[Swift-commit] r2443 - text/hpdc09submission

[noreply at svn.ci.uchicago.edu]

Author: wilde
Date: 2009-01-14 12:23:47 -0600 (Wed, 14 Jan 2009)
New Revision: 2443

Modified:
   text/hpdc09submission/paper.latex
Log:
Added a stub of an example for BLAST - just copied Allan's notes from SWFT wiki into here.


Modified: text/hpdc09submission/paper.latex
===================================================================
--- text/hpdc09submission/paper.latex	2009-01-14 14:38:43 UTC (rev 2442)
+++ text/hpdc09submission/paper.latex	2009-01-14 18:23:47 UTC (rev 2443)
@@ -865,10 +865,55 @@
 heterogeneity between sites. Large number of sites; automatic site file
 selection; and automatic app deployment there.
 
+\subsection{BLAST Application Example}
+
+The following is notes from the Wiki by Allan: needs much refinement, adding here as a placeholder.
+
+\begin{verbatim}
+type database;
+type query;
+type output;
+type error;
+
+(output out, error err) blastall(query i, database db) {
+ app {
+   blastall "-p" "blastp" "-F" "F" "-d" @filename(db) "-i"
+ at filename(i) "-v" "300" "-b" "300" "-m8" "-o" @filename(out)
+stderr=@filename(err);
+ }
+}
+
+database pir <simple_mapper;prefix="/disks/ci-gpfs/swift/blast/pir/UNIPROT_for_blast_14.0.seq">;
+output out <"test.out">;
+query i <"test.in">;
+error err <"test.err">;
+(out,err) = blastall(i, pir);
+\end{verbatim}
+
+The trick here is that blastall reads takes the prefix name of the database files that it will read (.phr, .seq and .pin files). So i made a dummy file called "UNIPROT_for_blast_14.0.seq" to satisfy the data dependency . So here is the final list of my files:
+
+\begin{verbatim}
+-rw-r--r--  1 aespinosa ci-users         0 Nov 15 13:49 UNIPROT_for_blast_14.0.seq
+-rw-r--r--  1 aespinosa ci-users 204106872 Oct 20 16:50 UNIPROT_for_blast_14.0.seq.00.phr
+-rw-r--r--  1 aespinosa ci-users  23001752 Oct 20 16:50 UNIPROT_for_blast_14.0.seq.00.pin
+-rw-r--r--  1 aespinosa ci-users 999999669 Oct 20 16:51 UNIPROT_for_blast_14.0.seq.00.psq
+-rw-r--r--  1 aespinosa ci-users 233680738 Oct 20 16:51 UNIPROT_for_blast_14.0.seq.01.phr
+-rw-r--r--  1 aespinosa ci-users  26330312 Oct 20 16:51 UNIPROT_for_blast_14.0.seq.01.pin
+-rw-r--r--  1 aespinosa ci-users 999999864 Oct 20 16:52 UNIPROT_for_blast_14.0.seq.01.psq
+-rw-r--r--  1 aespinosa ci-users  21034886 Oct 20 16:52 UNIPROT_for_blast_14.0.seq.02.phr
+-rw-r--r--  1 aespinosa ci-users   2370216 Oct 20 16:52 UNIPROT_for_blast_14.0.seq.02.pin
+-rw-r--r--  1 aespinosa ci-users 103755125 Oct 20 16:52 UNIPROT_for_blast_14.0.seq.02.psq
+-rw-r--r--  1 aespinosa ci-users       208 Oct 20 16:52 UNIPROT_for_blast_14.0.seq.pal
+\end{verbatim}
+
+I looked at the dock6 documentation for OSG. It looks that it recommends to transfer the datafiles to OSG sites manually via globus-url-copy. By my understanding of how swift works, it should be able to transfer my local files to the selected sites. I have yet to try this and will look more on examples in the data management side of Swift.
+
+Do you know other users who went in this approach? The documentation has only a few examples in managing data. I'll check the swift Wiki later and see what material we have and also post this email/ notes. 
+
 \subsection{fMRI Application Example}
 
 \begin{figure}[htbp]
-\includegraphics{IMG_fmridataset}
+\includegraphics[scale=0.5]{IMG_fmridataset}
 \caption{FMRI application}
 \end{figure}