[Swift-user] gsiftp filesystem mapper removes leading slash

[Allan Espinosa]

Hi,

I am trying to stage input data from a remote site to itself using
this workflow:
type database;
type query;
type output;
type error;

(output out, error err) blastall(query i, string pref, database db[]) {
  app {
    blastall "-p" "blastp" "-F" "F" "-d" pref "-i" @filename(i) "-v"
"300" "-b" "300" "-m8" "-o" @filename(out) stderr=@filename(err);
  }
}

string pirpref = "/work/01035/tg802895/pir/UNIPROT_for_blast_14.0.seq";
database pir[] <filesys_mapper;location="gsiftp://gridftp.ranger.tacc.teragrid.org/work/01035/tg802895/pir",
pattern="UNIPROT_for_blast_14.0.seq*">;
output out[] <ext;exec="mapper-out.sh">;
error err[] <ext;exec="mapper-err.sh">;
query input[] <ext;exec="mapper-in.sh">;

foreach data ,i in input {
  (out[i],err[i]) = blastall(data, pirpref, pir);
}


But gridftp internals in swift reports that it cannot get a directory
listing of "work/01035/tg802895/pir".  I was thinking that maybe the
leading slashes were removed.  Below is the program output:
~/swift/vdsk/bin/swift -config swift.properties -sites.file sites.xml
-tc.file tc.data blast.swift
Swift svn swift-r2490 cog-r2271

RunID: 20090203-1540-f00ydqsf
Progress:
Execution failed:
        java.lang.RuntimeException:
org.globus.cog.abstraction.impl.file.FileResourceException: Could not
get list of files in work/01035/tg802895/pir from server
Caused by:
        Server refused performing the request. Custom message:  (error
code 1) [Nested exception message:  Custom message: Unexpected reply:
500-Command failed. : System error in stat: No such file or directory
500-A system call failed: No such file or directory
500-
500 End.]
make: *** [remote] Error 2

but i was able to make a regular gridftp session:
 uberftp gridftp.ranger.tacc.teragrid.org
220 gridftp2.ranger.tacc.utexas.edu GridFTP Server 2.8 (gcc64,
1217607445-63) [Globus Toolkit 4.0.8] ready.
230 User tg802895 logged in.
uberftp> cd /work/01035/tg802895/pir
uberftp> ls
-rw-------  1  tg802895  G-81621  204106872 Nov 12 21:44
UNIPROT_for_blast_14.0.seq.00.phr
-rw-------  1  tg802895  G-81621   23001752 Nov 12 21:45
UNIPROT_for_blast_14.0.seq.00.pin
-rw-------  1  tg802895  G-81621  999999669 Nov 12 21:45
UNIPROT_for_blast_14.0.seq.00.psq
...

logfile: http://www.ci.uchicago.edu/~aespinosa/swift/blast-20090203-1540-f00ydqsf.log
sites.xml:
<config>

  <pool handle="RANGER">
    <profile namespace="karajan" key="initialScore">2</profile>
     <profile namespace="karajan" key="jobThrottle">1</profile>
     <filesystem provider="coaster"
url="gt2://gatekeeper.ranger.tacc.teragrid.org"/>
     <profile namespace="globus" key="coastersPerNode">16</profile>
     <execution provider="coaster"
url="gatekeeper.ranger.tacc.teragrid.org" jobManager="gt2:gt2:SGE"/>
     <workdirectory>/work/01035/tg802895</workdirectory>
  </pool>
</config>