mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
pbs_python egg changed from static to dynamic for the reasons explained
here: http://g2.trac.bx.psu.edu/wiki/ClusteringGalaxy#Anoteonlibtorque Also includes a rather ridiculous fix for compiling a fat dynamic libtorque on OS X due to some autoconf/libtool weirdness.
This commit is contained in:
Nate Coraor
@@ -46,7 +46,7 @@ wsgiref = 0.1.2 http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.z
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[tags]
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psycopg2 = _8.2.6_static
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pysqlite = _3.5.4_static
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pbs_python = _2.1.8_static
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pbs_python = _2.1.8
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MySQL_python = _5.0.51a_static
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python_lzo = _static
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flup = .dev_r2311
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+5
-3
@@ -75,10 +75,11 @@ class Egg:
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for orig_fn in z.namelist():
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fn = ( orig_fn.split( os.path.sep, 1 ) )[1]
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abs_fn = os.path.join( dir, fn )
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# could break things
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if "ez_setup" in abs_fn:
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continue
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if not os.access( os.path.dirname( abs_fn ), os.F_OK ):
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os.makedirs( os.path.dirname( abs_fn ) )
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if os.path.basename( abs_fn ) == "ez_setup.py":
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continue
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otf = open( abs_fn, "wb" )
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otf.write( z.read( orig_fn ) )
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otf.close()
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@@ -92,7 +93,8 @@ class Egg:
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# the top dir will now be an empty string
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if fn == "":
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continue
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if os.path.basename( abs_fn ) == "ez_setup.py":
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# could break things
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if "ez_setup" in abs_fn:
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continue
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if fn.endswith( os.path.sep ):
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if not os.access( os.path.dirname( abs_fn ), os.F_OK ):
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@@ -0,0 +1,154 @@
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import os, sys, subprocess, tarfile, shutil
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def unpack_prebuilt_torque():
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if not os.access( TORQUE_BINARY_ARCHIVE, os.F_OK ):
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print "unpack_prebuilt_torque(): No binary archive of Torque available for this platform - will build it now"
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build_torque()
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else:
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print "unpack_prebuilt_torque(): Found a previously built Torque binary archive for this platform."
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print "unpack_prebuilt_torque(): To force Torque to be rebuilt, remove the archive:"
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print " ", TORQUE_BINARY_ARCHIVE
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t = tarfile.open( TORQUE_BINARY_ARCHIVE, "r" )
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for fn in t.getnames():
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t.extract( fn )
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t.close()
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def build_torque():
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# download
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if not os.access( TORQUE_ARCHIVE, os.F_OK ):
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pkg_resources.require( "twill" )
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import twill.commands as tc
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import twill.errors as te
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try:
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print "build_torque(): Downloading Torque source archive from:"
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print " ", TORQUE_URL
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tc.go( TORQUE_URL )
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tc.code( 200 )
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tc.save_html( TORQUE_ARCHIVE )
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except te.TwillAssertionError, e:
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print "build_torque(): Unable to fetch Torque source archive from:"
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print " ", TORQUE_URL
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sys.exit( 1 )
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# untar
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print "build_torque(): Unpacking Torque source archive from:"
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print " ", TORQUE_ARCHIVE
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t = tarfile.open( TORQUE_ARCHIVE, "r" )
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for fn in t.getnames():
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t.extract( fn )
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t.close()
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# patch
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file = os.path.join( "torque-%s" %TORQUE_VERSION, "src", "include", "libpbs.h" )
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print "build_torque(): Patching", file
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if not os.access( "%s.orig" %file, os.F_OK ):
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shutil.copyfile( file, "%s.orig" %file )
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i = open( "%s.orig" %file, "r" )
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o = open( file, "w" )
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for line in i.readlines():
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if line == "#define NCONNECTS 5\n":
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line = "#define NCONNECTS 50\n"
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print >>o, line,
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i.close()
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o.close()
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# configure
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print "build_torque(): Running Torque configure script"
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p = subprocess.Popen( args = CONFIGURE, shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) )
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r = p.wait()
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if r != 0:
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print "build_torque(): Torque configure script failed"
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sys.exit( 1 )
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# compile
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print "build_torque(): Building Torque (make)"
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p = subprocess.Popen( args = "make", shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) )
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r = p.wait()
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# libtool won't pass -arch to the linker, maybe it's an old libtool? whatever, this works
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p = subprocess.Popen( args = "gcc -dynamiclib -undefined dynamic_lookup -o .libs/libtorque.0.0.0.dylib .libs/dis.o .libs/discui_.o .libs/discul_.o .libs/disi10d_.o .libs/disi10l_.o .libs/disiui_.o .libs/disp10d_.o .libs/disp10l_.o .libs/disrcs.o .libs/disrd.o .libs/disrf.o .libs/disrfcs.o .libs/disrfst.o .libs/disrl_.o .libs/disrl.o .libs/disrsc.o .libs/disrsi_.o .libs/disrsi.o .libs/disrsl_.o .libs/disrsl.o .libs/disrss.o .libs/disrst.o .libs/disruc.o .libs/disrui.o .libs/disrul.o .libs/disrus.o .libs/diswcs.o .libs/diswf.o .libs/diswl_.o .libs/diswsi.o .libs/diswsl.o .libs/diswui_.o .libs/diswui.o .libs/diswul.o .libs/advise.o .libs/dec_attrl.o .libs/dec_attropl.o .libs/dec_Authen.o .libs/dec_CpyFil.o .libs/dec_JobCred.o .libs/dec_JobFile.o .libs/dec_JobId.o .libs/dec_JobObit.o .libs/dec_Manage.o .libs/dec_MoveJob.o .libs/dec_MsgJob.o .libs/dec_QueueJob.o .libs/dec_Reg.o .libs/dec_ReqExt.o .libs/dec_ReqHdr.o .libs/dec_Resc.o .libs/dec_rpyc.o .libs/dec_rpys.o .libs/dec_RunJob.o .libs/dec_Shut.o .libs/dec_Sig.o .libs/dec_Status.o .libs/dec_svrattrl.o .libs/dec_Track.o .libs/enc_attrl.o .libs/enc_attropl.o .libs/enc_CpyFil.o .libs/enc_JobCred.o .libs/enc_JobFile.o .libs/enc_JobId.o .libs/enc_JobObit.o .libs/enc_Manage.o .libs/enc_MoveJob.o .libs/enc_MsgJob.o .libs/enc_QueueJob.o .libs/enc_Reg.o .libs/enc_reply.o .libs/enc_ReqExt.o .libs/enc_ReqHdr.o .libs/enc_RunJob.o .libs/enc_Shut.o .libs/enc_Sig.o .libs/enc_Status.o .libs/enc_svrattrl.o .libs/enc_Track.o .libs/get_svrport.o .libs/nonblock.o .libs/PBS_attr.o .libs/pbsD_alterjo.o .libs/pbsD_asyrun.o .libs/PBS_data.o .libs/pbsD_connect.o .libs/pbsD_deljob.o .libs/pbsD_holdjob.o .libs/pbsD_locjob.o .libs/PBSD_manage2.o .libs/pbsD_manager.o .libs/pbsD_movejob.o .libs/PBSD_manager_caps.o .libs/PBSD_msg2.o .libs/pbsD_msgjob.o .libs/pbsD_orderjo.o .libs/PBSD_rdrpy.o .libs/pbsD_rerunjo.o .libs/pbsD_resc.o .libs/pbsD_rlsjob.o .libs/pbsD_runjob.o .libs/pbsD_selectj.o .libs/PBSD_sig2.o .libs/pbsD_sigjob.o .libs/pbsD_stagein.o .libs/pbsD_statjob.o .libs/pbsD_statnode.o .libs/pbsD_statque.o .libs/pbsD_statsrv.o .libs/PBSD_status2.o .libs/PBSD_status.o .libs/pbsD_submit.o .libs/PBSD_submit_caps.o .libs/pbsD_termin.o .libs/pbs_geterrmg.o .libs/pbs_statfree.o .libs/rpp.o .libs/tcp_dis.o .libs/tm.o .libs/list_link.o .libs/ck_job_name.o .libs/cnt2server.o .libs/cvtdate.o .libs/get_server.o .libs/locate_job.o .libs/parse_at.o .libs/parse_depend.o .libs/parse_destid.o .libs/parse_equal.o .libs/parse_jobid.o .libs/parse_stage.o .libs/prepare_path.o .libs/prt_job_err.o .libs/set_attr.o .libs/set_resource.o .libs/chk_file_sec.o .libs/log_event.o .libs/pbs_log.o .libs/pbs_messages.o .libs/setup_env.o .libs/get_hostaddr.o .libs/get_hostname.o .libs/md5.o .libs/net_client.o .libs/net_server.o .libs/net_set_clse.o .libs/rm.o .libs/port_forwarding.o -lkvm -Wl,-syslibroot -Wl,/Developer/SDKs/MacOSX10.4u.sdk -install_name /usr/local/lib/libtorque.0.dylib -compatibility_version 1 -current_version 1.0 -arch i386 -arch ppc", shell = True, cwd = os.getcwd()+"/torque-%s/src/lib/Libpbs" %TORQUE_VERSION )
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r = p.wait()
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p = subprocess.Popen( args = "make", shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) )
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r = p.wait()
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if r != 0:
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print "build_torque(): Building Torque (make) failed"
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sys.exit( 1 )
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# install
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print "build_torque(): Installing Torque (make install_lib)"
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p = subprocess.Popen( args = "make DESTDIR=%s/torque install_lib" %os.getcwd(), shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) )
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r = p.wait()
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if r != 0:
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print "build_torque(): Installing Torque (make install_lib) failed"
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sys.exit( 1 )
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# pack
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print "build_torque(): Creating binary Torque archive for future builds of pbs_python"
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t = tarfile.open( TORQUE_BINARY_ARCHIVE, "w:bz2" )
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t.add( "torque" )
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t.close()
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# change back to the build dir
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if os.path.dirname( sys.argv[0] ) != "":
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os.chdir( os.path.dirname( sys.argv[0] ) )
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# find setuptools
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scramble_lib = os.path.join( "..", "..", "..", "lib" )
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sys.path.append( scramble_lib )
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try:
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from setuptools import *
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import pkg_resources
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except:
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from ez_setup import use_setuptools
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use_setuptools( download_delay=8, to_dir=scramble_lib )
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from setuptools import *
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import pkg_resources
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# get the tag
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if os.access( ".galaxy_tag", os.F_OK ):
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tagfile = open( ".galaxy_tag", "r" )
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tag = tagfile.readline().strip()
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else:
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tag = None
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TORQUE_VERSION = ( tag.split( "_" ) )[1]
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TORQUE_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s.tar.gz" %TORQUE_VERSION ) )
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TORQUE_BINARY_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s-%s.tar.bz2" %( TORQUE_VERSION, pkg_resources.get_platform() ) ) )
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TORQUE_URL = "http://www.clusterresources.com/downloads/torque/torque-%s.tar.gz" %TORQUE_VERSION
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CONFIGURE = "CFLAGS='-O -g -isysroot /Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc' "
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CONFIGURE += "LDFLAGS='-Wl,-syslibroot,/Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc' "
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CONFIGURE += "./configure --prefix=/usr/local --disable-dependency-tracking --without-tcl --without-tk"
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# clean, in case you're running this by hand from a dirty module source dir
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for dir in [ "build", "dist", "torque-%s" %TORQUE_VERSION ]:
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if os.access( dir, os.F_OK ):
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print "scramble_it.py: removing dir:", dir
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shutil.rmtree( dir )
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# build/unpack Torque
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unpack_prebuilt_torque()
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print "scramble_it(): Running pbs_python configure script"
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p = subprocess.Popen( args = "sh configure --with-pbsdir=torque/usr/local/lib", shell = True )
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r = p.wait()
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if r != 0:
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print "scramble_it(): pbs_python configure script failed"
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sys.exit( 1 )
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# version string in 2.9.4 setup.py is wrong
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file = "setup.py"
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print "scramble_it(): Patching", file
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if not os.access( "%s.orig" %file, os.F_OK ):
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shutil.copyfile( file, "%s.orig" %file )
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i = open( "%s.orig" %file, "r" )
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o = open( file, "w" )
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for line in i.readlines():
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if line == " version = '2.9.0',\n":
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line = " version = '2.9.4',\n"
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print >>o, line,
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i.close()
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o.close()
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# tag
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me = sys.argv[0]
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sys.argv = [ me ]
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if tag is not None:
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sys.argv.append( "egg_info" )
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sys.argv.append( "--tag-build=%s" %tag )
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sys.argv.append( "bdist_egg" )
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# go
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execfile( "setup.py", globals(), locals() )
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@@ -65,7 +65,7 @@ def build_torque():
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sys.exit( 1 )
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# install
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print "build_torque(): Installing Torque (make install_lib)"
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p = subprocess.Popen( args = "make install_lib", shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) )
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p = subprocess.Popen( args = "make DESTDIR=%s/torque install_lib" %os.getcwd(), shell = True, cwd = os.path.join( os.getcwd(), "torque-%s" %TORQUE_VERSION) )
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r = p.wait()
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if r != 0:
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print "build_torque(): Installing Torque (make install_lib) failed"
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@@ -103,14 +103,7 @@ TORQUE_VERSION = ( tag.split( "_" ) )[1]
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TORQUE_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s.tar.gz" %TORQUE_VERSION ) )
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TORQUE_BINARY_ARCHIVE = os.path.abspath( os.path.join( "..", "..", "..", "archives", "torque-%s-%s.tar.bz2" %( TORQUE_VERSION, pkg_resources.get_platform() ) ) )
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TORQUE_URL = "http://www.clusterresources.com/downloads/torque/torque-%s.tar.gz" %TORQUE_VERSION
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# there's no need to have a completely separate build script for this
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if pkg_resources.get_platform() == "macosx-10.3-fat":
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CONFIGURE = "CFLAGS='-O -g -isysroot /Developer/SDKs/MacOSX10.4u.sdk -arch i386 -arch ppc' "
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CONFIGURE += "LDFLAGS='-arch i386 -arch ppc' "
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CONFIGURE += "LD='gcc -mmacosx-version-min=10.4 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -nostartfiles -arch i386 -arch ppc' "
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CONFIGURE += "./configure --prefix=%s/torque --disable-shared --disable-dependency-tracking --without-tcl --without-tk" %os.getcwd()
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else:
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CONFIGURE = "CFLAGS='-fPIC' ./configure --prefix=%s/torque --disable-shared --without-tcl --without-tk" %os.getcwd()
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CONFIGURE = "CFLAGS='-fPIC' ./configure --prefix=/usr/local --without-tcl --without-tk"
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# clean, in case you're running this by hand from a dirty module source dir
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for dir in [ "build", "dist", "torque-%s" %TORQUE_VERSION ]:
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@@ -122,7 +115,7 @@ for dir in [ "build", "dist", "torque-%s" %TORQUE_VERSION ]:
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unpack_prebuilt_torque()
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print "scramble_it(): Running pbs_python configure script"
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p = subprocess.Popen( args = "sh configure --with-pbsdir=torque/lib", shell = True )
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p = subprocess.Popen( args = "sh configure --with-pbsdir=torque/usr/local/lib", shell = True )
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r = p.wait()
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if r != 0:
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print "scramble_it(): pbs_python configure script failed"
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@@ -141,19 +134,6 @@ for line in i.readlines():
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print >>o, line,
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i.close()
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o.close()
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# need to change this to an extern declaration
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file = os.path.join( "src", "log.h" )
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print "build_torque(): Patching", file
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if not os.access( "%s.orig" %file, os.F_OK ):
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shutil.copyfile( file, "%s.orig" %file )
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i = open( "%s.orig" %file, "r" )
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o = open( file, "w" )
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for line in i.readlines():
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if line == 'char *msg_daemonname = "pbs_python";\n':
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line = 'extern char *msg_daemonname;\n'
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print >>o, line,
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i.close()
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o.close()
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# tag
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me = sys.argv[0]
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Reference in New Issue
Block a user