[Bioclusters] help with running mpiBLAST-1.2.0

Richard Huang bioclusters@bioinformatics.org
Tue, 18 Nov 2003 23:53:01 -0800


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Hi,

I'm trying to run mpiBLAST on the nr peptide database using the first =
entry as the query. I've installed the NCBI toolbox and also MPI. I get =
the following error when I try to run:

[ryhuang@frontend-0 mpiBLAST-1.2.0]$ mpirun -np 5 -nolocal -machinefile =
machines /home/ryhuang/mpiBLAST-1.2.0/bin/mpiblast --debug =
--log-file=3D/home/ryhuang/mpiBLAST-1.2.0/log3 -p blastp -d nr_092602.fa =
-i query2.fas -o result.txt
logging to /home/ryhuang/mpiBLAST-1.2.0/log3.1
logging to /home/ryhuang/mpiBLAST-1.2.0/log3.2
logging to logging to /home/ryhuang/mpiBLAST-1.2.0/log3.4
/home/ryhuang/mpiBLAST-1.2.0/log3.0
logging to /home/ryhuang/mpiBLAST-1.2.0/log3.3
[blastall] ERROR: ncbiapi [000.000]  ObjMgrChoice: pointer [0] type [1] =
not found



The log file from the master node shows the following:

[0] 0.040438 initializing ncbi ...blastall -p blastp -i query2.fas -o =
result.txt -d /home/ryhuang/mpiBLAST-1.2.0/share/nr_092602.fa=20
[0] 0.143636=20
(0) done initializing ncbi.
[0] 0.302399 Init blast error code 0
[0] 0.30255 Received fragments from node 1
[0] 0.364905 Received fragments from node 2
[0] 0.378383 Received fragments from node 3
[0] 0.378404 Received fragments from node 4
[0] 0.400909 broadcasting file size of 897
[0] 0.401013 file size broadcasted
[0] 0.401043 broadcasting file
[0] 0.401079 file broadcasted
[0] 0.401132 node 1 has fragments 1 4=20
[0] 0.401147 node 2 has fragments 2 4=20
[0] 0.401159 node 3 has fragments 3 4=20
[0] 0.40117 node 4 has fragments 0 4=20
[0] 0.401896 Master got message with tag 10 from node 1
[0] 0.40193 Giving node 1 assignment 2 on fragment 1
[0] 0.402008 Master got message with tag 10 from node 2
[0] 0.402022 Giving node 2 assignment 2 on fragment 2
[0] 0.40207 Master got message with tag 10 from node 3
[0] 0.402084 Giving node 3 assignment 2 on fragment 3
[0] 0.402133 Master got message with tag 10 from node 4
[0] 0.402147 Giving node 4 assignment 2 on fragment 0
[0] 7.76659 Master got message with tag 7 from node 2
[0] 7.76809 Receiving 1 successful query results (2)
[0] 7.76813 receiveResults(2) to read 1 records
[0] 7.76877 (2) read 1 records in 533 bytes
[0] 7.7688 Receive was successful -- about to merge (2)
[0] 7.76882 Query results have been merged
[0] 7.80605 Master got message with tag 10 from node 2
[0] 7.80607 Giving node 2 assignment 2 on fragment 4
[0] 7.87957 Master got message with tag 7 from node 1
[0] 7.88007 Receiving 1 successful query results (1)
[0] 7.88008 receiveResults(1) to read 1 records
[0] 7.88196 (1) read 1 records in 3047 bytes
[0] 7.88203 Receive was successful -- about to merge (1)
[0] 7.88461 Query results have been merged
[0] 7.88467 Master got message with tag 10 from node 1
[0] 7.88469 Giving node 1 assignment 0 on fragment 0
[0] 7.94558 Master got message with tag 7 from node 3
[0] 7.94657 Receiving 1 successful query results (3)
[0] 7.94658 receiveResults(3) to read 1 records
[0] 7.94723 (3) read 1 records in 1029 bytes
[0] 7.94727 Receive was successful -- about to merge (3)
[0] 7.94731 Query results have been merged
[0] 7.98606 Master got message with tag 10 from node 3
[0] 7.98611 Giving node 3 assignment 0 on fragment 0
[0] 8.34605 Master got message with tag 7 from node 4
[0] 8.34703 Receiving 1 successful query results (4)
[0] 8.34706 receiveResults(4) to read 1 records
[0] 8.34893 (4) read 1 records in 3505 bytes
[0] 8.34895 Receive was successful -- about to merge (4)
[0] 8.349 Query results have been merged
[0] 8.34903 Master got message with tag 10 from node 4
[0] 8.34905 Giving node 4 assignment 0 on fragment 0
[0] 14.7292 Master got message with tag 7 from node 2
[0] 14.7302 Receiving 1 successful query results (2)
[0] 14.7302 receiveResults(2) to read 1 records
[0] 14.7321 (2) read 1 records in 3139 bytes
[0] 14.7321 Receive was successful -- about to merge (2)
[0] 14.7322 Query results have been merged
[0] 14.7322 Master got message with tag 10 from node 2
[0] 14.7323 Giving node 2 assignment 0 on fragment 0
[0] 14.7323 <<<<<<<<<<< Start merge >>>>>>>>>>>
[0] 14.7323 Enabling MPI Distributed DB queries
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<DIV><FONT face=3DArial size=3D2>Hi,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I'm trying to run mpiBLAST on the nr =
peptide=20
database using the first entry as the query. I've installed the NCBI =
toolbox and=20
also MPI. I get the following error when I try to run:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>[ryhuang@frontend-0 mpiBLAST-1.2.0]$ =
mpirun -np 5=20
-nolocal -machinefile machines /home/ryhuang/mpiBLAST-1.2.0/bin/mpiblast =
--debug=20
--log-file=3D/home/ryhuang/mpiBLAST-1.2.0/log3 -p blastp -d nr_092602.fa =
-i=20
query2.fas -o result.txt<BR>logging to=20
/home/ryhuang/mpiBLAST-1.2.0/log3.1<BR>logging to=20
/home/ryhuang/mpiBLAST-1.2.0/log3.2<BR>logging to logging to=20
/home/ryhuang/mpiBLAST-1.2.0/log3.4<BR>/home/ryhuang/mpiBLAST-1.2.0/log3.=
0<BR>logging=20
to /home/ryhuang/mpiBLAST-1.2.0/log3.3<BR>[blastall] ERROR: ncbiapi=20
[000.000]&nbsp; ObjMgrChoice: pointer [0] type [1] not =
found</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>The log file from the master node shows =
the=20
following:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>[0]&nbsp;0.040438&nbsp;initializing =
ncbi=20
...blastall -p blastp -i query2.fas -o result.txt -d=20
/home/ryhuang/mpiBLAST-1.2.0/share/nr_092602.fa=20
<BR>[0]&nbsp;0.143636&nbsp;<BR>(0) done initializing=20
ncbi.<BR>[0]&nbsp;0.302399&nbsp;Init blast error code=20
0<BR>[0]&nbsp;0.30255&nbsp;Received fragments from node=20
1<BR>[0]&nbsp;0.364905&nbsp;Received fragments from node=20
2<BR>[0]&nbsp;0.378383&nbsp;Received fragments from node=20
3<BR>[0]&nbsp;0.378404&nbsp;Received fragments from node=20
4<BR>[0]&nbsp;0.400909&nbsp;broadcasting file size of=20
897<BR>[0]&nbsp;0.401013&nbsp;file size=20
broadcasted<BR>[0]&nbsp;0.401043&nbsp;broadcasting=20
file<BR>[0]&nbsp;0.401079&nbsp;file =
broadcasted<BR>[0]&nbsp;0.401132&nbsp;node 1=20
has fragments 1 4 <BR>[0]&nbsp;0.401147&nbsp;node 2 has fragments 2 4=20
<BR>[0]&nbsp;0.401159&nbsp;node 3 has fragments 3 4=20
<BR>[0]&nbsp;0.40117&nbsp;node 4 has fragments 0 4=20
<BR>[0]&nbsp;0.401896&nbsp;Master got message with tag 10 from node=20
1<BR>[0]&nbsp;0.40193&nbsp;Giving node 1 assignment 2 on fragment=20
1<BR>[0]&nbsp;0.402008&nbsp;Master got message with tag 10 from node=20
2<BR>[0]&nbsp;0.402022&nbsp;Giving node 2 assignment 2 on fragment=20
2<BR>[0]&nbsp;0.40207&nbsp;Master got message with tag 10 from node=20
3<BR>[0]&nbsp;0.402084&nbsp;Giving node 3 assignment 2 on fragment=20
3<BR>[0]&nbsp;0.402133&nbsp;Master got message with tag 10 from node=20
4<BR>[0]&nbsp;0.402147&nbsp;Giving node 4 assignment 2 on fragment=20
0<BR>[0]&nbsp;7.76659&nbsp;Master got message with tag 7 from node=20
2<BR>[0]&nbsp;7.76809&nbsp;Receiving 1 successful query results=20
(2)<BR>[0]&nbsp;7.76813&nbsp;receiveResults(2) to read 1=20
records<BR>[0]&nbsp;7.76877&nbsp;(2) read 1 records in 533=20
bytes<BR>[0]&nbsp;7.7688&nbsp;Receive was successful -- about to merge=20
(2)<BR>[0]&nbsp;7.76882&nbsp;Query results have been=20
merged<BR>[0]&nbsp;7.80605&nbsp;Master got message with tag 10 from node =

2<BR>[0]&nbsp;7.80607&nbsp;Giving node 2 assignment 2 on fragment=20
4<BR>[0]&nbsp;7.87957&nbsp;Master got message with tag 7 from node=20
1<BR>[0]&nbsp;7.88007&nbsp;Receiving 1 successful query results=20
(1)<BR>[0]&nbsp;7.88008&nbsp;receiveResults(1) to read 1=20
records<BR>[0]&nbsp;7.88196&nbsp;(1) read 1 records in 3047=20
bytes<BR>[0]&nbsp;7.88203&nbsp;Receive was successful -- about to merge=20
(1)<BR>[0]&nbsp;7.88461&nbsp;Query results have been=20
merged<BR>[0]&nbsp;7.88467&nbsp;Master got message with tag 10 from node =

1<BR>[0]&nbsp;7.88469&nbsp;Giving node 1 assignment 0 on fragment=20
0<BR>[0]&nbsp;7.94558&nbsp;Master got message with tag 7 from node=20
3<BR>[0]&nbsp;7.94657&nbsp;Receiving 1 successful query results=20
(3)<BR>[0]&nbsp;7.94658&nbsp;receiveResults(3) to read 1=20
records<BR>[0]&nbsp;7.94723&nbsp;(3) read 1 records in 1029=20
bytes<BR>[0]&nbsp;7.94727&nbsp;Receive was successful -- about to merge=20
(3)<BR>[0]&nbsp;7.94731&nbsp;Query results have been=20
merged<BR>[0]&nbsp;7.98606&nbsp;Master got message with tag 10 from node =

3<BR>[0]&nbsp;7.98611&nbsp;Giving node 3 assignment 0 on fragment=20
0<BR>[0]&nbsp;8.34605&nbsp;Master got message with tag 7 from node=20
4<BR>[0]&nbsp;8.34703&nbsp;Receiving 1 successful query results=20
(4)<BR>[0]&nbsp;8.34706&nbsp;receiveResults(4) to read 1=20
records<BR>[0]&nbsp;8.34893&nbsp;(4) read 1 records in 3505=20
bytes<BR>[0]&nbsp;8.34895&nbsp;Receive was successful -- about to merge=20
(4)<BR>[0]&nbsp;8.349&nbsp;Query results have been=20
merged<BR>[0]&nbsp;8.34903&nbsp;Master got message with tag 10 from node =

4<BR>[0]&nbsp;8.34905&nbsp;Giving node 4 assignment 0 on fragment=20
0<BR>[0]&nbsp;14.7292&nbsp;Master got message with tag 7 from node=20
2<BR>[0]&nbsp;14.7302&nbsp;Receiving 1 successful query results=20
(2)<BR>[0]&nbsp;14.7302&nbsp;receiveResults(2) to read 1=20
records<BR>[0]&nbsp;14.7321&nbsp;(2) read 1 records in 3139=20
bytes<BR>[0]&nbsp;14.7321&nbsp;Receive was successful -- about to merge=20
(2)<BR>[0]&nbsp;14.7322&nbsp;Query results have been=20
merged<BR>[0]&nbsp;14.7322&nbsp;Master got message with tag 10 from node =

2<BR>[0]&nbsp;14.7323&nbsp;Giving node 2 assignment 0 on fragment=20
0<BR>[0]&nbsp;14.7323&nbsp;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt;&lt; =
Start=20
merge=20
&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;<BR>[0]&nbsp;14.7323&nbsp;Ena=
bling=20
MPI Distributed DB queries</FONT></DIV></BODY></HTML>

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