2011-04-08 22:35:05,102-0500 DEBUG Loader Max heap: 252641280 2011-04-08 22:35:05,102-0500 DEBUG Loader kmlversion is >30874f6f-a397-4693-8421-6ed17cfd2d62< 2011-04-08 22:35:05,102-0500 DEBUG Loader build version is >30874f6f-a397-4693-8421-6ed17cfd2d62< 2011-04-08 22:35:05,103-0500 DEBUG Loader Recompilation suppressed. 2011-04-08 22:35:05,291-0500 INFO VDL2ExecutionContext Stack dump: Level 1 [iA = 0, iB = 0, bA = false, bB = false] vdl:instanceconfigfile = cf vdl:instanceconfig = Swift configuration [cf] vdl:operation = run PATH_SEPARATOR = / swift.home = /home/ketan/swift-0.92/bin/.. 2011-04-08 22:35:05,904-0500 INFO unknown Using sites file: bionimbus-coaster-with-provider-staging.xml 2011-04-08 22:35:05,937-0500 INFO unknown Using tc.data: tc 2011-04-08 22:35:06,058-0500 INFO AbstractScheduler Setting resources to: {localhost=localhost} 2011-04-08 22:35:06,549-0500 INFO unknown Swift svn swift-r4157 cog-r3056 2011-04-08 22:35:06,550-0500 INFO unknown RUNID id=run:20110408-2235-en2fi70c 2011-04-08 22:35:06,582-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000001 path=$ 2011-04-08 22:35:06,582-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000001 VALUE=2.5 2011-04-08 22:35:06,583-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000002 path=$ 2011-04-08 22:35:06,583-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000002 VALUE=input/4TRA.pdb 2011-04-08 22:35:06,584-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000003 path=$ 2011-04-08 22:35:06,584-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000003 VALUE=n 2011-04-08 22:35:06,584-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000004 path=$ 2011-04-08 22:35:06,584-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000004 VALUE=.pdb 2011-04-08 22:35:06,584-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000005 path=$ 2011-04-08 22:35:06,584-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000005 VALUE=.dat 2011-04-08 22:35:06,585-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000006 path=$ 2011-04-08 22:35:06,585-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000006 VALUE=list 2011-04-08 22:35:06,585-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000007 path=$ 2011-04-08 22:35:06,585-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000007 VALUE=-root 2011-04-08 22:35:06,585-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000008 path=$ 2011-04-08 22:35:06,585-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000008 VALUE=-static 2011-04-08 22:35:06,586-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000009 path=$ 2011-04-08 22:35:06,586-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000009 VALUE=-angle_step 2011-04-08 22:35:06,586-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000010 path=$ 2011-04-08 22:35:06,586-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000010 VALUE=m 2011-04-08 22:35:06,586-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000011 path=$ 2011-04-08 22:35:06,586-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000011 VALUE=-keep 2011-04-08 22:35:06,586-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000012 path=$ 2011-04-08 22:35:06,587-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000012 VALUE=-modulo 2011-04-08 22:35:06,587-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000013 path=$ 2011-04-08 22:35:06,587-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000013 VALUE=1 2011-04-08 22:35:06,587-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000014 path=$ 2011-04-08 22:35:06,587-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000014 VALUE=10 2011-04-08 22:35:06,587-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000015 path=$ 2011-04-08 22:35:06,587-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000015 VALUE=-calculate_grid 2011-04-08 22:35:06,588-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000016 path=$ 2011-04-08 22:35:06,588-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000016 VALUE=: 2011-04-08 22:35:06,588-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000017 path=$ 2011-04-08 22:35:06,588-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000017 VALUE=grid 2011-04-08 22:35:06,589-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000018 path=$ 2011-04-08 22:35:06,589-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000018 VALUE=_ 2011-04-08 22:35:06,589-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000019 path=$ 2011-04-08 22:35:06,589-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000019 VALUE=-noelec 2011-04-08 22:35:06,589-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000020 path=$ 2011-04-08 22:35:06,589-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000020 VALUE=output 2011-04-08 22:35:06,590-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000021 path=$ 2011-04-08 22:35:06,590-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000021 VALUE=input/ 2011-04-08 22:35:06,590-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000022 path=$ 2011-04-08 22:35:06,590-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000022 VALUE=-mobile 2011-04-08 22:35:06,590-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000023 path=$ 2011-04-08 22:35:06,590-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000023 VALUE=100 2011-04-08 22:35:06,591-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000024 path=$ 2011-04-08 22:35:06,591-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000024 VALUE=0 2011-04-08 22:35:06,591-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000025 path=$ 2011-04-08 22:35:06,591-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000025 VALUE=1 2011-04-08 22:35:06,591-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000026 path=$ 2011-04-08 22:35:06,591-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000026 VALUE=32 2011-04-08 22:35:06,592-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000027 path=$ 2011-04-08 22:35:06,592-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000027 VALUE=3 2011-04-08 22:35:06,594-0500 INFO vdl:parameterlog PARAM thread=0 direction=intermediate variable=modulus provenanceid=dataset:20110408-2235-a6nbrxh1:720000000028 2011-04-08 22:35:06,648-0500 INFO vdl:parameterlog PARAM thread=0 direction=intermediate variable=str_roots provenanceid=dataset:20110408-2235-a6nbrxh1:720000000029 2011-04-08 22:35:06,664-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000030 path=$ 2011-04-08 22:35:06,664-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000030 VALUE=100 2011-04-08 22:35:06,664-0500 INFO VDLFunction FUNCTION: arg() 2011-04-08 22:35:06,664-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000031 path=$ 2011-04-08 22:35:06,664-0500 INFO SetFieldValue Set: modulus=100 2011-04-08 22:35:06,664-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000031 VALUE=pdb.list.1 2011-04-08 22:35:06,665-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000028 path=$ 2011-04-08 22:35:06,665-0500 INFO VDLFunction FUNCTION: arg() 2011-04-08 22:35:06,665-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000028 VALUE=100 2011-04-08 22:35:06,666-0500 INFO vdl:parameterlog PARAM thread=0-1 direction=output variable=TODO_name_or_pos provenanceid=dataset:20110408-2235-a6nbrxh1:720000000029 2011-04-08 22:35:06,666-0500 INFO vdl:parameterlog PARAM thread=0-1 direction=input variable=TODO_name_or_pos provenanceid=dataset:20110408-2235-a6nbrxh1:720000000031 2011-04-08 22:35:06,666-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000032 path=[0] 2011-04-08 22:35:06,666-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000032 VALUE=3bg0-1 2011-04-08 22:35:06,666-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000029 path=$ 2011-04-08 22:35:06,667-0500 INFO AbstractDataNode CONTAINMENT parent=dataset:20110408-2235-a6nbrxh1:720000000029 child=dataset:20110408-2235-a6nbrxh1:720000000032 2011-04-08 22:35:06,667-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000032 path=[0] 2011-04-08 22:35:06,667-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000032 VALUE=3bg0-1 2011-04-08 22:35:06,669-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=str_file_static provenanceid=dataset:20110408-2235-a6nbrxh1:720000000033 2011-04-08 22:35:06,670-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=str_file_mobile provenanceid=dataset:20110408-2235-a6nbrxh1:720000000034 2011-04-08 22:35:06,672-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=file_static provenanceid=dataset:20110408-2235-a6nbrxh1:720000000035 2011-04-08 22:35:06,674-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=file_mobile provenanceid=dataset:20110408-2235-a6nbrxh1:720000000036 2011-04-08 22:35:06,675-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=swift#mapper#17017 provenanceid=dataset:20110408-2235-a6nbrxh1:720000000037 2011-04-08 22:35:06,676-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=swift#mapper#17018 provenanceid=dataset:20110408-2235-a6nbrxh1:720000000038 2011-04-08 22:35:06,677-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=swift#mapper#17020 provenanceid=dataset:20110408-2235-a6nbrxh1:720000000039 2011-04-08 22:35:06,678-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=swift#mapper#17022 provenanceid=dataset:20110408-2235-a6nbrxh1:720000000040 2011-04-08 22:35:06,679-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000041 path=$ 2011-04-08 22:35:06,679-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000041 VALUE=output 2011-04-08 22:35:06,680-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000042 path=$ 2011-04-08 22:35:06,680-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000042 VALUE=.dat 2011-04-08 22:35:06,681-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=dat_files provenanceid=dataset:20110408-2235-a6nbrxh1:720000000043 2011-04-08 22:35:06,682-0500 INFO vdl:parameterlog PARAM thread=0-2-1 direction=intermediate variable=n provenanceid=dataset:20110408-2235-a6nbrxh1:720000000044 2011-04-08 22:35:06,684-0500 INFO SetFieldValue Set: str_file_mobile=input/4TRA.pdb 2011-04-08 22:35:06,684-0500 INFO SetFieldValue Set: swift#mapper#17017=3 2011-04-08 22:35:06,685-0500 INFO SetFieldValue Set: swift#mapper#17018=output 2011-04-08 22:35:06,685-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000037 path=$ 2011-04-08 22:35:06,685-0500 INFO SetFieldValue Set: swift#mapper#17022=.dat 2011-04-08 22:35:06,685-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000038 path=$ 2011-04-08 22:35:06,685-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000040 path=$ 2011-04-08 22:35:06,685-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000037 VALUE=3 2011-04-08 22:35:06,685-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000040 VALUE=.dat 2011-04-08 22:35:06,685-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000038 VALUE=output 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000045 path=$ 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000045 VALUE=3bg0-1_ 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000047 path=$ 2011-04-08 22:35:06,686-0500 INFO VDLFunction FUNCTION: strcat() 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000046 path=$ 2011-04-08 22:35:06,686-0500 INFO SetFieldValue Set: swift#mapper#17020=3bg0-1_ 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000047 VALUE=1 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000046 VALUE=input/3bg0-1.pdb 2011-04-08 22:35:06,686-0500 INFO VDLFunction FUNCTION: arg() 2011-04-08 22:35:06,686-0500 INFO VDLFunction FUNCTION: strcat() 2011-04-08 22:35:06,686-0500 INFO SetFieldValue Set: str_file_static=input/3bg0-1.pdb 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000048 path=$ 2011-04-08 22:35:06,686-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000048 VALUE=1 2011-04-08 22:35:06,687-0500 INFO VDLFunction FUNCTION: toint() 2011-04-08 22:35:06,687-0500 INFO SetFieldValue Set: n=1 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000044 path=$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000036 path=$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000039 path=$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode Found data org.griphyn.vdl.mapping.RootDataNode identifier dataset:20110408-2235-a6nbrxh1:720000000036 type file_pdb with no value at dataset=file_mobile (closed).$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000044 VALUE=1 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000035 path=$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000039 VALUE=3bg0-1_ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode Found data org.griphyn.vdl.mapping.RootDataNode identifier dataset:20110408-2235-a6nbrxh1:720000000035 type file_pdb with no value at dataset=file_static (closed).$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000034 path=$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000033 path=$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000034 VALUE=input/4TRA.pdb 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000049 path=$ 2011-04-08 22:35:06,687-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000033 VALUE=input/3bg0-1.pdb 2011-04-08 22:35:06,688-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000049 VALUE=0 2011-04-08 22:35:06,688-0500 INFO operators OPERATOR thread=0-2-1-8 operator=subtraction lhs=dataset:20110408-2235-a6nbrxh1:720000000044 rhs=dataset:20110408-2235-a6nbrxh1:720000000025 result=dataset:20110408-2235-a6nbrxh1:720000000049 2011-04-08 22:35:06,688-0500 INFO vdl:parameterlog PARAM thread=0-2-1-0 direction=input variable=TODO_name_or_pos provenanceid=dataset:20110408-2235-a6nbrxh1:720000000032 2011-04-08 22:35:06,688-0500 WARN trace SwiftScript trace: 3bg0-1 2011-04-08 22:35:06,691-0500 INFO vdl:mains ARRAYRANGE thread=0-2-1-8 array=dataset:20110408-2235-a6nbrxh1:720000000050 from=dataset:20110408-2235-a6nbrxh1:720000000024 to=dataset:20110408-2235-a6nbrxh1:720000000049 step=none 2011-04-08 22:35:06,693-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000051 path=$ 2011-04-08 22:35:06,694-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000051 VALUE=0 2011-04-08 22:35:06,694-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000050 path=$ 2011-04-08 22:35:06,696-0500 INFO vdl:parameterlog PARAM thread=0-2-1-8-1 direction=intermediate variable=str_modulo provenanceid=dataset:20110408-2235-a6nbrxh1:720000000052 2011-04-08 22:35:06,697-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000054 path=$ 2011-04-08 22:35:06,697-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000054 VALUE=0:100 2011-04-08 22:35:06,697-0500 INFO VDLFunction FUNCTION: strcat() 2011-04-08 22:35:06,697-0500 INFO SetFieldValue Set: str_modulo=0:100 2011-04-08 22:35:06,697-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000052 path=$ 2011-04-08 22:35:06,697-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000052 VALUE=0:100 2011-04-08 22:35:06,698-0500 INFO vdl:parameterlog PARAM thread=0-2-1-8-1-1 direction=input variable=param_root provenanceid=dataset:20110408-2235-a6nbrxh1:720000000032 2011-04-08 22:35:06,699-0500 INFO vdl:parameterlog PARAM thread=0-2-1-8-1-1 direction=input variable=param_modulo provenanceid=dataset:20110408-2235-a6nbrxh1:720000000052 2011-04-08 22:35:06,700-0500 INFO vdl:parameterlog PARAM thread=0-2-1-8-1-1 direction=input variable=param_file_static provenanceid=dataset:20110408-2235-a6nbrxh1:720000000035 2011-04-08 22:35:06,701-0500 INFO vdl:parameterlog PARAM thread=0-2-1-8-1-1 direction=input variable=param_file_mobile provenanceid=dataset:20110408-2235-a6nbrxh1:720000000036 2011-04-08 22:35:06,702-0500 INFO vdl:parameterlog PARAM thread=0-2-1-8-1-1 direction=output variable=dat_file provenanceid=dataset:20110408-2235-a6nbrxh1:720000000053 2011-04-08 22:35:06,712-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000055 path=$ 2011-04-08 22:35:06,712-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000055 VALUE=0:100 2011-04-08 22:35:06,713-0500 INFO VDLFunction FUNCTION: filename() 2011-04-08 22:35:06,713-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000056 path=$ 2011-04-08 22:35:06,713-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000056 VALUE=3bg0-1 2011-04-08 22:35:06,713-0500 INFO VDLFunction FUNCTION: filename() 2011-04-08 22:35:06,714-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000057 path=$ 2011-04-08 22:35:06,714-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000057 VALUE=input/3bg0-1.pdb 2011-04-08 22:35:06,714-0500 INFO VDLFunction FUNCTION: filename() 2011-04-08 22:35:06,714-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000058 path=$ 2011-04-08 22:35:06,714-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000058 VALUE=input/4TRA.pdb 2011-04-08 22:35:06,714-0500 INFO VDLFunction FUNCTION: filename() 2011-04-08 22:35:06,715-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000059 path=$ 2011-04-08 22:35:06,715-0500 INFO AbstractDataNode VALUE dataset=dataset:20110408-2235-a6nbrxh1:720000000059 VALUE=10 2011-04-08 22:35:06,715-0500 INFO VDLFunction FUNCTION: arg() 2011-04-08 22:35:06,722-0500 INFO vdl:execute START thread=0-2-1-8-1-1 tr=modftdock 2011-04-08 22:35:06,735-0500 INFO WeightedHostScoreScheduler CONTACT_SELECTED host=localhost, score=99.854 2011-04-08 22:35:06,737-0500 INFO GlobalSubmitQueue No global submit throttle set. Using default (1024) 2011-04-08 22:35:06,738-0500 INFO LateBindingScheduler JobQueue: 0 2011-04-08 22:35:06,739-0500 INFO LateBindingScheduler JobQueue: 0 2011-04-08 22:35:06,768-0500 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-2-1-8-1-1-1-1302320105917) is /bin/bash _swiftwrap.staging -e /home/ketan/swift-labs/bionimbus-coaster-modftdock/app/modftdock.sh -out stdout.txt -err stderr.txt -i -d output -if input/3bg0-1.pdb|input/4TRA.pdb -of output/3bg0-1_000.dat -k -cdmfile -status provider -a 32 -modulo 0:100 -root 3bg0-1 -static input/3bg0-1.pdb -mobile input/4TRA.pdb -calculate_grid 10 -angle_step 10 -keep 10 -noelec 2011-04-08 22:35:06,789-0500 WARN RemoteConfiguration Find: http://localhost:1984 2011-04-08 22:35:06,790-0500 WARN RemoteConfiguration Find: keepalive(120), reconnect - http://localhost:1984 2011-04-08 22:35:06,793-0500 INFO AbstractKarajanChannel MetaChannel: 1014593217[1248040939: {}] -> null: Disabling heartbeats (disabled in config) 2011-04-08 22:35:06,811-0500 INFO AbstractStreamKarajanChannel$Multiplexer Multiplexer 0 started 2011-04-08 22:35:06,811-0500 INFO AbstractStreamKarajanChannel$Multiplexer (0) Scheduling SC-null for addition 2011-04-08 22:35:06,811-0500 INFO AbstractStreamKarajanChannel$Multiplexer Multiplexer 1 started 2011-04-08 22:35:06,812-0500 INFO AbstractStreamKarajanChannel nullChannel started 2011-04-08 22:35:06,852-0500 INFO ChannelConfigurationCommand Got reply 2011-04-08 22:35:06,852-0500 INFO AbstractStreamKarajanChannel Channel configured 2011-04-08 22:35:06,852-0500 INFO MetaChannel MetaChannel: 1014593217[1248040939: {}] -> null.bind -> SC-null 2011-04-08 22:35:07,567-0500 INFO PutFileHandler Source: /home/ketan/swift-labs/bionimbus-coaster-modftdock/workdir/ftdock-20110408-2235-en2fi70c-g-modftdock-gdyrqf8k/wrapper.log 2011-04-08 22:35:07,567-0500 INFO PutFileHandler Destination: file://localhost/ftdock-20110408-2235-en2fi70c.d/modftdock-gdyrqf8k.info 2011-04-08 22:35:07,576-0500 INFO WeightedHostScoreScheduler CONTACT_SELECTED host=localhost, score=99.854 2011-04-08 22:35:07,583-0500 INFO GridExec TASK_DEFINITION: Task(type=JOB_SUBMISSION, identity=urn:0-2-1-8-1-1-1-1302320105920) is /bin/bash _swiftwrap.staging -e /home/ketan/swift-labs/bionimbus-coaster-modftdock/app/modftdock.sh -out stdout.txt -err stderr.txt -i -d output -if input/3bg0-1.pdb|input/4TRA.pdb -of output/3bg0-1_000.dat -k -cdmfile -status provider -a 32 -modulo 0:100 -root 3bg0-1 -static input/3bg0-1.pdb -mobile input/4TRA.pdb -calculate_grid 10 -angle_step 10 -keep 10 -noelec 2011-04-08 22:35:08,132-0500 INFO PutFileHandler Source: /home/ketan/swift-labs/bionimbus-coaster-modftdock/workdir/ftdock-20110408-2235-en2fi70c-i-modftdock-idyrqf8k/wrapper.log 2011-04-08 22:35:08,133-0500 INFO PutFileHandler Destination: file://localhost/ftdock-20110408-2235-en2fi70c.d/modftdock-idyrqf8k.info 2011-04-08 22:35:08,136-0500 INFO vdl:execute END_FAILURE thread=0-2-1-8-1-1 tr=modftdock 2011-04-08 22:35:08,138-0500 INFO vdl:execute Exception in modftdock: Arguments: [32, -modulo, 0:100, -root, 3bg0-1, -static, input/3bg0-1.pdb, -mobile, input/4TRA.pdb, -calculate_grid, 10, -angle_step, 10, -keep, 10, -noelec] Host: localhost Directory: ftdock-20110408-2235-en2fi70c/jobs/i/modftdock-idyrqf8kTODO: outs ---- Caused by: Job failed with an exit code of 254 Caused by: org.globus.cog.abstraction.impl.common.execution.JobException: Job failed with an exit code of 254 2011-04-08 22:35:08,140-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000053 path=[0] 2011-04-08 22:35:08,140-0500 INFO AbstractDataNode FILENAME dataset=dataset:20110408-2235-a6nbrxh1:720000000053 filename=file://localhost/output/3bg0-1_000.dat 2011-04-08 22:35:08,142-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000043 path=$ 2011-04-08 22:35:08,142-0500 INFO AbstractDataNode CONTAINMENT parent=dataset:20110408-2235-a6nbrxh1:720000000043 child=dataset:20110408-2235-a6nbrxh1:720000000053 2011-04-08 22:35:08,142-0500 INFO AbstractDataNode ROOTPATH dataset=dataset:20110408-2235-a6nbrxh1:720000000053 path=[0] 2011-04-08 22:35:08,142-0500 INFO AbstractDataNode FILENAME dataset=dataset:20110408-2235-a6nbrxh1:720000000053 filename=file://localhost/output/3bg0-1_000.dat 2011-04-08 22:35:08,151-0500 INFO vdl:mains Errors detected. Cleanup not done. 2011-04-08 22:35:08,153-0500 DEBUG VDL2ExecutionContext sys:throw @ vdl.k, line: 165: Execution completed with errors Execution completed with errors at org.globus.cog.karajan.workflow.nodes.FlowNode.fail(FlowNode.java:422) at org.globus.cog.karajan.workflow.nodes.FlowNode.fail(FlowNode.java:426) at org.globus.cog.karajan.workflow.nodes.GenerateErrorNode.post(GenerateErrorNode.java:28) at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192) at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181) at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309) at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58) at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28) at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50) at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:26) at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63) at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:238) at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:289) at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:402) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:343) at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:230) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:44) at edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431) at edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668) at java.lang.Thread.run(Thread.java:662) 2011-04-08 22:35:08,154-0500 INFO ExecutionContext Detailed exception: Execution completed with errors at org.globus.cog.karajan.workflow.nodes.FlowNode.fail(FlowNode.java:422) at org.globus.cog.karajan.workflow.nodes.FlowNode.fail(FlowNode.java:426) at org.globus.cog.karajan.workflow.nodes.GenerateErrorNode.post(GenerateErrorNode.java:28) at org.globus.cog.karajan.workflow.nodes.AbstractSequentialWithArguments.childCompleted(AbstractSequentialWithArguments.java:192) at org.globus.cog.karajan.workflow.nodes.Sequential.notificationEvent(Sequential.java:32) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:340) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.nodes.FlowNode.fireNotificationEvent(FlowNode.java:181) at org.globus.cog.karajan.workflow.nodes.FlowNode.complete(FlowNode.java:309) at org.globus.cog.karajan.workflow.nodes.FlowContainer.post(FlowContainer.java:58) at org.globus.cog.karajan.workflow.nodes.functions.AbstractFunction.post(AbstractFunction.java:28) at org.globus.cog.karajan.workflow.nodes.Sequential.startNext(Sequential.java:50) at org.globus.cog.karajan.workflow.nodes.Sequential.executeChildren(Sequential.java:26) at org.globus.cog.karajan.workflow.nodes.FlowContainer.execute(FlowContainer.java:63) at org.globus.cog.karajan.workflow.nodes.FlowNode.restart(FlowNode.java:238) at org.globus.cog.karajan.workflow.nodes.FlowNode.start(FlowNode.java:289) at org.globus.cog.karajan.workflow.nodes.FlowNode.controlEvent(FlowNode.java:402) at org.globus.cog.karajan.workflow.nodes.FlowNode.event(FlowNode.java:343) at org.globus.cog.karajan.workflow.FlowElementWrapper.event(FlowElementWrapper.java:230) at org.globus.cog.karajan.workflow.events.EventBus.send(EventBus.java:173) at org.globus.cog.karajan.workflow.events.EventTargetPair.run(EventTargetPair.java:44) at edu.emory.mathcs.backport.java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:431) at edu.emory.mathcs.backport.java.util.concurrent.FutureTask.run(FutureTask.java:166) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:643) at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:668) at java.lang.Thread.run(Thread.java:662) 2011-04-08 22:35:08,154-0500 DEBUG Loader Swift finished with errors