This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C3198D.324A63C8 Content-Type: text/plain; charset="big5" I'm not sure why you don't have an nr.dbs, I just started installing mpiblast (taking most of the day so far) and I did get an nr.dbs in my shared storage directory. I have other problems though, for instance I get a 3 line (null).pal in my shared storage directory instead of the nr.pal it is looking for. Anyone know what happened with this? In addition, when I run mpiformatdb and tell it to break it into 20 chunks it creates 21, from 0 to 20. Pretty annoying. The other problem I ran into when I was running mpiformatdb (on nr, is there preformatted stuff I can download now?) is that it took really long. Sure enough, it was only running on one machine and when I peaked at the mpiformatdb.cpp I noticed there were no MPI_ function calls...?! No big deal, but I find the name of the program somewhat misleading. Anybody solve these problems? I'm using 1.1.0. I actually tried using an earlier version of mpiblast before but I couldn't get it to compile. Still seems more promising than the non-MPI query splitting variant I have been using in the past since each mini database should be able to fit into RAM on our nodes. -John -----Original Message----- From: kwLee [mailto:g912803@student.thu.edu.tw] Sent: Monday, May 12, 2003 10:32 PM To: bioclusters@bioinformatics.org Subject: [Bioclusters] [mpiBLAST]how to "mpiformatdb nr"~~?THX~ i think i have installed mpiblast already i can use "mpiformatdb" to format yeast.nt database into same fragment then use "mpiblast blastn" to search sequence so i try "nr" database i have formated nr database(use mpiformat) but when i use "mpiblast blastp" to search it says that "ERROR opening...nr.dbs" i don't know why it has no nr.dbs THX~ ------_=_NextPart_001_01C3198D.324A63C8 Content-Type: text/html; charset="big5" <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML><HEAD> <META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=big5"> <META content="MSHTML 6.00.2800.1141" name=GENERATOR> <STYLE></STYLE> </HEAD> <BODY bgColor=#ffffff> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>I'm not sure why you don't have an nr.dbs, I just started installing mpiblast (taking most of the day so far)</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>and I did get an nr.dbs in my shared storage directory.</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2></FONT></SPAN> </DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>I have other problems though, for instance I get a 3 line (null).pal in my shared storage directory instead of the</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>nr.pal it is looking for. Anyone know what happened with this?</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2></FONT></SPAN> </DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>In addition, when I run mpiformatdb and tell it to break it into 20 chunks it creates 21, from 0 to 20.</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>Pretty annoying.</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2></FONT></SPAN> </DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>The other problem I ran into when I was running mpiformatdb (on nr, is there preformatted stuff I can</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2> download now?) is that it took really long. Sure enough, it was only running on one machine and when I</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>peaked at the mpiformatdb.cpp I noticed there were no MPI_ function calls...?! No big deal, but I find the</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>name of the program somewhat misleading.</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2></FONT></SPAN> </DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>Anybody solve these problems? I'm using 1.1.0. I actually tried using an earlier version of mpiblast before but I couldn't get it to</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>compile. Still seems more promising than the non-MPI query splitting variant I have been using in the past since each mini</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2>database should be able to fit into RAM on our nodes.</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2></FONT></SPAN> </DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2> -John</FONT></SPAN></DIV> <DIV><SPAN class=758550920-13052003><FONT face=Arial color=#0000ff size=2></FONT></SPAN> </DIV> <BLOCKQUOTE dir=ltr style="MARGIN-RIGHT: 0px"> <DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma size=2>-----Original Message-----<BR><B>From:</B> kwLee [mailto:g912803@student.thu.edu.tw]<BR><B>Sent:</B> Monday, May 12, 2003 10:32 PM<BR><B>To:</B> bioclusters@bioinformatics.org<BR><B>Subject:</B> [Bioclusters] [mpiBLAST]how to "mpiformatdb nr"~~?THX~<BR><BR></FONT></DIV> <DIV><FONT size=2>i think i have installed mpiblast already</FONT></DIV> <DIV>i can use "mpiformatdb" to format yeast.nt database into same fragment</DIV> <DIV>then use "mpiblast blastn" to search sequence</DIV> <DIV>so i try "nr" database</DIV> <DIV>i have formated nr database(use mpiformat)</DIV> <DIV>but when i use "mpiblast blastp" to search</DIV> <DIV>it says that "ERROR opening...nr.dbs"</DIV> <DIV><FONT size=2>i don't know why it has no nr.dbs</FONT></DIV> <DIV>THX~</DIV> <DIV> </DIV></BLOCKQUOTE></BODY></HTML> ------_=_NextPart_001_01C3198D.324A63C8--