Hi Aaron, Thanks for the reply. I was able to split the database into 38 fragments.
My next question is: I'm new to this mailing list so maybe this has been answered, sorry in advance. Are there works in progress to split the output processing across the mpi grig. I have clearly hit the limit of user process memory for a 32 bit architecture (>3GB) during output processing. thanks, -- Drew > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] Behalf Of Aaron > Darling > Sent: Wednesday, January 25, 2006 10:25 AM > To: [email protected] > Subject: Re: [Mpiblast-users] mpiformatdb - vertebrate_mammalian > > > Ah. Sorry, I should have looked more closely at your e-mail. > > It seems that you're having issues with NCBI formatdb's > built-in notion > that it shouldn't ever create a fragment larger than 1GB. Whenever > formatdb is about to exceed 1gb in a fragment it > automatically starts a > new fragment. That is why you're ending up with files with > numberings > like 000.00 and 000.01 instead of just 000, 001, ..., 004. > It may be possible to change ncbi/tools/readdb.c in the NCBI > toolbox to > change this behavior. > Specifically, try changing > #define SEQFILE_SIZE_MAX 1000000000UL > to something larger, then recompile the toolbox and relink > mpiblast with > the new toolbox. > > The alternative is to simply make enough fragments so that > each fragment > is less than 1gb in size. mpiblast can handle cases where there are > more fragments than compute nodes/mpi processes. > > -Aaron > > > > Drew Bullard wrote: > > >Hi, > > > >Thanks for the reply. > > > >The disk space has 172GB as shown below. The odd thing about > the 005.ntm is > >that I have requested the data be split in 5 parts, 0-4. > That's why I don't > >understand the 6th part. It is like it created the 6th part > and then tried > >to open the 3rd part (002.ntm). > > > >thanks again, > > > >-- Drew > > > > > > > >>-----Original Message----- > >>From: [EMAIL PROTECTED] > >>[mailto:[EMAIL PROTECTED] > Behalf Of Aaron > >>Darling > >>Sent: Wednesday, January 25, 2006 6:06 AM > >>To: [email protected] > >>Subject: Re: [Mpiblast-users] mpiformatdb - vertebrate_mammalian > >> > >> > >>Hi Drew, > >> > >>The .ntm files are temporary files that the NCBI library uses when > >>constructing the database indices. > >>This seems to be the relevant error message: > >> > >>NOTE: CoreLib [002.003] > >>FileOpen("/opt/blast/newdb/vertebrate_mammalian.002.ntm" > >>,"r") failed > >>ERROR: [000.000] SORTFiles failed, change TMPDIR to a > >>partition with more > >>free s > >>pace or use -s option > >> > >> > >>Is it true that the machine is running out of space in > >>/opt/blast/newdb? It's possible to check drive space on many unix > >>machines with the `df` command. > >> > >>-Aaron > >> > >> > >> > >>Drew Bullard wrote: > >> > >> > >> > >>>Hi all, > >>> > >>>Has anyone successfully formatted the vertebrate_mammalian > >>> > >>> > >>NCBI database > >> > >> > >>>using mpiformatdb. I have tried several iterations to format > >>> > >>> > >>the data into 5 > >> > >> > >>>chunks. > >>> > >>>Here's my latest: > >>> > >>>$ echo $TMPDIR > >>>/opt/blast/tmpdir > >>>$ df -h /opt/blast > >>>Filesystem Size Used Avail Use% Mounted on > >>>api-lcbkup-1:/blast 545G 374G 172G 69% /opt/blast > >>> > >>>$ cat .ncbirc > >>>[NCBI] > >>>Data=/opt/blast/data > >>> > >>>[BLAST] > >>>BLASTDB=/opt/blast/newdb > >>>BLASTMAT=/opt/blast/data > >>> > >>>[mpiBLAST] > >>>Shared=/opt/blast/newdb > >>>Local=/opt/blast/tmpdir > >>> > >>>Here's the database: > >>>$ ls -lh /opt/blast/download/vertebrate_mammalian > >>>-rw-r--r-- 1 dbullard ri 34G Dec 17 05:04 > >>>/opt/blast/download/vertebrate_mammalian > >>> > >>>Here's the command: > >>>mpiformatdb -N 5 -i /opt/blast/download/vertebrate_mammalian -p > >>>F --skip-reorder > >>> > >>>Here's the log: > >>> > >>>========================[ Jan 24, 2006 7:03 AM > >>> > >>> > >>]======================== > >> > >> > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Closing volume /opt/blast/newdb/vertebrate_mammalian.001 with 10402 > >>>sequences, 3 > >>>,873,748,360 letters(.nsq file = 1006885366 bytes; .nhr file > >>> > >>> > >>= 1401461 > >> > >> > >>>bytes) > >>>Formatted 10402 sequences in volume 1 > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Closing volume /opt/blast/newdb/vertebrate_mammalian.002 with 10894 > >>>sequences, 3 > >>>,880,693,254 letters(.nsq file = 1002450993 bytes; .nhr file > >>> > >>> > >>= 1467235 > >> > >> > >>>bytes) > >>>Formatted 10894 sequences in volume 2 > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Closing volume /opt/blast/newdb/vertebrate_mammalian.003 with 8985 > >>>sequences, 3, > >>>912,490,460 letters(.nsq file = 1011952328 bytes; .nhr file > >>> > >>> > >>= 1212563 bytes) > >> > >> > >>>Formatted 8985 sequences in volume 3 > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Closing volume /opt/blast/newdb/vertebrate_mammalian.000 with 9760 > >>>sequences, 3, > >>>914,162,677 letters(.nsq file = 1002394425 bytes; .nhr file > >>> > >>> > >>= 1319243 bytes) > >> > >> > >>>Formatted 9760 sequences in volume 0 > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Closing volume /opt/blast/newdb/vertebrate_mammalian.004 with 8487 > >>>sequences, 3, > >>>925,218,720 letters(.nsq file = 1000860920 bytes; .nhr file > >>> > >>> > >>= 1145719 bytes) > >> > >> > >>>Formatted 8487 sequences in volume 4 > >>>Version 2.2.10 [Oct-19-2004] > >>>Started database file "/opt/blast/download/vertebrate_mammalian" > >>>Formatted 31345 sequences in volume 1 > >>>NOTE: CoreLib [002.003] > >>>FileOpen("/opt/blast/newdb/vertebrate_mammalian.002.ntm" > >>>,"r") failed > >>>ERROR: [000.000] SORTFiles failed, change TMPDIR to a > >>> > >>> > >>partition with more > >> > >> > >>>free s > >>>pace or use -s option > >>> > >>>Here's a listing of the final directory, NOTE the 005.ntm > >>> > >>> > >>file? What is > >> > >> > >>>that? > >>> > >>>$ ls -l /opt/blast/newdb/ > >>>total 6611631 > >>>-rw-r--r-- 1 dbullard ri 1319243 Jan 24 08:05 > >>>vertebrate_mammalian.000.00.nhr > >>>-rw-r--r-- 1 dbullard ri 117228 Jan 24 08:05 > >>>vertebrate_mammalian.000.00.nin > >>>-rw-r--r-- 1 dbullard ri 78080 Jan 24 08:05 > >>>vertebrate_mammalian.000.00.nnd > >>>-rw-r--r-- 1 dbullard ri 356 Jan 24 08:05 > >>>vertebrate_mammalian.000.00.nni > >>>-rw-r--r-- 1 dbullard ri 1955463 Jan 24 08:05 > >>>vertebrate_mammalian.000.00.nsd > >>>-rw-r--r-- 1 dbullard ri 45207 Jan 24 08:05 > >>>vertebrate_mammalian.000.00.nsi > >>>-rw-r--r-- 1 dbullard ri 997954313 Jan 24 08:05 > >>>vertebrate_mammalian.000.00.nsq > >>>-rw-r--r-- 1 dbullard ri 4131317 Jan 24 08:51 > >>>vertebrate_mammalian.000.01.nhr > >>>-rw-r--r-- 1 dbullard ri 376248 Jan 24 08:51 > >>>vertebrate_mammalian.000.01.nin > >>>-rw-r--r-- 1 dbullard ri 250760 Jan 24 08:51 > >>>vertebrate_mammalian.000.01.nnd > >>>-rw-r--r-- 1 dbullard ri 1028 Jan 24 08:51 > >>>vertebrate_mammalian.000.01.nni > >>>-rw-r--r-- 1 dbullard ri 6720507 Jan 24 08:51 > >>>vertebrate_mammalian.000.01.nsd > >>>-rw-r--r-- 1 dbullard ri 156680 Jan 24 08:51 > >>>vertebrate_mammalian.000.01.nsi > >>>-rw-r--r-- 1 dbullard ri 875184322 Jan 24 08:51 > >>>vertebrate_mammalian.000.01.nsq > >>>-rw-r--r-- 1 dbullard ri 1401461 Jan 24 08:04 > >>>vertebrate_mammalian.001.nhr > >>>-rw-r--r-- 1 dbullard ri 124932 Jan 24 08:04 > >>>vertebrate_mammalian.001.nin > >>>-rw-r--r-- 1 dbullard ri 83216 Jan 24 08:04 > >>>vertebrate_mammalian.001.nnd > >>>-rw-r--r-- 1 dbullard ri 372 Jan 24 08:04 > >>>vertebrate_mammalian.001.nni > >>>-rw-r--r-- 1 dbullard ri 2122526 Jan 24 08:04 > >>>vertebrate_mammalian.001.nsd > >>>-rw-r--r-- 1 dbullard ri 49005 Jan 24 08:04 > >>>vertebrate_mammalian.001.nsi > >>>-rw-r--r-- 1 dbullard ri 989185886 Jan 24 08:04 > >>>vertebrate_mammalian.001.nsq > >>>-rw-r--r-- 1 dbullard ri 3618358 Jan 24 08:51 > >>>vertebrate_mammalian.002.nhr > >>>-rw-r--r-- 1 dbullard ri 330624 Jan 24 08:52 > >>>vertebrate_mammalian.002.nin > >>>-rw-r--r-- 1 dbullard ri 220344 Jan 24 08:51 > >>>vertebrate_mammalian.002.nnd > >>>-rw-r--r-- 1 dbullard ri 908 Jan 24 08:51 > >>>vertebrate_mammalian.002.nni > >>>-rw-r--r-- 1 dbullard ri 0 Jan 24 08:51 > >>>vertebrate_mammalian.002.nsd > >>>-rw-r--r-- 1 dbullard ri 648 Jan 24 08:04 > >>>vertebrate_mammalian.002.nsi > >>>-rw-r--r-- 1 dbullard ri 994808643 Jan 24 08:51 > >>>vertebrate_mammalian.002.nsq > >>>-rw-r--r-- 1 dbullard ri 3408746 Jan 24 08:51 > >>>vertebrate_mammalian.003.nhr > >>>-rw-r--r-- 1 dbullard ri 107928 Jan 24 08:05 > >>>vertebrate_mammalian.003.nin > >>>-rw-r--r-- 1 dbullard ri 71880 Jan 24 08:05 > >>>vertebrate_mammalian.003.nnd > >>>-rw-r--r-- 1 dbullard ri 332 Jan 24 08:05 > >>>vertebrate_mammalian.003.nni > >>>-rw-r--r-- 1 dbullard ri 1815511 Jan 24 08:05 > >>>vertebrate_mammalian.003.nsd > >>>-rw-r--r-- 1 dbullard ri 161 Jan 24 08:05 > >>>vertebrate_mammalian.003.nsi > >>>-rw-r--r-- 1 dbullard ri 998850878 Jan 24 08:52 > >>>vertebrate_mammalian.003.nsq > >>>-rw-r--r-- 1 dbullard ri 3653467 Jan 24 08:51 > >>>vertebrate_mammalian.004.nhr > >>>-rw-r--r-- 1 dbullard ri 101952 Jan 24 08:06 > >>>vertebrate_mammalian.004.nin > >>>-rw-r--r-- 1 dbullard ri 67896 Jan 24 08:06 > >>>vertebrate_mammalian.004.nnd > >>>-rw-r--r-- 1 dbullard ri 316 Jan 24 08:06 > >>>vertebrate_mammalian.004.nni > >>>-rw-r--r-- 1 dbullard ri 1705972 Jan 24 08:06 > >>>vertebrate_mammalian.004.nsd > >>>-rw-r--r-- 1 dbullard ri 388 Jan 24 08:06 > >>>vertebrate_mammalian.004.nsi > >>>-rw-r--r-- 1 dbullard ri 999163733 Jan 24 08:51 > >>>vertebrate_mammalian.004.nsq > >>>-rw-r--r-- 1 dbullard ri 3611609 Jan 24 08:51 > >>>vertebrate_mammalian.005.nhr > >>>-rw-r--r-- 1 dbullard ri 0 Jan 24 08:06 > >>>vertebrate_mammalian.005.nin > >>>-rw-r--r-- 1 dbullard ri 871563163 Jan 24 08:52 > >>>vertebrate_mammalian.005.nsq > >>>-rw-r--r-- 1 dbullard ri 5937997 Jan 24 08:52 > >>>vertebrate_mammalian.005.ntm > >>>-rw-r--r-- 1 dbullard ri 339 Jan 24 08:51 > >>>vertebrate_mammalian.nal > >>> > >>>Here's the nal file: > >>>$ cat /opt/blast/newdb/*.nal > >>># > >>># Alias file created Tue Jan 24 08:51:22 2006 > >>># > >>># > >>>TITLE /opt/blast/newdb/vertebrate_mammalian > >>># > >>>DBLIST /opt/blast/newdb/vertebrate_mammalian.000 > >>>/opt/blast/newdb/vertebrate_mammalian.001 > >>>/opt/blast/newdb/vertebrate_mammalian.002 > >>>/opt/blast/newdb/vertebrate_mammalian.003 > >>>/opt/blast/newdb/vertebrate_mammalian.004 > >>># > >>>#GILIST > >>># > >>>#OIDLIST > >>># > >>> > >>>thanks, > >>>-- Drew > >>> > >>> > >>> > >>> > >>>------------------------------------------------------- > >>>This SF.net email is sponsored by: Splunk Inc. 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