Beispiel #1
0
    def configure_step(self):
        """Configure build:
        - set required environment variables (for netCDF, JasPer)
        - patch compile script and ungrib Makefile for non-default install paths of WRF and JasPer
        - run configure script and figure how to select desired build option
        - patch configure.wps file afterwards to fix 'serial compiler' setting
        """

        # netCDF dependency check + setting env vars (NETCDF, NETCDFF)
        set_netcdf_env_vars(self.log)
        self.netcdf_mod_cmds = get_netcdf_module_set_cmds(self.log)

        # WRF dependency check
        wrf = get_software_root('WRF')
        if wrf:
            majver = get_software_version('WRF').split('.')[0]
            self.wrfdir = os.path.join(wrf, "WRFV%s" % majver)
        else:
            self.log.error("WRF module not loaded?")

        # patch compile script so that WRF is found
        self.compile_script = "compile"
        try:
            for line in fileinput.input(self.compile_script, inplace=1, backup='.orig.wrf'):
                line = re.sub(r"^(\s*set\s*WRF_DIR_PRE\s*=\s*)\${DEV_TOP}(.*)$", r"\1%s\2" % self.wrfdir, line)
                sys.stdout.write(line)
        except IOError, err:
            self.log.error("Failed to patch %s script: %s" % (self.compile_script, err))
Beispiel #2
0
    def configure_step(self):
        """Configure build:
            - set some magic environment variables
            - run configure script
            - adjust configure.wrf file if needed
        """

        wrfdir = os.path.join(self.builddir, self.wrfsubdir)

        # define $NETCDF* for netCDF dependency (used when creating WRF module file)
        set_netcdf_env_vars(self.log)

        # HDF5 (optional) dependency
        hdf5 = get_software_root('HDF5')
        if hdf5:
            env.setvar('HDF5', hdf5)
            # check if this is parallel HDF5
            phdf5_bins = ['h5pcc', 'ph5diff']
            parallel_hdf5 = True
            for f in phdf5_bins:
                if not os.path.exists(os.path.join(hdf5, 'bin', f)):
                    parallel_hdf5 = False
                    break
            if parallel_hdf5:
                env.setvar('PHDF5', hdf5)
            else:
                self.log.info(
                    "Parallel HDF5 module not loaded, assuming that's OK...")
        else:
            self.log.info("HDF5 module not loaded, assuming that's OK...")

        # Parallel netCDF (optional) dependency
        pnetcdf = get_software_root('PnetCDF')
        if pnetcdf:
            env.setvar('PNETCDF', pnetcdf)

        # JasPer dependency check + setting env vars
        jasper = get_software_root('JasPer')
        if jasper:
            jasperlibdir = os.path.join(jasper, "lib")
            env.setvar('JASPERINC', os.path.join(jasper, "include"))
            env.setvar('JASPERLIB', jasperlibdir)

        else:
            if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
                raise EasyBuildError(
                    "JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?"
                )
            else:
                self.log.info(
                    "JasPer module not loaded, assuming that's OK...")

        # enable support for large file support in netCDF
        env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')

        # patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
        if LooseVersion(self.version) < LooseVersion('4.0'):
            patch_perl_script_autoflush(
                os.path.join(wrfdir, "arch", "Config_new.pl"))

        # determine build type option to look for
        build_type_option = None
        self.comp_fam = self.toolchain.comp_family()
        if self.comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
            if LooseVersion(self.version) >= LooseVersion('3.7'):
                build_type_option = "INTEL\ \(ifort\/icc\)"
            else:
                build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"

        elif self.comp_fam == toolchain.GCC:  # @UndefinedVariable
            if LooseVersion(self.version) >= LooseVersion('3.7'):
                build_type_option = "GNU\ \(gfortran\/gcc\)"
            else:
                build_type_option = "x86_64 Linux, gfortran compiler with gcc"

        else:
            raise EasyBuildError(
                "Don't know how to figure out build type to select.")

        # fetch selected build type (and make sure it makes sense)
        known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
        self.parallel_build_types = ["dmpar", "dm+sm"]
        bt = self.cfg['buildtype']

        if bt not in known_build_types:
            raise EasyBuildError(
                "Unknown build type: '%s'. Supported build types: %s", bt,
                known_build_types)

        # Escape the "+" in "dm+sm" since it's being used in a regexp below.
        bt = bt.replace('+', r'\+')

        # fetch option number based on build type option and selected build type
        if LooseVersion(self.version) >= LooseVersion('3.7'):
            # the two relevant lines in the configure output for WRF 3.8 are:
            #  13. (serial)  14. (smpar)  15. (dmpar)  16. (dm+sm)   INTEL (ifort/icc)
            #  32. (serial)  33. (smpar)  34. (dmpar)  35. (dm+sm)   GNU (gfortran/gcc)
            build_type_question = "\s*(?P<nr>[0-9]+)\.\ \(%s\).*%s" % (
                bt, build_type_option)
        else:
            # the relevant lines in the configure output for WRF 3.6 are:
            #  13.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (serial)
            #  14.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (smpar)
            #  15.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (dmpar)
            #  16.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (dm+sm)
            #  32.  x86_64 Linux, gfortran compiler with gcc   (serial)
            #  33.  x86_64 Linux, gfortran compiler with gcc   (smpar)
            #  34.  x86_64 Linux, gfortran compiler with gcc   (dmpar)
            #  35.  x86_64 Linux, gfortran compiler with gcc   (dm+sm)
            build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (
                build_type_option, bt)

        # run configure script
        cmd = "./configure"
        qa = {
            # named group in match will be used to construct answer
            "Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:":
            "1",
            "Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:":
            "0"
        }
        no_qa = [
            "testing for fseeko and fseeko64",
            r"If you wish to change the default options, edit the file:[\s\n]*arch/configure_new.defaults"
        ]
        std_qa = {
            # named group in match will be used to construct answer
            r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
            "%(nr)s",
        }

        run_cmd_qa(cmd,
                   qa,
                   no_qa=no_qa,
                   std_qa=std_qa,
                   log_all=True,
                   simple=True)

        cfgfile = 'configure.wrf'

        # make sure correct compilers are being used
        comps = {
            'SCC': os.getenv('CC'),
            'SFC': os.getenv('F90'),
            'CCOMP': os.getenv('CC'),
            'DM_FC': os.getenv('MPIF90'),
            'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
        }
        regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v)
                      for (k, v) in comps.items()]
        apply_regex_substitutions(cfgfile, regex_subs)

        # rewrite optimization options if desired
        if self.cfg['rewriteopts']:

            # replace default -O3 option in configure.wrf with CFLAGS/FFLAGS from environment
            self.log.info("Rewriting optimization options in %s" % cfgfile)

            # set extra flags for Intel compilers
            # see http://software.intel.com/en-us/forums/showthread.php?t=72109&p=1#146748
            if self.comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable

                # -O3 -heap-arrays is required to resolve compilation error
                for envvar in ['CFLAGS', 'FFLAGS']:
                    val = os.getenv(envvar)
                    if '-O3' in val:
                        env.setvar(envvar, '%s -heap-arrays' % val)
                        self.log.info("Updated %s to '%s'" %
                                      (envvar, os.getenv(envvar)))

            # replace -O3 with desired optimization options
            regex_subs = [
                (r"^(FCOPTIM.*)(\s-O3)(\s.*)$",
                 r"\1 %s \3" % os.getenv('FFLAGS')),
                (r"^(CFLAGS_LOCAL.*)(\s-O3)(\s.*)$",
                 r"\1 %s \3" % os.getenv('CFLAGS')),
            ]
            apply_regex_substitutions(cfgfile, regex_subs)
Beispiel #3
0
    def configure_step(self):
        """Configure build:
            - set some magic environment variables
            - run configure script
            - adjust configure.wrf file if needed
        """
        # define $NETCDF* for netCDF dependency (used when creating WRF module file)
        set_netcdf_env_vars(self.log)

        # HDF5 (optional) dependency
        hdf5 = get_software_root('HDF5')
        if hdf5:
            # check if this is parallel HDF5
            phdf5_bins = ['h5pcc', 'ph5diff']
            parallel_hdf5 = True
            for f in phdf5_bins:
                if not os.path.exists(os.path.join(hdf5, 'bin', f)):
                    parallel_hdf5 = False
                    break
            if not (hdf5 or parallel_hdf5):
                raise EasyBuildError("Parallel HDF5 module not loaded?")
            else:
                env.setvar('PHDF5', hdf5)
        else:
            self.log.info("HDF5 module not loaded, assuming that's OK...")

        # JasPer dependency check + setting env vars
        jasper = get_software_root('JasPer')
        if jasper:
            jasperlibdir = os.path.join(jasper, "lib")
            env.setvar('JASPERINC', os.path.join(jasper, "include"))
            env.setvar('JASPERLIB', jasperlibdir)

        else:
            if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
                raise EasyBuildError("JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?")
            else:
                self.log.info("JasPer module not loaded, assuming that's OK...")

        # enable support for large file support in netCDF
        env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')

        # patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
        patch_perl_script_autoflush(os.path.join("arch", "Config_new.pl"))

        # determine build type option to look for
        build_type_option = None
        self.comp_fam = self.toolchain.comp_family()
        if self.comp_fam == toolchain.INTELCOMP:  #@UndefinedVariable
            if LooseVersion(self.version) >= LooseVersion('3.7'):
                build_type_option = "INTEL\ \(ifort\/icc\)"
            else:
                build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"

        elif self.comp_fam == toolchain.GCC:  #@UndefinedVariable
            if LooseVersion(self.version) >= LooseVersion('3.7'):
                build_type_option = "GNU\ \(gfortran\/gcc\)"
            else:
                build_type_option = "x86_64 Linux, gfortran compiler with gcc"

        else:
            raise EasyBuildError("Don't know how to figure out build type to select.")

        # fetch selected build type (and make sure it makes sense)
        known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
        self.parallel_build_types = ["dmpar", "smpar", "dm+sm"]
        bt = self.cfg['buildtype']

        if not bt in known_build_types:
            raise EasyBuildError("Unknown build type: '%s'. Supported build types: %s", bt, known_build_types)

        # fetch option number based on build type option and selected build type
        if LooseVersion(self.version) >= LooseVersion('3.7'):
            # the two relevant lines in the configure output for WRF 3.8 are:
            #  13. (serial)  14. (smpar)  15. (dmpar)  16. (dm+sm)   INTEL (ifort/icc)
            #  32. (serial)  33. (smpar)  34. (dmpar)  35. (dm+sm)   GNU (gfortran/gcc)
            build_type_question = "\s*(?P<nr>[0-9]+)\.\ \(%s\).*%s" % (bt, build_type_option)
        else:
            # the relevant lines in the configure output for WRF 3.6 are:
            #  13.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (serial)
            #  14.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (smpar)
            #  15.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (dmpar)
            #  16.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (dm+sm)
            #  32.  x86_64 Linux, gfortran compiler with gcc   (serial)
            #  33.  x86_64 Linux, gfortran compiler with gcc   (smpar)
            #  34.  x86_64 Linux, gfortran compiler with gcc   (dmpar)
            #  35.  x86_64 Linux, gfortran compiler with gcc   (dm+sm)
            build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (build_type_option, bt)

        # run configure script
        cmd = "./configure"
        qa = {
              # named group in match will be used to construct answer
              "Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:": "1",
              "Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:": "0"
             }
        no_qa = [
                 "testing for fseeko and fseeko64",
                 r"If you wish to change the default options, edit the file:[\s\n]*arch/configure_new.defaults"
                ]
        std_qa = {
                  # named group in match will be used to construct answer
                  r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question: "%(nr)s",
                 }

        run_cmd_qa(cmd, qa, no_qa=no_qa, std_qa=std_qa, log_all=True, simple=True)

        cfgfile = 'configure.wrf'

        # make sure correct compilers are being used
        comps = {
                 'SCC': os.getenv('CC'),
                 'SFC': os.getenv('F90'),
                 'CCOMP': os.getenv('CC'),
                 'DM_FC': os.getenv('MPIF90'),
                 'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
                }
        regex_subs = [(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v) for (k, v) in comps.items()]
        apply_regex_substitutions(cfgfile, regex_subs)

        # rewrite optimization options if desired
        if self.cfg['rewriteopts']:

            # replace default -O3 option in configure.wrf with CFLAGS/FFLAGS from environment
            self.log.info("Rewriting optimization options in %s" % cfgfile)

            # set extra flags for Intel compilers
            # see http://software.intel.com/en-us/forums/showthread.php?t=72109&p=1#146748
            if self.comp_fam == toolchain.INTELCOMP:  #@UndefinedVariable

                # -O3 -heap-arrays is required to resolve compilation error
                for envvar in ['CFLAGS', 'FFLAGS']:
                    val = os.getenv(envvar)
                    if '-O3' in val:
                        env.setvar(envvar, '%s -heap-arrays' % val)
                        self.log.info("Updated %s to '%s'" % (envvar, os.getenv(envvar)))

            # replace -O3 with desired optimization options
            regex_subs = [
                (r"^(FCOPTIM.*)(\s-O3)(\s.*)$", r"\1 %s \3" % os.getenv('FFLAGS')),
                (r"^(CFLAGS_LOCAL.*)(\s-O3)(\s.*)$", r"\1 %s \3" % os.getenv('CFLAGS')),
            ]
            apply_regex_substitutions(cfgfile, regex_subs)
    def configure_step(self):
        """Configure build:
            - set some magic environment variables
            - run configure script
            - adjust configure.wrf file if needed
        """

        # netCDF dependency
        set_netcdf_env_vars(self.log)
        self.netcdf_mod_cmds = get_netcdf_module_set_cmds(self.log)

        # HDF5 (optional) dependency
        hdf5 = get_software_root('HDF5')
        if hdf5:
            # check if this is parallel HDF5
            phdf5_bins = ['h5pcc', 'ph5diff']
            parallel_hdf5 = True
            for f in phdf5_bins:
                if not os.path.exists(os.path.join(hdf5, 'bin', f)):
                    parallel_hdf5 = False
                    break
            if not (hdf5 or parallel_hdf5):
                self.log.error("Parallel HDF5 module not loaded?")
            else:
                env.setvar('PHDF5', hdf5)
        else:
            self.log.info("HDF5 module not loaded, assuming that's OK...")

        # JasPer dependency check + setting env vars
        jasper = get_software_root('JasPer')
        if jasper:
            jasperlibdir = os.path.join(jasper, "lib")
            env.setvar('JASPERINC', os.path.join(jasper, "include"))
            env.setvar('JASPERLIB', jasperlibdir)

        else:
            if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
                self.log.error(
                    "JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?"
                )
            else:
                self.log.info(
                    "JasPer module not loaded, assuming that's OK...")

        # enable support for large file support in netCDF
        env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')

        # patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
        patch_perl_script_autoflush(os.path.join("arch", "Config_new.pl"))

        # determine build type option to look for
        build_type_option = None
        self.comp_fam = self.toolchain.comp_family()
        if self.comp_fam == toolchain.INTELCOMP:  #@UndefinedVariable
            build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"

        elif self.comp_fam == toolchain.GCC:  #@UndefinedVariable
            build_type_option = "x86_64 Linux, gfortran compiler with gcc"

        else:
            self.log.error(
                "Don't know how to figure out build type to select.")

        # fetch selected build type (and make sure it makes sense)
        known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
        self.parallel_build_types = ["dmpar", "smpar", "dm+sm"]
        bt = self.cfg['buildtype']

        if not bt in known_build_types:
            self.log.error(
                "Unknown build type: '%s'. Supported build types: %s" %
                (bt, known_build_types))

        # fetch option number based on build type option and selected build type
        build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (
            build_type_option, bt)

        # run configure script
        cmd = "./configure"
        qa = {
            # named group in match will be used to construct answer
            "Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:":
            "1",
            "Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:":
            "0"
        }
        no_qa = [
            "testing for fseeko and fseeko64",
            r"If you wish to change the default options, edit the file:[\s\n]*arch/configure_new.defaults"
        ]
        std_qa = {
            # named group in match will be used to construct answer
            r"%s.*\n(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
            "%(nr)s",
        }

        run_cmd_qa(cmd,
                   qa,
                   no_qa=no_qa,
                   std_qa=std_qa,
                   log_all=True,
                   simple=True)

        cfgfile = 'configure.wrf'

        # make sure correct compilers are being used
        comps = {
            'SCC': os.getenv('CC'),
            'SFC': os.getenv('F90'),
            'CCOMP': os.getenv('CC'),
            'DM_FC': os.getenv('MPIF90'),
            'DM_CC': "%s -DMPI2_SUPPORT" % os.getenv('MPICC'),
        }
        for line in fileinput.input(cfgfile, inplace=1, backup='.orig.comps'):
            for (k, v) in comps.items():
                line = re.sub(r"^(%s\s*=\s*).*$" % k, r"\1 %s" % v, line)
            sys.stdout.write(line)

        # rewrite optimization options if desired
        if self.cfg['rewriteopts']:

            # replace default -O3 option in configure.wrf with CFLAGS/FFLAGS from environment
            self.log.info("Rewriting optimization options in %s" % cfgfile)

            # set extra flags for Intel compilers
            # see http://software.intel.com/en-us/forums/showthread.php?t=72109&p=1#146748
            if self.comp_fam == toolchain.INTELCOMP:  #@UndefinedVariable

                # -O3 -heap-arrays is required to resolve compilation error
                for envvar in ['CFLAGS', 'FFLAGS']:
                    val = os.getenv(envvar)
                    if '-O3' in val:
                        env.setvar(envvar, '%s -heap-arrays' % val)
                        self.log.info("Updated %s to '%s'" %
                                      (envvar, os.getenv(envvar)))

            # replace -O3 with desired optimization options
            for line in fileinput.input(cfgfile,
                                        inplace=1,
                                        backup='.orig.rewriteopts'):
                line = re.sub(r"^(FCOPTIM.*)(\s-O3)(\s.*)$",
                              r"\1 %s \3" % os.getenv('FFLAGS'), line)
                line = re.sub(r"^(CFLAGS_LOCAL.*)(\s-O3)(\s.*)$",
                              r"\1 %s \3" % os.getenv('CFLAGS'), line)
                sys.stdout.write(line)
Beispiel #5
0
    def configure_step(self):
        """Configure build:
        - set required environment variables (for netCDF, JasPer)
        - patch compile script and ungrib Makefile for non-default install paths of WRF and JasPer
        - run configure script and figure how to select desired build option
        - patch configure.wps file afterwards to fix 'serial compiler' setting
        """

        # netCDF dependency check + setting env vars (NETCDF, NETCDFF)
        set_netcdf_env_vars(self.log)

        # WRF dependency check
        wrf = get_software_root('WRF')
        if wrf:
            wrfdir = os.path.join(wrf,
                                  det_wrf_subdir(get_software_version('WRF')))
        else:
            raise EasyBuildError("WRF module not loaded?")

        self.compile_script = 'compile'

        if LooseVersion(self.version) >= LooseVersion('4.0.3'):
            # specify install location of WRF via $WRF_DIR (supported since WPS 4.0.3)
            # see https://github.com/wrf-model/WPS/pull/102
            env.setvar('WRF_DIR', wrfdir)
        else:
            # patch compile script so that WRF is found
            regex_subs = [(r"^(\s*set\s*WRF_DIR_PRE\s*=\s*)\${DEV_TOP}(.*)$",
                           r"\1%s\2" % wrfdir)]
            apply_regex_substitutions(self.compile_script, regex_subs)

        # libpng dependency check
        libpng = get_software_root('libpng')
        zlib = get_software_root('zlib')
        if libpng:
            paths = [libpng]
            if zlib:
                paths.insert(0, zlib)
            libpnginc = ' '.join(
                ['-I%s' % os.path.join(path, 'include') for path in paths])
            libpnglib = ' '.join(
                ['-L%s' % os.path.join(path, 'lib') for path in paths])
        else:
            # define these as empty, assume that libpng will be available via OS (e.g. due to --filter-deps=libpng)
            libpnglib = ""
            libpnginc = ""

        # JasPer dependency check + setting env vars
        jasper = get_software_root('JasPer')
        if jasper:
            env.setvar('JASPERINC', os.path.join(jasper, "include"))
            jasperlibdir = os.path.join(jasper, "lib")
            env.setvar('JASPERLIB', jasperlibdir)
            jasperlib = "-L%s" % jasperlibdir
        else:
            raise EasyBuildError("JasPer module not loaded?")

        # patch ungrib Makefile so that JasPer is found
        jasperlibs = "%s -ljasper %s -lpng" % (jasperlib, libpnglib)
        regex_subs = [
            (r"^(\s*-L\.\s*-l\$\(LIBTARGET\))(\s*;.*)$",
             r"\1 %s\2" % jasperlibs),
            (r"^(\s*\$\(COMPRESSION_LIBS\))(\s*;.*)$",
             r"\1 %s\2" % jasperlibs),
        ]
        apply_regex_substitutions(os.path.join('ungrib', 'src', 'Makefile'),
                                  regex_subs)

        # patch arch/Config.pl script, so that run_cmd_qa receives all output to answer questions
        patch_perl_script_autoflush(os.path.join("arch", "Config.pl"))

        # configure

        # determine build type option to look for
        self.comp_fam = self.toolchain.comp_family()
        build_type_option = None

        if LooseVersion(self.version) >= LooseVersion("3.4"):

            knownbuildtypes = {'smpar': 'serial', 'dmpar': 'dmpar'}

            if self.comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
                build_type_option = " Linux x86_64, Intel compiler"

            elif self.comp_fam == toolchain.GCC:  # @UndefinedVariable
                if LooseVersion(self.version) >= LooseVersion("3.6"):
                    build_type_option = "Linux x86_64, gfortran"
                else:
                    build_type_option = "Linux x86_64 g95"

            else:
                raise EasyBuildError(
                    "Don't know how to figure out build type to select.")

        else:

            knownbuildtypes = {'smpar': 'serial', 'dmpar': 'DM parallel'}

            if self.comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
                build_type_option = "PC Linux x86_64, Intel compiler"

            elif self.comp_fam == toolchain.GCC:  # @UndefinedVariable
                build_type_option = "PC Linux x86_64, gfortran compiler,"
                knownbuildtypes['dmpar'] = knownbuildtypes['dmpar'].upper()

            else:
                raise EasyBuildError(
                    "Don't know how to figure out build type to select.")

        # check and fetch selected build type
        bt = self.cfg['buildtype']

        if bt not in knownbuildtypes.keys():
            raise EasyBuildError(
                "Unknown build type: '%s'. Supported build types: %s", bt,
                knownbuildtypes.keys())

        # fetch option number based on build type option and selected build type
        build_type_question = r"\s*(?P<nr>[0-9]+).\s*%s\s*\(?%s\)?\s*\n" % (
            build_type_option, knownbuildtypes[bt])

        cmd = ' '.join(
            [self.cfg['preconfigopts'], './configure', self.cfg['configopts']])
        qa = {}
        no_qa = [".*compiler is.*"]
        std_qa = {
            # named group in match will be used to construct answer
            r"%s(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question:
            "%(nr)s",
        }

        run_cmd_qa(cmd,
                   qa,
                   no_qa=no_qa,
                   std_qa=std_qa,
                   log_all=True,
                   simple=True)

        # make sure correct compilers and compiler flags are being used
        comps = {
            'SCC': "%s -I$(JASPERINC) %s" % (os.getenv('CC'), libpnginc),
            'SFC': os.getenv('F90'),
            'DM_FC': os.getenv('MPIF90'),
            'DM_CC': os.getenv('MPICC'),
            'FC': os.getenv('MPIF90'),
            'CC': os.getenv('MPICC'),
        }
        if self.toolchain.options.get('openmp', None):
            comps.update({
                'LDFLAGS':
                '%s %s' %
                (self.toolchain.get_flag('openmp'), os.environ['LDFLAGS'])
            })

        regex_subs = [(r"^(%s\s*=\s*).*$" % key, r"\1 %s" % val)
                      for (key, val) in comps.items()]
        apply_regex_substitutions('configure.wps', regex_subs)
Beispiel #6
0
    def configure_step(self):
        """Configure build:
        - set required environment variables (for netCDF, JasPer)
        - patch compile script and ungrib Makefile for non-default install paths of WRF and JasPer
        - run configure script and figure how to select desired build option
        - patch configure.wps file afterwards to fix 'serial compiler' setting
        """

        # netCDF dependency check + setting env vars (NETCDF, NETCDFF)
        set_netcdf_env_vars(self.log)

        # WRF dependency check
        wrf = get_software_root('WRF')
        if wrf:
            wrfdir = os.path.join(wrf, det_wrf_subdir(get_software_version('WRF')))
        else:
            raise EasyBuildError("WRF module not loaded?")

        # patch compile script so that WRF is found
        self.compile_script = "compile"
        regex_subs = [(r"^(\s*set\s*WRF_DIR_PRE\s*=\s*)\${DEV_TOP}(.*)$", r"\1%s\2" % wrfdir)]
        apply_regex_substitutions(self.compile_script, regex_subs)

        # libpng dependency check
        libpng = get_software_root('libpng')
        zlib = get_software_root('zlib')
        if libpng:
            paths = [libpng]
            if zlib:
                paths.insert(0, zlib)
            libpnginc = ' '.join(['-I%s' % os.path.join(path, 'include') for path in paths])
            libpnglib = ' '.join(['-L%s' % os.path.join(path, 'lib') for path in paths])
        else:
            # define these as empty, assume that libpng will be available via OS (e.g. due to --filter-deps=libpng)
            libpnglib = ""
            libpnginc = ""

        # JasPer dependency check + setting env vars
        jasper = get_software_root('JasPer')
        if jasper:
            env.setvar('JASPERINC', os.path.join(jasper, "include"))
            jasperlibdir = os.path.join(jasper, "lib")
            env.setvar('JASPERLIB', jasperlibdir)
            jasperlib = "-L%s" % jasperlibdir
        else:
            raise EasyBuildError("JasPer module not loaded?")

        # patch ungrib Makefile so that JasPer is found
        jasperlibs = "%s -ljasper %s -lpng" % (jasperlib, libpnglib)
        regex_subs = [
            (r"^(\s*-L\.\s*-l\$\(LIBTARGET\))(\s*;.*)$", r"\1 %s\2" % jasperlibs),
            (r"^(\s*\$\(COMPRESSION_LIBS\))(\s*;.*)$", r"\1 %s\2" % jasperlibs),
        ]
        apply_regex_substitutions(os.path.join('ungrib', 'src', 'Makefile'), regex_subs)

        # patch arch/Config.pl script, so that run_cmd_qa receives all output to answer questions
        patch_perl_script_autoflush(os.path.join("arch", "Config.pl"))

        # configure

        # determine build type option to look for
        self.comp_fam = self.toolchain.comp_family()
        build_type_option = None

        if LooseVersion(self.version) >= LooseVersion("3.4"):

            knownbuildtypes = {
                'smpar': 'serial',
                'dmpar': 'dmpar'
            }

            if self.comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
                build_type_option = " Linux x86_64, Intel compiler"

            elif self.comp_fam == toolchain.GCC:  # @UndefinedVariable
                build_type_option = "Linux x86_64 g95 compiler"

            else:
                raise EasyBuildError("Don't know how to figure out build type to select.")

        else:

            knownbuildtypes = {
                'smpar': 'serial',
                'dmpar': 'DM parallel'
            }

            if self.comp_fam == toolchain.INTELCOMP:  # @UndefinedVariable
                build_type_option = "PC Linux x86_64, Intel compiler"

            elif self.comp_fam == toolchain.GCC:  # @UndefinedVariable
                build_type_option = "PC Linux x86_64, gfortran compiler,"
                knownbuildtypes['dmpar'] = knownbuildtypes['dmpar'].upper()

            else:
                raise EasyBuildError("Don't know how to figure out build type to select.")

        # check and fetch selected build type
        bt = self.cfg['buildtype']

        if bt not in knownbuildtypes.keys():
            raise EasyBuildError("Unknown build type: '%s'. Supported build types: %s", bt, knownbuildtypes.keys())

        # fetch option number based on build type option and selected build type
        build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(?%s\)?\s*\n" % (build_type_option, knownbuildtypes[bt])

        cmd = "./configure"
        qa = {}
        no_qa = [".*compiler is.*"]
        std_qa = {
            # named group in match will be used to construct answer
            r"%s(.*\n)*Enter selection\s*\[[0-9]+-[0-9]+\]\s*:" % build_type_question: "%(nr)s",
        }

        run_cmd_qa(cmd, qa, no_qa=no_qa, std_qa=std_qa, log_all=True, simple=True)

        # make sure correct compilers and compiler flags are being used
        comps = {
            'SCC': "%s -I$(JASPERINC) %s" % (os.getenv('CC'), libpnginc),
            'SFC': os.getenv('F90'),
            'DM_FC': os.getenv('MPIF90'),
            'DM_CC': os.getenv('MPICC'),
            'FC': os.getenv('MPIF90'),
            'CC': os.getenv('MPICC'),
        }
        regex_subs = [(r"^(%s\s*=\s*).*$" % key, r"\1 %s" % val) for (key, val) in comps.items()]
        apply_regex_substitutions('configure.wps', regex_subs)
Beispiel #7
0
Datei: wrf.py Projekt: rdrake/JSC
    def configure_step(self):
        """Configure build:
            - set some magic environment variables
            - run configure script
            - adjust configure.wrf file if needed
        """
        # define $NETCDF* for netCDF dependency (used when creating WRF module file)
        set_netcdf_env_vars(self.log)

        # HDF5 (optional) dependency
        hdf5 = get_software_root('HDF5')
        if hdf5:
            # check if this is parallel HDF5
            phdf5_bins = ['h5pcc', 'ph5diff']
            parallel_hdf5 = True
            for f in phdf5_bins:
                if not os.path.exists(os.path.join(hdf5, 'bin', f)):
                    parallel_hdf5 = False
                    break
            if not (hdf5 or parallel_hdf5):
                raise EasyBuildError("Parallel HDF5 module not loaded?")
            else:
                env.setvar('PHDF5', hdf5)
        else:
            self.log.info("HDF5 module not loaded, assuming that's OK...")

        # JasPer dependency check + setting env vars
        jasper = get_software_root('JasPer')
        if jasper:
            jasperlibdir = os.path.join(jasper, "lib")
            env.setvar('JASPERINC', os.path.join(jasper, "include"))
            env.setvar('JASPERLIB', jasperlibdir)

        else:
            if os.getenv('JASPERINC') or os.getenv('JASPERLIB'):
                raise EasyBuildError("JasPer module not loaded, but JASPERINC and/or JASPERLIB still set?")
            else:
                self.log.info("JasPer module not loaded, assuming that's OK...")

        # enable support for large file support in netCDF
        env.setvar('WRFIO_NCD_LARGE_FILE_SUPPORT', '1')

        # patch arch/Config_new.pl script, so that run_cmd_qa receives all output to answer questions
        patch_perl_script_autoflush(os.path.join("arch", "Config_new.pl"))

        # determine build type option to look for
        build_type_option = None
        self.comp_fam = self.toolchain.comp_family()
        if self.comp_fam == toolchain.INTELCOMP:  #@UndefinedVariable
            if LooseVersion(self.version) >= LooseVersion('3.7'):
                build_type_option = "INTEL\ \(ifort\/icc\)"
            else:
                build_type_option = "Linux x86_64 i486 i586 i686, ifort compiler with icc"

        elif self.comp_fam == toolchain.GCC:  #@UndefinedVariable
            if LooseVersion(self.version) >= LooseVersion('3.7'):
                build_type_option = "GNU\ \(gfortran\/gcc\)"
            else:
                build_type_option = "x86_64 Linux, gfortran compiler with gcc"

        else:
            raise EasyBuildError("Don't know how to figure out build type to select.")

        # fetch selected build type (and make sure it makes sense)
        known_build_types = ['serial', 'smpar', 'dmpar', 'dm+sm']
        self.parallel_build_types = ["dmpar", "smpar", "dm+sm"]
        bt = self.cfg['buildtype']

        if not bt in known_build_types:
            raise EasyBuildError("Unknown build type: '%s'. Supported build types: %s", bt, known_build_types)

        # fetch option number based on build type option and selected build type
        if LooseVersion(self.version) >= LooseVersion('3.7'):
            # the two relevant lines in the configure output for WRF 3.8 are:
            #  13. (serial)  14. (smpar)  15. (dmpar)  16. (dm+sm)   INTEL (ifort/icc)
            #  32. (serial)  33. (smpar)  34. (dmpar)  35. (dm+sm)   GNU (gfortran/gcc)
            build_type_question = "\s*(?P<nr>[0-9]+)\.\ \(%s\).*%s" % (bt, build_type_option)
        else:
            # the relevant lines in the configure output for WRF 3.6 are:
            #  13.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (serial)
            #  14.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (smpar)
            #  15.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (dmpar)
            #  16.  Linux x86_64 i486 i586 i686, ifort compiler with icc  (dm+sm)
            #  32.  x86_64 Linux, gfortran compiler with gcc   (serial)
            #  33.  x86_64 Linux, gfortran compiler with gcc   (smpar)
            #  34.  x86_64 Linux, gfortran compiler with gcc   (dmpar)
            #  35.  x86_64 Linux, gfortran compiler with gcc   (dm+sm)
            build_type_question = "\s*(?P<nr>[0-9]+).\s*%s\s*\(%s\)" % (build_type_option, bt)

        # run configure script
        cmd = "./configure"
        qa = {
              # named group in match will be used to construct answer
              "Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default 1]:": "1",
              "Compile for nesting? (0=no nesting, 1=basic, 2=preset moves, 3=vortex following) [default 0]:": "0"
             }
        no_qa = [
                 "testing for fseeko and fseeko64",
                 r"If you wish to change the default options, edit the file:[\s
]*arch/configure_new.defaults"
                ]