This is a multi-part message in MIME format. ------=_NextPart_000_00F7_01C3AE2F.19A9A4F0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable 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 ------=_NextPart_000_00F7_01C3AE2F.19A9A4F0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML><HEAD> <META http-equiv=3DContent-Type content=3D"text/html; = charset=3Diso-8859-1"> <META content=3D"MSHTML 6.00.2800.1276" name=3DGENERATOR> <STYLE></STYLE> </HEAD> <BODY bgColor=3D#ffffff> <DIV><FONT face=3DArial size=3D2>Hi,</FONT></DIV> <DIV><FONT face=3DArial size=3D2></FONT> </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> </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] ObjMgrChoice: pointer [0] type [1] not = found</FONT></DIV> <DIV><FONT face=3DArial size=3D2></FONT> </DIV> <DIV><FONT face=3DArial size=3D2></FONT> </DIV> <DIV><FONT face=3DArial size=3D2></FONT> </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> </DIV> <DIV><FONT face=3DArial size=3D2>[0] 0.040438 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] 0.143636 <BR>(0) done initializing=20 ncbi.<BR>[0] 0.302399 Init blast error code=20 0<BR>[0] 0.30255 Received fragments from node=20 1<BR>[0] 0.364905 Received fragments from node=20 2<BR>[0] 0.378383 Received fragments from node=20 3<BR>[0] 0.378404 Received fragments from node=20 4<BR>[0] 0.400909 broadcasting file size of=20 897<BR>[0] 0.401013 file size=20 broadcasted<BR>[0] 0.401043 broadcasting=20 file<BR>[0] 0.401079 file = broadcasted<BR>[0] 0.401132 node 1=20 has fragments 1 4 <BR>[0] 0.401147 node 2 has fragments 2 4=20 <BR>[0] 0.401159 node 3 has fragments 3 4=20 <BR>[0] 0.40117 node 4 has fragments 0 4=20 <BR>[0] 0.401896 Master got message with tag 10 from node=20 1<BR>[0] 0.40193 Giving node 1 assignment 2 on fragment=20 1<BR>[0] 0.402008 Master got message with tag 10 from node=20 2<BR>[0] 0.402022 Giving node 2 assignment 2 on fragment=20 2<BR>[0] 0.40207 Master got message with tag 10 from node=20 3<BR>[0] 0.402084 Giving node 3 assignment 2 on fragment=20 3<BR>[0] 0.402133 Master got message with tag 10 from node=20 4<BR>[0] 0.402147 Giving node 4 assignment 2 on fragment=20 0<BR>[0] 7.76659 Master got message with tag 7 from node=20 2<BR>[0] 7.76809 Receiving 1 successful query results=20 (2)<BR>[0] 7.76813 receiveResults(2) to read 1=20 records<BR>[0] 7.76877 (2) read 1 records in 533=20 bytes<BR>[0] 7.7688 Receive was successful -- about to merge=20 (2)<BR>[0] 7.76882 Query results have been=20 merged<BR>[0] 7.80605 Master got message with tag 10 from node = 2<BR>[0] 7.80607 Giving node 2 assignment 2 on fragment=20 4<BR>[0] 7.87957 Master got message with tag 7 from node=20 1<BR>[0] 7.88007 Receiving 1 successful query results=20 (1)<BR>[0] 7.88008 receiveResults(1) to read 1=20 records<BR>[0] 7.88196 (1) read 1 records in 3047=20 bytes<BR>[0] 7.88203 Receive was successful -- about to merge=20 (1)<BR>[0] 7.88461 Query results have been=20 merged<BR>[0] 7.88467 Master got message with tag 10 from node = 1<BR>[0] 7.88469 Giving node 1 assignment 0 on fragment=20 0<BR>[0] 7.94558 Master got message with tag 7 from node=20 3<BR>[0] 7.94657 Receiving 1 successful query results=20 (3)<BR>[0] 7.94658 receiveResults(3) to read 1=20 records<BR>[0] 7.94723 (3) read 1 records in 1029=20 bytes<BR>[0] 7.94727 Receive was successful -- about to merge=20 (3)<BR>[0] 7.94731 Query results have been=20 merged<BR>[0] 7.98606 Master got message with tag 10 from node = 3<BR>[0] 7.98611 Giving node 3 assignment 0 on fragment=20 0<BR>[0] 8.34605 Master got message with tag 7 from node=20 4<BR>[0] 8.34703 Receiving 1 successful query results=20 (4)<BR>[0] 8.34706 receiveResults(4) to read 1=20 records<BR>[0] 8.34893 (4) read 1 records in 3505=20 bytes<BR>[0] 8.34895 Receive was successful -- about to merge=20 (4)<BR>[0] 8.349 Query results have been=20 merged<BR>[0] 8.34903 Master got message with tag 10 from node = 4<BR>[0] 8.34905 Giving node 4 assignment 0 on fragment=20 0<BR>[0] 14.7292 Master got message with tag 7 from node=20 2<BR>[0] 14.7302 Receiving 1 successful query results=20 (2)<BR>[0] 14.7302 receiveResults(2) to read 1=20 records<BR>[0] 14.7321 (2) read 1 records in 3139=20 bytes<BR>[0] 14.7321 Receive was successful -- about to merge=20 (2)<BR>[0] 14.7322 Query results have been=20 merged<BR>[0] 14.7322 Master got message with tag 10 from node = 2<BR>[0] 14.7323 Giving node 2 assignment 0 on fragment=20 0<BR>[0] 14.7323 <<<<<<<<<<< = Start=20 merge=20 >>>>>>>>>>><BR>[0] 14.7323 Ena= bling=20 MPI Distributed DB queries</FONT></DIV></BODY></HTML> ------=_NextPart_000_00F7_01C3AE2F.19A9A4F0--