[Bioclusters] mpiblast on the smallest possible cluster

[Fernan Aguero]

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+----[ To bioclusters <fernan@iib.unsam.edu.ar> (28.Jan.2004 11:05):
|
| +----[ Joe Landman <landman@scalableinformatics.com> (28.Jan.2004 03:36):
| |
| | Hi Fernan
| 
| Hi Joe, and thanks for your reply.

[snipped]
  
| This is also reflected in the mpiblast output that I get
| using --debug (attached to this message).
| 
|
+----]

Forgot to attach the file. My fault. Here it is,

Fernan

-- 
F e r n a n   A g u e r o
http://genoma.unsam.edu.ar/~fernan

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Content-Disposition: attachment; filename="mpiblast.out"

Script started on Wed Jan 28 10:52:40 2004
You have 56 mail messages.
[fernan@pi] mpirun -np 2 /usr/local/bin/mpiblast --debug -i query_1.fa -d sprot. 
fasta -p blastp -o query.mpiblast ; exit
[0]	0.001786[	initializing ncbi ...blastall -i query_1.fa -p blastp -o query.mpiblast -d /databases/sprot.fasta 
[0]	0.015419	
(01]	0.002395	Temp name base: /usr/local/databases/sprot.fastaXXXXXX
[1]	0.013901	Got temp name: /usr/local/databases/sprot.fastaK2qJKa
[1]	0.025655	Temp name base: /usr/local/databases/query.mpiblast.1XXXXXX
[1]	0.029522	Got temp name: /usr/local/databases/query.mpiblast.10k3pgO
[1) done initializing ncbi.
]	0.032222	Temp name base: /usr/local/databases/query_1.faXXXXXX
[1]	0.035613	Got temp name: /usr/local/databases/query_1.fa02gGWq
[1]	0.038407	initializing ncbi ...blastall -p blastp[0]	0.060075	Init blast error code 0
[0]	0.069457	Received fragments from node 1
[0]	0.077183	broadcasting file size of 995
[ -z 51029181 -i /usr/local/databases/query_1.fa02gGWq -m 11 -o /usr/local/databases/query.mpiblast.10k3pgO -d /usr/local/databases/sprot.fastaK2qJKa -J 
[1]	0.043391	
(1) done initializing ncbi.
[1]	0.051084	Fragment list sent.
[1]	0.053768	waiting for file size broadcast
[1]	0.083969	received file size broadcast of 995
[1]	0]	0.084502	file size broadcasted
[0]	0.097861	broadcasting file
[0]	0.1053630.087141	opening receive file /usr/local/databases/query_1.fa02gGWq
[1]	0.090229	receiving file to /usr/local/databases/query_1.fa02gGWq
[1]	0.105868	received file broadcast
[1]	0.108453	file broadcasted
[0]	0.118464	node 1 has fragments 0 1 
[0]	0.13679	Master got message with tag 10 from node 1
[0]	0.144054	Giving node 1 assignment 2 on fragment 0
	Query file received as /usr/local/databases/query_1.fa
[1]	0.111766	Idle message sent
[1]	0.152809	Assignment received is 2
[1]	0.155304	got fragment assignment 0
[1]	0.159049	node 1 fragid: 00
[1]	0.162068	node 1 Executing BLAST search
[[0]	16.3238	Master got message with tag 7 from node 1
[0]	16.3274	Receiving 1 successful query results (1)
[0]	16.3296	receiveResults(1) to read 1 records
1]	16.3194	node 1 blast retcode= 0
[1]	16.3231	Sending 1 successful query results
[1]	16.3301	Idle message sent[
0]	16.3368	(1) read 1 records in 1104 bytes
[0]	16.342	Receive was successful -- about to merge (1)
[0]	16.3421	Query results have been merged
[0]	16.3423	Master got message with tag 10 from node 1
[0]	16.3424	Giving node 1 assignment 2 on fragment 1
[1]	16.3432	Assignment received is 2
[1]	16.346	got fragment assignment 1
[1]	16.3495	node 1 fragid: 01
[1]	16.3531	node 1 Executing BLAST search
[[0]	32.2477	Master got message with tag 7 from node 1
[0]	32.2505	Receiving 1 successful query results (1)
[0]	32.2539	receiveResults(1) to read 1 records
1]	32.2415	node 1 blast retcode= 0
[1]	32.2451	Sending 1 successful query results
[1]	32.2591	Idle message sent[0]	32.268	(1) read 1 records in 5238 bytes
[0]	32.2682	Receive was successful -- about to merge (1)
[0]	32.2684	Query results have been merged
[0]	32.2686	Master got message with tag 10 from node 1
[0]	32.2687	Giving node 1 assignment 0 on fragment 0
[0]	32.2689	<<<<<<<<<<< Start merge >>>>>>>>>>>
[0]	32.269	Enabling MPI Distributed DB queries

[1]	32.2698	Assignment received is 0
[1]	32.2735	node 1 fragid: 00
[1]	32.2765	node 1 fragid: 01
[1]	32.2801	Enabling Bioseq Fetch
[1]	32.2842	Bioseq Fetch Enabled
[1]	32.2868	Looking up bioseq
[1]	32.299	Looking up bioseq
[1]	32.3095	Looking up bioseq
[1]	32.316	Looking up bioseq
[1]	32.3257	Looking up bioseq
[1]	32.3351	Looking up bioseq
[1]	32.347	Looking up bioseq
[1]	32.3567	Looking up bioseq
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mpiblast in free(): warning: chunk is already free[1]	32.3669	Looking up bioseq
[1]	32.3726	Looking up bioseq
[1]	32.3803	Looking up bioseq

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mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
mpiblast in free(): warning: chunk is already free
[0]	32.5237	*********** Finished merge ***********
[0]	32.5242	rank 0 exiting successfully
[0]	32.5243	MPI startup  time is 0
[1]	32.5247	Assignment received is 3
[1]	32.5559	rank 1 exiting successfully
[1]	32.5588	MPI startup  time is 0.015625
exit

Script done on Wed Jan 28 10:53:17 2004

--Qxx1br4bt0+wmkIi--