the included template.c, or Doxygen documentation for information on how to write analysis tools using the library. Existing tools have not (yet) been converted. * g_tune_pme: For a given number of processes or threads this tool systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It also checks whether performance can be enhanced by shifting load between the real and the reciprocal space part of the Ewald sum. * g_membed: a very convenient utility for rapidly embedding membrane proteins into equilibrated lipid bilayers * g_pme_error: estimates the error of the electrostatic forces if using the SPME algorithm. TO be incorporated in g_tune_pme Changes that might affect your results * grompp by default sets the new nstcalcenergy parameter equal to nstlist, this has no effect on the integration, only on the energy averages stored in ener.edr * grompp by default sets the new nsttcouple parameter equal to nstlist, this means T-coupling is done less frequently; grompp checks if tau_t is large enough * grompp by default sets the new nstpcouple parameter equal to nstlist, this means P-coupling is done less frequently; grompp checks if tau_p is large enough * mdrun results with old tpr files with twin-range non-bonded interactions will be different, because of the new symplectic integrator * for free-energy calculations sc-sigma now also sets the minimum soft-core sigma (old tpr files retain the old behavior, which can be enforced by setting the env.var. GMX_SCSIGMA_MIN to 0)
2010-09-03 22:52:39 +02:00
CONFIGURE_ARGS+= --disable-gcc41-check
Import GROMACS 4.0.7 as biology/gromacs. From pkgsrc-wip, packaged originally by Peter Ibsen Hansen. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
2010-03-15 15:08:49 +01:00
.include "options.mk"
USE_TOOLS+= perl:run
REPLACE_PERL= scripts/demux.pl scripts/xplor2gmx.pl
Update to Gromacs 4.5.5 Notable changes in Gromacs 4.5.5: * Improved pdb2gmx -chainsep option and reintroduced the -merge option. * Fixed mdrun file appending truncating files to 0 bytes when continuation runs stopped before writing new output. * Fixed COM pulling with multiple constraints checking the convergence of one constraint instead of all. * Fixed some dihedrals in sugars in Gromos53a5/6 working on the wrong atoms. * AmberGS force field is now based on Amber94 instead of Amber96. * Moved hydrogens in Charmm27 protein termini to separate charge groups and added ACE and CT3 residue types. * Many small fixes which avoid termination with fatal errors or crashes in mdrun and tools. * Many small updates to the manual pages of programs.
2012-01-14 01:38:18 +01:00
.include "../../mk/bsd.prefs.mk"
.if $(MACHINE_ARCH) == "i386"
CFLAGS+= -msse -msse2
.endif
Import GROMACS 4.0.7 as biology/gromacs. From pkgsrc-wip, packaged originally by Peter Ibsen Hansen. GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
2010-03-15 15:08:49 +01:00
.include "../../math/fftw/buildlink3.mk"
.include "../../math/gsl/buildlink3.mk" # optional
.include "../../textproc/libxml2/buildlink3.mk" # optional
.include "../../mk/bsd.pkg.mk"
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