Package gromacs: Specfile
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 | %define fftw_major_ver 3 %define fftw_ver %fftw_major_ver.0.1 %define mpi_impl openmpi %define mpidir %_libdir/%mpi_impl %def_disable static Name: gromacs Version: 4.0.7 Release: alt8 Summary: Molecular dynamics package License: GPL Group: Sciences/Chemistry Url: http://www.gromacs.org Source: ftp://ftp.gromacs.org/pub/gromacs/%name-%version.tar.gz Patch: gromacs-4.0.3-alt-LIBS-LDADD.patch Packager: Michael Shigorin <mike@altlinux.org> Requires: %name-common = %version-%release %set_libtool_version 1.5 # Automatically added by buildreq on Thu Mar 24 2011 # optimized out: gcc-c++ gcc-fortran glibc-pthread libICE-devel libatlas-devel libgfortran-devel libstdc++-devel mpi-selector openmpi xorg-xproto-devel BuildRequires: imake libSM-devel libX11-devel libfftw3-devel libgsl-devel liblapack-devel openmpi-devel xorg-cf-files BuildRequires: libfftw%fftw_major_ver-devel >= %fftw_ver BuildRequires: gcc-fortran %mpi_impl-devel chrpath BuildRequires: libX11-devel libgsl-devel BuildRequires: liblapack-devel BuildRequires: libopenmotif-devel %description GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package provides single and double precision binaries. The documentation is in the package gromacs-common. N.B. All binaries have names starting with g_, for example mdrun has been renamed to g_mdrun. %package libs Summary: GROMACS libraries Group: Sciences/Chemistry Requires: gromacs-common = %version-%release %description libs GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package provides runtime libraries needed for the single and double precision binaries. %package mpi Summary: GROMACS MPI binaries Group: Sciences/Chemistry Requires: gromacs-common = %version-%release %description mpi GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package provides MPI single precision and double precision binaries. %package common Summary: GROMACS shared data and man pages Group: Sciences/Chemistry BuildArch: noarch %description common GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package includes architecture independent data and man pages. %package devel Summary: GROMACS header files and development libraries Group: Sciences/Chemistry Requires: gromacs-common = %version-%release Requires: gromacs-libs = %version-%release %description devel GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package contains header files, development libraries, and a program example for the GROMACS molecular dynamics software. You need it if you want to write your own analysis programs. %package mpi-devel Summary: GROMACS MPI development libraries Group: Sciences/Chemistry Requires: gromacs-mpi-libs = %version-%release Requires: gromacs-devel = %version-%release %description mpi-devel GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package contains development libraries for GROMACS MPI. You need it if you want to write your own analysis programs. %package mpi-libs Summary: GROMACS libraries Group: Sciences/Chemistry Requires: gromacs-common = %version-%release %description mpi-libs GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package provides runtime libraries needed for the MPI single and double precision binaries. %package shell-extensions Summary: GROMACS shell extensions Group: Sciences/Chemistry Obsoletes: %name-bash Obsoletes: %name-zsh Obsoletes: %name-csh %description shell-extensions GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package provides the needed shell extensions for GROMACS %package tutor Summary: GROMACS tutorial files Group: Sciences/Chemistry BuildArch: noarch %description tutor GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package provides tutorials for the use of GROMACS. %package doc Summary: Documentation for GROMACS Group: Development/Documentation BuildArch: noarch %description doc This package contains documentation for GROMACS. %prep %setup %patch -p0 %ifarch x86_64 sed -i 's|lib/openmpi|lib64/openmpi|' configure.ac %endif sed -i 's|^\(AM_CPPFLAGS.*\)|\1 -g|' $(find ./ -name Makefile.am) %build # Set MPI environment mpi-selector --set `mpi-selector --list | grep %mpi_impl` source %_sysconfdir/profile.d/mpi-selector.sh export OMPI_LDFLAGS="-Wl,--as-needed,-rpath,%mpidir/lib -L%mpidir/lib" sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=|g' acinclude.m4 %autoreconf # params: # $1 - float/double precision # $2 - enable/disable MPI # $3 - program suffix function buildThis() { ln -s ../configure . %configure \ --disable-rpath \ --enable-static=no \ --enable-shared \ --enable-$1 \ --enable-mpi \ --enable-prefetch-forces \ --enable-fortran \ --with-gnu-ld \ --with-fft=fftw%fftw_major_ver \ --with-x \ --with-gsl \ --$2-mpi \ --program-suffix=$3 \ --with-external-blas=-lopenblas sed -i 's|^hardcode_libdir_flag_spec=.*|hardcode_libdir_flag_spec=""|g' \ libtool sed -i 's|^runpath_var=LD_RUN_PATH|runpath_var=DIE_RPATH_DIE|g' libtool %make_build } # Single precision mkdir single pushd single buildThis float disable popd # Double precision mkdir double pushd double buildThis double disable _d popd # MPI, single precision mkdir mpi-single pushd mpi-single buildThis float enable _mpi popd # MPI, double precision mkdir mpi-double pushd mpi-double buildThis double enable _mpi_d popd %install export OMPI_LDFLAGS="-Wl,--as-needed,-rpath,%mpidir/lib -L%mpidir/lib" # Single precision pushd single %makeinstall_std popd # Double precision pushd double %makeinstall_std popd # MPI, single precision pushd mpi-single %makeinstall_std popd # MPI, double precision pushd mpi-double %makeinstall_std popd # Rename binaries and man pages to prevent clashes # (This is done here so that we don't need to mess with machine generated makefiles. for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr \ gmxcheck gmxdump grompp highway luck make_edi make_ndx mdrun mk_angndx ngmx \ pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps \ xrama do mv %buildroot%_bindir/$bin %buildroot%_bindir/g_$bin mv %buildroot%_bindir/${bin}_d %buildroot%_bindir/g_${bin}_d done for bin in demux.pl xplor2gmx.pl; do mv %buildroot%_bindir/$bin %buildroot%_bindir/g_$bin done # MPI-enabled binaries (list will continue when the makefile has # the possibility to compile all mpi-enabled files for mpibin in mdrun; do mv %buildroot%_bindir/${mpibin}_mpi %buildroot%_bindir/g_${mpibin}_mpi mv %buildroot%_bindir/${mpibin}_mpi_d %buildroot%_bindir/g_${mpibin}_mpi_d done # Man pages for bin in anadock do_dssp editconf eneconv genbox genconf genion genrestr \ gmxcheck gmxdump grompp highway make_edi make_ndx mdrun mk_angndx ngmx \ pdb2gmx protonate sigeps tpbconv trjcat trjconv trjorder wheel x2top xpm2ps \ xrama do mv %buildroot%_man1dir/$bin.1 %buildroot%_man1dir/g_$bin.1 mv %buildroot%_man1dir/${bin}_d.1 %buildroot%_man1dir/g_${bin}_d.1 done # Move completion files around chmod a-x %buildroot%_bindir/completion.* # Zsh mkdir -p %buildroot%_datadir/zsh/site-functions mv %buildroot%_bindir/completion.zsh \ %buildroot%_datadir/zsh/site-functions/gromacs # Bash mkdir -p %buildroot%_sysconfdir/bash_completion.d mv %buildroot%_bindir/completion.bash %buildroot%_sysconfdir/bash_completion.d/gromacs # Tcsh mv %buildroot%_bindir/completion.csh . # Remove .la files rm -rf %buildroot/%_libdir/*.la mv mpi-single/src/mdlib/.libs/libmd_mpi.so* %buildroot%_libdir/ mv mpi-double/src/mdlib/.libs/libmd_mpi_d.so* %buildroot%_libdir/ for i in %buildroot%_bindir/* %buildroot%_libdir/*.so.* do chrpath -r %mpidir/lib $i ||: done %files %_bindir/* %exclude %_bindir/g_mdrun_mpi %exclude %_bindir/g_mdrun_mpi_d %exclude %_bindir/GMXRC.csh %exclude %_bindir/GMXRC.zsh %files libs %_libdir/libgmx.so.* %_libdir/libgmx_d.so.* %_libdir/libgmxana.so.* %_libdir/libgmxana_d.so.* %_libdir/libmd.so.* %_libdir/libmd_d.so.* %files mpi %_bindir/g_mdrun_mpi %_bindir/g_mdrun_mpi_d %files mpi-libs %_libdir/libgmx_mpi.so.* %_libdir/libgmx_mpi_d.so.* %_libdir/libgmxana_mpi.so.* %_libdir/libgmxana_mpi_d.so.* %_libdir/libmd_mpi.so.* %_libdir/libmd_mpi_d.so.* %files common %doc AUTHORS COPYING README #_bindir/GMXRC #_bindir/GMXRC.bash %_man1dir/* %_datadir/%name %exclude %_datadir/%name/template %exclude %_datadir/%name/tutor %exclude %_datadir/%name/html %files devel %_includedir/%name %_libdir/libgmx.so %_libdir/libgmx_d.so %_libdir/libgmxana.so %_libdir/libgmxana_d.so %_libdir/libmd.so %_libdir/libmd_d.so %_datadir/%name/template %files mpi-devel %_libdir/libgmx_mpi.so %_libdir/libgmx_mpi_d.so %_libdir/libgmxana_mpi.so %_libdir/libgmxana_mpi_d.so %_libdir/libmd_mpi.so %_libdir/libmd_mpi_d.so %files shell-extensions %_datadir/zsh/site-functions/gromacs %_bindir/GMXRC.zsh %config(noreplace) %_sysconfdir/bash_completion.d/gromacs %doc completion.csh %_bindir/GMXRC.csh %files tutor %_datadir/%name/tutor %files doc %_datadir/%name/html %changelog * Sat Aug 11 2012 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.7-alt8 - Built with OpenBLAS instead of GotoBLAS2 * Thu Jul 05 2012 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.7-alt7 - Rebuilt with OpenMPI 1.6 * Sat Feb 04 2012 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.7-alt6 - Fixed RPATH * Sun Apr 17 2011 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.7-alt5 - Built with GotoBLAS2 instead of ATLAS * Thu Mar 24 2011 Michael Shigorin <mike@altlinux.org> 4.0.7-alt4 - merged fixups by led@: + dropped superfluous BR + enabled parallel build - re-adopting the package - buildreq -u - spec cleanup * Fri Mar 18 2011 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.7-alt3 - Rebuilt for debuginfo - Enabled optimization (-O2) * Thu Oct 14 2010 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.7-alt2 - Fixed overlinking of libraries * Wed Jun 30 2010 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.7-alt1 - Version 4.0.7 * Mon May 25 2009 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.5-alt1 - Version 4.0.5 * Wed Apr 29 2009 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.4-alt1 - Version 4.0.4 * Fri Mar 06 2009 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.3-alt3 - enable GSL extensions * Tue Feb 10 2009 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.3-alt2 - disable GSL extensions - merge shell extensions into one package * Thu Jan 29 2009 Eugeny A. Rostovtsev (REAL) <real at altlinux.org> 4.0.3-alt1 - 4.0.3 * Thu Jan 04 2007 Michael Shigorin <mike@altlinux.org> 3.3.1-alt1 - built for ALT Linux (based on Mandriva contrib spec by Lenny Cartier <lenny/mandriva.com> and original one by Erik Lindahl <lindahl/gromacs.org>) - disable GUI build by default * Tue Apr 11 2006 Lenny Cartier <lenny@mandriva.com> 3.3.1-1mdk - 3.3.1 * Mon Nov 07 2005 Nicolas L\xe9cureuil <neoclust@mandriva.org> 3.3-2mdk - Fix BuildRequires * Thu Oct 20 2005 Lenny Cartier <lenny@mandriva.com> 3.3-1mdk - 3.3 * Fri Jun 04 2004 Lenny Cartier <lenny@mandrakesoft.com> 3.2.1-1mdk - 3.2.1 * Wed Apr 30 2003 Lenny Cartier <lenny@mandrakesoft.com> 3.1.4-3mdk - buildrequires * Sun Feb 02 2003 Lenny Cartier <lenny@mandrakesoft.com> 3.1.4-2mdk - rebuild * Tue Dec 05 2002 Lenny Cartier <lenny@mandrakesoft.com> 3.1.4-1mdk - from Austin Acton <aacton@yorkul.ca> : - initial package for Mandrake 9.0+ |