From schmidt at stein.cshl.org  Tue Oct  2 15:55:27 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Tue, 02 Oct 2001 15:55:27 -0400
Subject: gramene -> gruyere and chevre
Message-ID: <3BBA1BAF.F52FE5ED@cshl.org>

Instead of
http://www.gramene.org:8000/perl/contigview   etc.
we now have
http://www.gramene.org/perl/contigview   etc.

Also, the contig viewer,  and other ensembl pages on chevre
are accessible from outside the firewall by

http://www.brie2:8085/perl/contigview  etc.

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


From lstein at stein.cshl.org  Tue Oct  2 18:07:11 2001
From: lstein at stein.cshl.org (Lincoln Stein)
Date: Tue, 2 Oct 2001 18:07:11 -0400
Subject: gramene -> gruyere and chevre
In-Reply-To: <3BBA1BAF.F52FE5ED@cshl.org>
References: <3BBA1BAF.F52FE5ED@cshl.org>
Message-ID: <15290.14991.896036.383996@formaggio.cshl.org>

Very nice!

Lincoln

Steven Schmidt writes:
 > Instead of
 > http://www.gramene.org:8000/perl/contigview   etc.
 > we now have
 > http://www.gramene.org/perl/contigview   etc.
 > 
 > Also, the contig viewer,  and other ensembl pages on chevre
 > are accessible from outside the firewall by
 > 
 > http://www.brie2:8085/perl/contigview  etc.
 > 
 > --
 > Steven Schmidt
 > snp.cshl.org     www.gramene.org
 > Cold Spring Harbor Laboratory
 > 516-367-6977

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY

NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
PLEASE WRITE FOR DETAILS.
========================================================================


From schmidt at stein.cshl.org  Wed Oct  3 16:26:50 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Wed, 03 Oct 2001 16:26:50 -0400
Subject: Permissions
Message-ID: <3BBB748A.9F25776E@cshl.org>

All the gramene project directories have group gramene and permissions
g+s
so that files created in them will also have group gramene.

All gramene files should be group readable and writeable.

Please make sure you keep this true:

Your umask should be 002, not 022  (since the default group is your
own private one, this does not open anything up)
Put  umask 002 in your
.cshrc file  (csh or tcsh users)
.bash_profile  file (bash users)
.profile   file    (ksh users)
This is probably correct on swiss and chevre, and probably needs to be
fixed
on brie and brie2.

If you copy files to a gramene directory using cp -p
then they will keep their original group.  So you must
chgrp gramene ...  before or after copying.

Some directories used by web servers for temporary files may have
group nobody instead of gramene, but we would rarely copy anything
to these.

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From schmidt at stein.cshl.org  Wed Oct  3 17:35:07 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Wed, 03 Oct 2001 17:35:07 -0400
Subject: cvs directories
Message-ID: <3BBB848B.CF25D0FB@cshl.org>

To add a new directory to CVS, just do
     cvs add directoryname
No commit is needed.  The parent directory must already be in cvs.

To create the directory in other copies of the project, do not use
mkdir,
use
cvs update -d directoryname

and in general when you update, use -d if there might be new
subdirectories.

-Steve

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From schmidt at stein.cshl.org  Wed Oct  3 17:54:25 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Wed, 03 Oct 2001 17:54:25 -0400
Subject: gruyere -> chevre
Message-ID: <3BBB8911.D38D698E@cshl.org>

Code on gruyere that we want to keep using should be
added to cvs ( in /home/ensembl/gramene_ensembl) and committed and then
checked out on chevre in
/export/share_more/ensembl/gramene_ensembl

This includes web code, static html pages, scripts used to
load the database, and documentation.

The web server is running on chevre and a lot of stuff already works.
You can access it from outside the firewall using
http://www.brie2:8085/perl/.....

Tell me when all your code works, so brie and brie2 can point
to chevre instead of gruyere.

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From schmidt at stein.cshl.org  Thu Oct  4 15:33:18 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Thu, 04 Oct 2001 15:33:18 -0400
Subject: gruyere -> chevre
References: <3BBB8911.D38D698E@cshl.org>
Message-ID: <3BBCB97E.4ECE66A3@cshl.org>

Hi all,

Lincoln wants us to be off gruyere next week.

Also

I should have said

The web server is running on chevre and a lot of stuff already works.
You can access it from outside the firewall using
http://brie2.cshl.org:8085/perl/.....

And, as Wei pointed out, it wasn't working correctly.
But it's fixed now.

-STeve


Steven Schmidt wrote:

> Code on gruyere that we want to keep using should be
> added to cvs ( in /home/ensembl/gramene_ensembl) and committed and then
> checked out on chevre in
> /export/share_more/ensembl/gramene_ensembl
>
> This includes web code, static html pages, scripts used to
> load the database, and documentation.
>
> The web server is running on chevre and a lot of stuff already works.
> You can access it from outside the firewall using
> http://www.brie2:8085/perl/.....
>
> Tell me when all your code works, so brie and brie2 can point
> to chevre instead of gruyere.
>
> --
> Steven Schmidt
> snp.cshl.org     www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From schmidt at stein.cshl.org  Wed Oct 10 15:03:00 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Wed, 10 Oct 2001 15:03:00 -0400
Subject: gruyere -> chevre
References: <Pine.LNX.4.33.0110091312120.17791-100000@brahman.logsoft.com>
Message-ID: <3BC49B64.40F29D46@cshl.org>

Hi Ken & all

Yes, brie2:8085 is blocked by the firewall.
So now brie2:8082/perl  goes to chevre.
You can still use www.gramene.org/perl to go to gruyere for comparison.

-Steve


"Ken Y. Clark" wrote:

> On Thu, 4 Oct 2001, Steven Schmidt wrote:
>
> > Date: Thu, 04 Oct 2001 15:33:18 -0400
> > From: Steven Schmidt <schmidt at cshl.org>
> > To: gramene at brie.cshl.org, changku at cshl.org, zhaow at cshl.org,
> >      kclark at logsoft.com
> > Subject: Re: gruyere -> chevre
> >
> > Hi all,
> >
> > Lincoln wants us to be off gruyere next week.
> >
> > Also
> >
> > I should have said
> >
> > The web server is running on chevre and a lot of stuff already works.
> > You can access it from outside the firewall using
> > http://brie2.cshl.org:8085/perl/.....
> >
> > And, as Wei pointed out, it wasn't working correctly.
> > But it's fixed now.
> >
> > -STeve
>
> Steve and/or Peter,
>
> I seem to be unable to raise brie2.cshl.org:8085 from outside the
> firewall.  Is there a firewall blocking access?
>
> ky
>
> --
> # -----------------------------
> # k e n            Ken Y. Clark
> # r   y      kclark at logsoft.com
> # a l c            972-542-7923
> # -----------------------------

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From pan at stein.cshl.org  Sat Oct 13 22:22:49 2001
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Sat, 13 Oct 2001 22:22:49 -0400 (EDT)
Subject: Oracle database on chevre.
In-Reply-To: <3BBCB97E.4ECE66A3@cshl.org>
Message-ID: <Pine.GSO.4.05.10110132216030.27312-100000@phage.cshl.org>


    Ok. The Oracle database on chevre has been fixed. It should be no
problems when you create, drop tables, or update data in any account.
Please try it.

    Have a nice weekend!

    Xiaokang





From ware at phage.cshl.org  Sun Oct 14 21:10:09 2001
From: ware at phage.cshl.org (Doreen Ware)
Date: Sun, 14 Oct 2001 18:10:09 -0700
Subject: Oracle database on chevre.
In-Reply-To: <Pine.GSO.4.05.10110132216030.27312-100000@phage.cshl.org>
References: <Pine.GSO.4.05.10110132216030.27312-100000@phage.cshl.org>
Message-ID: <a05100301b7efe7c0f768@[24.47.90.110]>

Xiaokang,

Thanks for taking care of the problem.

Can you explain to me what happened on Monday.

Thanks,

doreen




>  Ok. The Oracle database on chevre has been fixed. It should be no
>problems when you create, drop tables, or update data in any account.
>Please try it.
>
>     Have a nice weekend!
>
>     Xiaokang


-- 
======================================================================
Doreen Ware
Cold Spring Harbor Laboratory			voice: (516) 367-6979
Freeman Bldg.					fax: (516) 367-8389
1 Bungtown Rd.					email: ware at cshl.org
Cold Spring Harbor, NY. 11724			url: www.gramene.org
======================================================================


From pan at stein.cshl.org  Sun Oct 14 19:50:35 2001
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Sun, 14 Oct 2001 19:50:35 -0400 (EDT)
Subject: Oracle database on chevre.
In-Reply-To: <a05100301b7efe7c0f768@[24.47.90.110]>
Message-ID: <Pine.GSO.4.05.10110141855580.869-100000@phage.cshl.org>


 Doreen,

      Actually, the database problem happened on Wednesday. When somebody
 tried to insert or delete a very large data sets, he/she thought that it
 took too long time to finish the job and then quit before the Oracle
 system committed the work. As a result, the system had to roll back
 the work slowly, which may significantly slow down the database. After
 that several people tried to create and drop tables in the database, they
 found that it took too long time to finish the jobs, so, they quit again.
 The system had to do more roll back work and it slowed down further. I
 was trying to shut down the database in normal option so that the system
 can be quickly recovered but I couldn't shut down it normally.

      I had been trying to fixed this problem since Wednesday. Last night,
 I found a method to fix it.

      Xiaokang


On Sun, 14 Oct 2001, Doreen Ware wrote:

> Xiaokang,
> 
> Thanks for taking care of the problem.
> 
> Can you explain to me what happened on Monday.
> 
> Thanks,
> 
> doreen
> 
> 
> 
> 
> >  Ok. The Oracle database on chevre has been fixed. It should be no
> >problems when you create, drop tables, or update data in any account.
> >Please try it.
> >
> >     Have a nice weekend!
> >
> >     Xiaokang
> 
> 
> -- 
> ======================================================================
> Doreen Ware
> Cold Spring Harbor Laboratory			voice: (516) 367-6979
> Freeman Bldg.					fax: (516) 367-8389
> 1 Bungtown Rd.					email: ware at cshl.org
> Cold Spring Harbor, NY. 11724			url: www.gramene.org
> ======================================================================
> 



From schmidt at stein.cshl.org  Mon Oct 15 20:04:58 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Mon, 15 Oct 2001 20:04:58 -0400
Subject: Contig viewer (on chevre)
Message-ID: <3BCB79AA.99EF4E92@cshl.org>

SSR's are on the contig viewer:
http://brie2.cshl.org:8082/perl/contigview?clone=AP001168

You can now search by BACend and by the Genbank accession of
a marker tag:
http://brie2.cshl.org:8082/perl/unisearch


A list of clones with maximal combinations of features
or pile-ups is attached.

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


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From srm4 at cornell.edu  Tue Oct 16 08:45:05 2001
From: srm4 at cornell.edu (Susan McCouch)
Date: Tue, 16 Oct 2001 08:45:05 -0400
Subject: Contig viewer (on chevre)
In-Reply-To: <3BCB79AA.99EF4E92@cshl.org>
References: <3BCB79AA.99EF4E92@cshl.org>
Message-ID: <p04320459b7f1d856b627@[128.253.184.48]>

Steve,

This looks great.  Thanks so much for adding the SSR information.

 From what I can see, the SSR info includes only those that have been 
mapped and characterized by our lab as RM markers.  It does not show 
SSR hits from the set of SSR-containing sequences released by 
Monsanto.  Is that true?

We have a new batch of SSR markers designed from the Monsanto 
sequence, and I'm trying to figure out how to deal with the 
nomenclature.  In some cases, we have more than one primer pair 
designed around the same SSR locus, which presents a challenge in 
terms of naming convention.

In any case, it would be helpful if I could see all the Monsanto 
SSR-containing sequences displayed on the contig viewer.  Only about 
1,000 of these SSR's have primer pairs designed or tested for them 
(unpublished data at this point) but there are more in the pipeline. 
Please see 
http://www.rice-research.org/cgi-bin/download.cgi/riceSSR_seq.fasta 
for a FASTA file of the Monsanto SSR-containing sequences.  I wonder 
if you could discuss with Doreen and Lincoln to see if you could 
position as many of these as possible onto the contig viewer using 
the Monsanto assigned ID's.  We would then convert the Monsanto ID's 
into RM nomenclature as primer pair information is verified.

Thanks, Susan


>SSR's are on the contig viewer:
>http://brie2.cshl.org:8082/perl/contigview?clone=AP001168
>
>You can now search by BACend and by the Genbank accession of
>a marker tag:
>http://brie2.cshl.org:8082/perl/unisearch
>
>
>A list of clones with maximal combinations of features
>or pile-ups is attached.
>
>--
>Steven Schmidt
>snp.cshl.org     www.gramene.org
>Cold Spring Harbor Laboratory
>516-367-6977
>
>
><http://brie2.cshl.org:8082/perl/contigview?clone=AB023482>AB023482 
>Genes=33 BACends=6 MarkerTag=2 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AB026295>AB026295 
>Genes=35 BACends=13 MarkerTag=5 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AC011806>AC011806 
>Genes=23 BACends=0 ssr=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AC016779>AC016779 
>Genes=0 BACends=4 ssr=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AC079022>AC079022 
>Genes=30 BACends=4 MarkerTag=8 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AC082644>AC082644 
>Genes=30 BACends=13 MarkerTag=7
><http://brie2.cshl.org:8082/perl/contigview?clone=AJ307662>AJ307662 
>Genes=56 BACends=0
><http://brie2.cshl.org:8082/perl/contigview?clone=AL442115>AL442115 
>Genes=30 BACends=11 MarkerTag=11
><http://brie2.cshl.org:8082/perl/contigview?clone=AL513003>AL513003 
>Genes=0 BACends=24 MarkerTag=1 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AL513004>AL513004 
>Genes=0 BACends=52 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP000391>AP000391 
>Genes=27 BACends=20 MarkerTag=3 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP000492>AP000492 
>Genes=33 BACends=5 MarkerTag=4 ssr=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AP001129>AP001129 
>Genes=38 BACends=9 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP001168>AP001168 
>Genes=28 BACends=18 MarkerTag=4 ssr=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AP001551>AP001551 
>Genes=32 BACends=18 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002482>AP002482 
>Genes=36 BACends=7 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002540>AP002540 
>Genes=34 BACends=6 MarkerTag=8
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002542>AP002542 
>Genes=33 BACends=4 MarkerTag=7 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002744>AP002744 
>Genes=36 BACends=5 MarkerTag=7
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002819>AP002819 
>Genes=26 BACends=21 MarkerTag=4 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002882>AP002882 
>Genes=32 BACends=10 MarkerTag=6
><http://brie2.cshl.org:8082/perl/contigview?clone=AP002953>AP002953 
>Genes=23 BACends=10 MarkerTag=6 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003047>AP003047 
>Genes=23 BACends=43 MarkerTag=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003048>AP003048 
>Genes=21 BACends=7 MarkerTag=5
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003076>AP003076 
>Genes=40 BACends=12 MarkerTag=3
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003277>AP003277 
>Genes=33 BACends=29 MarkerTag=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003747>AP003747 
>Genes=0 BACends=18 MarkerTag=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003904>AP003904 
>Genes=0 BACends=8 MarkerTag=7 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP003989>AP003989 
>Genes=0 BACends=0 ssr=4
><http://brie2.cshl.org:8082/perl/contigview?clone=AP004001>AP004001 
>Genes=0 BACends=10 ssr=2
><http://brie2.cshl.org:8082/perl/contigview?clone=AP004048>AP004048 
>Genes=0 BACends=12 MarkerTag=6 ssr=1
><http://brie2.cshl.org:8082/perl/contigview?clone=AP004065>AP004065 
>Genes=0 BACends=5 MarkerTag=3 ssr=3

******************************************
Susan McCouch
Dept of Plant Breeding
418 Bradfield Hall
Cornell University
Ithaca, NY  14853-1901
Phone: 607-255-0420
Fax: 607-255-6683
E-Mail: srm4 at cornell.edu

******************************************
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From schmidt at stein.cshl.org  Wed Oct 17 17:28:22 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Wed, 17 Oct 2001 17:28:22 -0400
Subject: Oracle database on chevre.
References: <Pine.GSO.4.05.10110141855580.869-100000@phage.cshl.org>
Message-ID: <3BCDF7F6.9B3098B8@cshl.org>

Xiaokang,

Is it better to delete a whole table or to drop it and re-create it?
Wei and I have heard conflicting advice on this.

-Steve


Xiaokang Pan wrote:

>  Doreen,
>
>       Actually, the database problem happened on Wednesday. When somebody
>  tried to insert or delete a very large data sets, he/she thought that it
>  took too long time to finish the job and then quit before the Oracle
>  system committed the work. As a result, the system had to roll back
>  the work slowly, which may significantly slow down the database. After
>  that several people tried to create and drop tables in the database, they
>  found that it took too long time to finish the jobs, so, they quit again.
>  The system had to do more roll back work and it slowed down further. I
>  was trying to shut down the database in normal option so that the system
>  can be quickly recovered but I couldn't shut down it normally.
>
>       I had been trying to fixed this problem since Wednesday. Last night,
>  I found a method to fix it.
>
>       Xiaokang
>
> On Sun, 14 Oct 2001, Doreen Ware wrote:
>
> > Xiaokang,
> >
> > Thanks for taking care of the problem.
> >
> > Can you explain to me what happened on Monday.
> >
> > Thanks,
> >
> > doreen
> >
> >
> >
> >
> > >  Ok. The Oracle database on chevre has been fixed. It should be no
> > >problems when you create, drop tables, or update data in any account.
> > >Please try it.
> > >
> > >     Have a nice weekend!
> > >
> > >     Xiaokang
> >
> >
> > --
> > ======================================================================
> > Doreen Ware
> > Cold Spring Harbor Laboratory                 voice: (516) 367-6979
> > Freeman Bldg.                                 fax: (516) 367-8389
> > 1 Bungtown Rd.                                        email: ware at cshl.org
> > Cold Spring Harbor, NY. 11724                 url: www.gramene.org
> > ======================================================================
> >

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From pan at stein.cshl.org  Wed Oct 17 18:06:29 2001
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Wed, 17 Oct 2001 18:06:29 -0400 (EDT)
Subject: Oracle database on chevre.
In-Reply-To: <3BCDF7F6.9B3098B8@cshl.org>
Message-ID: <Pine.GSO.4.05.10110171748550.19680-100000@phage.cshl.org>


 Steve,

      I also heard conflicting advice on this topic. From my experience by
 now, I think if the the table contains many records, it is better
 (faster) to drop it and then re-create it than to delete all of the data
 in the table. Both cases seem do not waste disk space.

      Xiaokang



On Wed, 17 Oct 2001, Steven Schmidt wrote:

> Xiaokang,
> 
> Is it better to delete a whole table or to drop it and re-create it?
> Wei and I have heard conflicting advice on this.
> 
> -Steve
> 
> 



From teytelma at stein.cshl.org  Wed Oct 17 18:34:18 2001
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Wed, 17 Oct 2001 18:34:18 -0400 (EDT)
Subject: Oracle database on chevre.
In-Reply-To: <3BCDF7F6.9B3098B8@cshl.org>
Message-ID: <Pine.GSO.4.05.10110171757240.405-100000@phage.cshl.org>

Guys,

If you want to get rid of all the records in a table and don't care about
rolling back in case of error, DO NOT use the 'delete from ...' command as
is.  The delete command will automatically log every single deletion and
will take forever on a large dataset.

Instead, use the 'truncate table_name' or 'drop table table_name' command.
'Drop table' instantaneously removes everything without logging.  Truncate
works similarly to 'delete', but does not remove the table definition.

Now, suppose you want to delete only certain records rather than
everything.  There is no way to use the drop or truncate commands in this
case.  However, even here you can avoid the delete command.  You  can
simply create a new table with only those records that you want to keep,
and then drop the original table.

So instead of 'delete from tbl_name where id>5000;' do,
'create table tbl_name2 as select * from tbl_name where id<=5000;'
'drop table tbl_name;'
'alter table tbl_name2 rename to tbl_name;'

Of course, you want to use your head in this case.  If you have 10 million
records and want to delete 5, it's better to use the delete command.

Also, it may be possible to turn off logging in a table on case-by-case
basis.

Lenny

> Xiaokang,
> 
> Is it better to delete a whole table or to drop it and re-create it?
> Wei and I have heard conflicting advice on this.
> 
> -Steve
> 
> 
> Xiaokang Pan wrote:
> 
> >  Doreen,
> >
> >       Actually, the database problem happened on Wednesday. When somebody
> >  tried to insert or delete a very large data sets, he/she thought that it
> >  took too long time to finish the job and then quit before the Oracle
> >  system committed the work. As a result, the system had to roll back
> >  the work slowly, which may significantly slow down the database. After
> >  that several people tried to create and drop tables in the database, they
> >  found that it took too long time to finish the jobs, so, they quit again.
> >  The system had to do more roll back work and it slowed down further. I
> >  was trying to shut down the database in normal option so that the system
> >  can be quickly recovered but I couldn't shut down it normally.
> >
> >       I had been trying to fixed this problem since Wednesday. Last night,
> >  I found a method to fix it.
> >
> >       Xiaokang
> >
> > On Sun, 14 Oct 2001, Doreen Ware wrote:
> >
> > > Xiaokang,
> > >
> > > Thanks for taking care of the problem.
> > >
> > > Can you explain to me what happened on Monday.
> > >
> > > Thanks,
> > >
> > > doreen
> > >
> > >
> > >
> > >
> > > >  Ok. The Oracle database on chevre has been fixed. It should be no
> > > >problems when you create, drop tables, or update data in any account.
> > > >Please try it.
> > > >
> > > >     Have a nice weekend!
> > > >
> > > >     Xiaokang
> > >
> > >
> > > --
> > > ======================================================================
> > > Doreen Ware
> > > Cold Spring Harbor Laboratory                 voice: (516) 367-6979
> > > Freeman Bldg.                                 fax: (516) 367-8389
> > > 1 Bungtown Rd.                                        email: ware at cshl.org
> > > Cold Spring Harbor, NY. 11724                 url: www.gramene.org
> > > ======================================================================
> > >
> 
> --
> Steven Schmidt
> snp.cshl.org     www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977
> 
> 
> 
> 




From schmidt at stein.cshl.org  Wed Oct 17 19:30:05 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Wed, 17 Oct 2001 19:30:05 -0400
Subject: changes on brie2
Message-ID: <3BCE147D.C6CF8644@cshl.org>

Because Ace::Browser::AceSubs
no longer exports AceInit and AceHeader
by default,

I edited these files in
brie2:/usr/local/gramene

cgi-perl/generic/xml
cgi-perl/searches/blast
cgi-perl/searches/browser
cgi-perl/searches/query
cgi-perl/searches/text
lib/perl/GrameneSubs.pm

to specifically ask for these to be exported
(along with :DEFAULT)

I didn't commit these  or
really test them.

I notice that
cgi-perl/generic/tree
cgi-perl/searches/text
have problems

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


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From steven at stein.cshl.org  Thu Oct 18 00:20:10 2001
From: steven at stein.cshl.org (Steven Schmidt)
Date: Thu, 18 Oct 2001 00:20:10 -0400 (EDT)
Subject: searches/text on brie2
Message-ID: <Pine.LNX.4.10.10110180015370.26642-100000@turunmaa.cshl.org>

Since 
AceSearchMenuBar() was removed from 
Ace::Browser::SearchSubs on brie2,
I put it in GrameneSubs, and made the
scripts that use it ask for it to be exported:
text, browser, and query in cgi-perl/searches
(again nothing committed)

Perhaps there is a better place for it.

Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977



From lstein at stein.cshl.org  Thu Oct 18 11:48:43 2001
From: lstein at stein.cshl.org (Lincoln Stein)
Date: Thu, 18 Oct 2001 11:48:43 -0400
Subject: changes on brie2
In-Reply-To: <3BCE147D.C6CF8644@cshl.org>
References: <3BCE147D.C6CF8644@cshl.org>
Message-ID: <15310.63963.136741.372023@formaggio.cshl.org>

Hi Steve,

You should probably get the new tree and text searches from the
AcePerl distribution.  I will install them.

Lincoln

Steven Schmidt writes:
 > Because Ace::Browser::AceSubs
 > no longer exports AceInit and AceHeader
 > by default,
 > 
 > I edited these files in
 > brie2:/usr/local/gramene
 > 
 > cgi-perl/generic/xml
 > cgi-perl/searches/blast
 > cgi-perl/searches/browser
 > cgi-perl/searches/query
 > cgi-perl/searches/text
 > lib/perl/GrameneSubs.pm
 > 
 > to specifically ask for these to be exported
 > (along with :DEFAULT)
 > 
 > I didn't commit these  or
 > really test them.
 > 
 > I notice that
 > cgi-perl/generic/tree
 > cgi-perl/searches/text
 > have problems
 > 
 > --
 > Steven Schmidt
 > snp.cshl.org     www.gramene.org
 > Cold Spring Harbor Laboratory
 > 516-367-6977
 > 
 > 
 > <!doctype html public "-//w3c//dtd html 4.0 transitional//en">
 > <html>
 > Because Ace::Browser::AceSubs
 > <br>no longer exports AceInit and AceHeader
 > <br>by default,
 > <p>I edited these files in
 > <br>brie2:/usr/local/gramene
 > <p>cgi-perl/generic/xml
 > <br>cgi-perl/searches/blast
 > <br>cgi-perl/searches/browser
 > <br>cgi-perl/searches/query
 > <br>cgi-perl/searches/text
 > <br>lib/perl/GrameneSubs.pm
 > <p>to specifically ask for these to be exported
 > <br>(along with :DEFAULT)
 > <p>I&nbsp;didn't commit these&nbsp; or
 > <br>really test them.
 > <p>I notice that
 > <br>cgi-perl/generic/tree
 > <br>cgi-perl/searches/text
 > <br>have problems
 > <pre>--&nbsp;
 > Steven Schmidt
 > snp.cshl.org&nbsp;&nbsp;&nbsp;&nbsp; www.gramene.org
 > Cold Spring Harbor Laboratory
 > 516-367-6977</pre>
 > &nbsp;</html>

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY

NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
PLEASE WRITE FOR DETAILS.
========================================================================


From schmidt at stein.cshl.org  Fri Oct 19 15:29:02 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Fri, 19 Oct 2001 15:29:02 -0400
Subject: mailing list archive
Message-ID: <3BD07EFE.BA08E022@cshl.org>

The mailing list archive is fixed.

The problem was that
/usr/local/gramene/html/mailarch
could not be accessed by majordomo
Now that directory and its contents belong to
      majordom
and their group is gramene.


--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From schmidt at stein.cshl.org  Fri Oct 19 18:35:58 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Fri, 19 Oct 2001 18:35:58 -0400
Subject: Std Operating Procedure
Message-ID: <3BD0AACE.880BDE23@cshl.org>

I put a rough first SOP in

brie2:/usr/local/gramene/html/sop/sequence_load.txt
viewable
http://brie2.cshl.org:8082/sop/sequence_load.txt

This is about
loading sequences into ensembl and what to do after
So it needs some contribution from Xiaokang and,
for the marker, etc., mapping, Lenny.

It's under CVS but not checked out on brie or
linked to from anywhere yet.



--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From pan at stein.cshl.org  Fri Oct 19 21:33:18 2001
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Fri, 19 Oct 2001 21:33:18 -0400 (EDT)
Subject: Connection from Brie2 to Oracle database on chevre
In-Reply-To: <3BD0AACE.880BDE23@cshl.org>
Message-ID: <Pine.GSO.4.05.10110192116220.23622-100000@phage.cshl.org>


Hi all,

     We can connect to the Oracle database "gramene" on chevere from Brie2
if using the following method:

     1. setting the environmental variable ORACLE_HOME to
        /usr/local/oracle/home in your profile.

     2. using connection string like 
        $dbh = DBI->connect("dbi:Oracle:", 
                            q{username/password@(DESCRIPTION=
                                        	(ADDRESS=(PROTOCOL=TCP)
                                        	(HOST=chevre)(PORT=1521))
				        	(CONNECT_DATA=(SID=gramene)))},
                            "");


     Would you like to try it?


     Have a nice weekend!

     Xiaokang
 
     



From schmidt at stein.cshl.org  Tue Oct 23 13:08:17 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Tue, 23 Oct 2001 13:08:17 -0400
Subject: GramenePage on chevre
Message-ID: <3BD5A401.2F395C54@cshl.org>

The web configuration has been fixed on chevre, so
that the GramenePage module can be used there.

Here's a simple example of how to use it:
/perl/gptest
(in /export/share_more/ensembl/gramene_ensembl)

Whatever you do should also work when moved
to brie or brie2.

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From teytelma at stein.cshl.org  Wed Oct 24 11:07:37 2001
From: teytelma at stein.cshl.org (Lenny Teytelman)
Date: Wed, 24 Oct 2001 11:07:37 -0400 (EDT)
Subject: Gramene Blast
In-Reply-To: <3BD5A401.2F395C54@cshl.org>
Message-ID: <Pine.GSO.4.05.10110241021150.15261-100000@phage.cshl.org>

At the request of Pankaj, I've added the Swissprot/Trembl Oryza proteins
to the Gramene Blast.  So blastp and blastx should now work.

Lenny


-----------------------------
Lenny Teytelman
Cold Spring Harbor Laboratory
516-367-8864
teytelma at cshl.org







From pj37 at cornell.edu  Thu Oct 25 10:42:01 2001
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Thu, 25 Oct 2001 10:42:01 -0400
Subject: Gramene Blast
References: <Pine.GSO.4.05.10110241021150.15261-100000@phage.cshl.org>
Message-ID: <3BD824B9.C49875D6@cornell.edu>

Thanks Lenny.,

It works great.
a comment. Is it possible to show some text saying the blast is running ! (after
submission button is hit) otherwise people might feel that there is a blank
field and something is wrong.

Pankaj


Lenny Teytelman wrote:

> At the request of Pankaj, I've added the Swissprot/Trembl Oryza proteins
> to the Gramene Blast.  So blastp and blastx should now work.
>
> Lenny
>
> -----------------------------
> Lenny Teytelman
> Cold Spring Harbor Laboratory
> 516-367-8864
> teytelma at cshl.org

--

**************************************************************
Pankaj Jaiswal, Ph.D.
Postdoctoral Associate
Dept. of plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   http://ars-genome.cornell.edu/rice
**************************************************************




From schmidt at stein.cshl.org  Thu Oct 25 18:53:54 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Thu, 25 Oct 2001 18:53:54 -0400
Subject: Appearance of Gramene Ensembl pages
Message-ID: <3BD89802.4D47B7F4@cshl.org>

The gramene banner has been fixed and navigation bar added for some
pages generated on chevre.

Examples:

http://brie2.cshl.org:8082/perl/unisearch
http://brie2.cshl.org:8082/perl/contigview?clone=AP002743
http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261
http://brie2.cshl.org:8082/perl/geneview?gene=Gene4261
http://brie2.cshl.org:8082/perl/seqentryview?seqentry=AP002743&contigid=AP002743.001

http://brie2.cshl.org:8082/perl/markerview?marker=C101
http://brie2.cshl.org:8082/genome/perl/SeqTable.cgi

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


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From lstein at stein.cshl.org  Fri Oct 26 11:38:25 2001
From: lstein at stein.cshl.org (Lincoln Stein)
Date: Fri, 26 Oct 2001 11:38:25 -0400
Subject: Appearance of Gramene Ensembl pages
In-Reply-To: <3BD89802.4D47B7F4@cshl.org>
References: <3BD89802.4D47B7F4@cshl.org>
Message-ID: <15321.33649.311361.389392@formaggio.cshl.org>

Thank you!

Lincoln

Steven Schmidt writes:
 > The gramene banner has been fixed and navigation bar added for some
 > pages generated on chevre.
 > 
 > Examples:
 > 
 > http://brie2.cshl.org:8082/perl/unisearch
 > http://brie2.cshl.org:8082/perl/contigview?clone=AP002743
 > http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261
 > http://brie2.cshl.org:8082/perl/geneview?gene=Gene4261
 > http://brie2.cshl.org:8082/perl/seqentryview?seqentry=AP002743&contigid=AP002743.001
 > 
 > http://brie2.cshl.org:8082/perl/markerview?marker=C101
 > http://brie2.cshl.org:8082/genome/perl/SeqTable.cgi
 > 
 > --
 > Steven Schmidt
 > snp.cshl.org     www.gramene.org
 > Cold Spring Harbor Laboratory
 > 516-367-6977
 > 
 > 
 > <!doctype html public "-//w3c//dtd html 4.0 transitional//en">
 > <html>
 > The gramene banner has been fixed and navigation bar added for some pages
 > generated on chevre.
 > <p>Examples:
 > <p><A HREF="http://brie2.cshl.org:8082/perl/unisearch">http://brie2.cshl.org:8082/perl/unisearch</A>
 > <br><A HREF="http://brie2.cshl.org:8082/perl/contigview?clone=AP002743">http://brie2.cshl.org:8082/perl/contigview?clone=AP002743</A>
 > <br><A HREF="http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261">http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261</A>
 > <br><A HREF="http://brie2.cshl.org:8082/perl/geneview?gene=Gene4261">http://brie2.cshl.org:8082/perl/geneview?gene=Gene4261</A>
 > <br><A HREF="http://brie2.cshl.org:8082/perl/seqentryview?seqentry=AP002743&contigid=AP002743.001">http://brie2.cshl.org:8082/perl/seqentryview?seqentry=AP002743&amp;contigid=AP002743.001</A>
 > <br><A HREF="http://brie2.cshl.org:8082/perl/markerview?marker=C101">http://brie2.cshl.org:8082/perl/markerview?marker=C101</A>
 > <br><A HREF="http://brie2.cshl.org:8082/genome/perl/SeqTable.cgi">http://brie2.cshl.org:8082/genome/perl/SeqTable.cgi</A>
 > <pre>--&nbsp;
 > Steven Schmidt
 > snp.cshl.org&nbsp;&nbsp;&nbsp;&nbsp; www.gramene.org
 > Cold Spring Harbor Laboratory
 > 516-367-6977</pre>
 > &nbsp;</html>

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY

NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
PLEASE WRITE FOR DETAILS.
========================================================================


From kclark at logsoft.com  Fri Oct 26 11:45:25 2001
From: kclark at logsoft.com (Ken Y. Clark)
Date: Fri, 26 Oct 2001 11:45:25 -0400 (EDT)
Subject: Appearance of Gramene Ensembl pages
In-Reply-To: <3BD89802.4D47B7F4@cshl.org>
Message-ID: <Pine.LNX.4.33.0110261140570.3636-100000@brahman.logsoft.com>

On Thu, 25 Oct 2001, Steven Schmidt wrote:

> Date: Thu, 25 Oct 2001 18:53:54 -0400
> From: Steven Schmidt <schmidt at brie.cshl.org>
> Reply-To: gramene at brie.cshl.org
> To: gramene at brie.cshl.org
> Subject: Appearance of Gramene Ensembl pages
>
> The gramene banner has been fixed and navigation bar added for some
> pages generated on chevre.
>
> Examples:
>
> http://brie2.cshl.org:8082/perl/unisearch
> http://brie2.cshl.org:8082/perl/contigview?clone=AP002743
> http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261

I checked out the above three examples using Konqueror (on my iBook
running YellowDog Linux 2.0), and the background comes up as black.  I
see in the source that the <BODY>'s background attribute is set to the
empty string ("").  In Netscape and Mozilla, it displays as a white
background.  Perhaps the value should be stated absolutely.

ky

-- 
# -----------------------------
# k e n            Ken Y. Clark
# r   y      kclark at logsoft.com
# a l c            972-542-7923
# -----------------------------



From pan at stein.cshl.org  Fri Oct 26 13:14:33 2001
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Fri, 26 Oct 2001 13:14:33 -0400 (EDT)
Subject: Connections from Brie to Oracle DBs on chevre and gruyere 
In-Reply-To: <Pine.LNX.4.33.0110261140570.3636-100000@brahman.logsoft.com>
Message-ID: <Pine.GSO.4.05.10110261303540.4256-100000@phage.cshl.org>


    The port for firewall exceptions was opened from Brie to chevre and
gruyere. An Oracle client and DBD have also installed on Brie. So, after
setting the environmental variable ORACLE_HOME to /usr/local/oracle/home,
you can connect to the Oracle databases on chevre and gruyere separately
from Brie.

    Xiaokang





From schmidt at stein.cshl.org  Fri Oct 26 14:20:47 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Fri, 26 Oct 2001 14:20:47 -0400
Subject: Appearance of Gramene Ensembl pages
References: <Pine.LNX.4.33.0110261140570.3636-100000@brahman.logsoft.com>
Message-ID: <3BD9A97F.B68BF4B8@cshl.org>

Hi Ken,

I got rid of the  background="" .
Does it make a difference?

What about the pages on brie2 (and brie)?
http://brie2.cshl.org:8082/
also has    background="" in  <body>

-Steve


"Ken Y. Clark" wrote:

> On Thu, 25 Oct 2001, Steven Schmidt wrote:
>
> > Date: Thu, 25 Oct 2001 18:53:54 -0400
> > From: Steven Schmidt <schmidt at brie.cshl.org>
> > Reply-To: gramene at brie.cshl.org
> > To: gramene at brie.cshl.org
> > Subject: Appearance of Gramene Ensembl pages
> >
> > The gramene banner has been fixed and navigation bar added for some
> > pages generated on chevre.
> >
> > Examples:
> >
> > http://brie2.cshl.org:8082/perl/unisearch
> > http://brie2.cshl.org:8082/perl/contigview?clone=AP002743
> > http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261
>
> I checked out the above three examples using Konqueror (on my iBook
> running YellowDog Linux 2.0), and the background comes up as black.  I
> see in the source that the <BODY>'s background attribute is set to the
> empty string ("").  In Netscape and Mozilla, it displays as a white
> background.  Perhaps the value should be stated absolutely.
>
> ky
>
> --
> # -----------------------------
> # k e n            Ken Y. Clark
> # r   y      kclark at logsoft.com
> # a l c            972-542-7923
> # -----------------------------

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977


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From kclark at logsoft.com  Fri Oct 26 14:27:33 2001
From: kclark at logsoft.com (Ken Y. Clark)
Date: Fri, 26 Oct 2001 14:27:33 -0400 (EDT)
Subject: Appearance of Gramene Ensembl pages
In-Reply-To: <3BD9A97F.B68BF4B8@cshl.org>
Message-ID: <Pine.LNX.4.33.0110261424140.3636-100000@brahman.logsoft.com>

On Fri, 26 Oct 2001, Steven Schmidt wrote:

> Date: Fri, 26 Oct 2001 14:20:47 -0400
> From: Steven Schmidt <schmidt at brie.cshl.org>
> Reply-To: gramene at brie.cshl.org
> To: gramene at brie.cshl.org
> Subject: Re: Appearance of Gramene Ensembl pages
>
> Hi Ken,
>
> I got rid of the  background="" .
> Does it make a difference?
>
> What about the pages on brie2 (and brie)?
> http://brie2.cshl.org:8082/
> also has    background="" in  <body>
>
> -Steve

Steve,

Oddely enough, even with the bgcolor attribute set to "white," I'm
still getting a black background when viewing the following URLs with
Konqueror:

http://brie2.cshl.org:8082/perl/unisearch
http://brie2.cshl.org:8082/perl/contigview?clone=AP002743
http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261

However, the following two URLs look just fine:

http://brie2.cshl.org:8082/
http://www.gramene.org/

I can't explain it.

ky

-- 
# -----------------------------
# k e n            Ken Y. Clark
# r   y      kclark at logsoft.com
# a l c            972-542-7923
# -----------------------------



From pj37 at cornell.edu  Fri Oct 26 14:47:16 2001
From: pj37 at cornell.edu (Pankaj Jaiswal)
Date: Fri, 26 Oct 2001 14:47:16 -0400
Subject: Appearance of Gramene Ensembl pages
References: <Pine.LNX.4.33.0110261140570.3636-100000@brahman.logsoft.com> <3BD9A97F.B68BF4B8@cshl.org>
Message-ID: <3BD9AFB4.FFE17D64@cornell.edu>

hi,
check the print preview. the background behind GRAMENE and teh rice plant image
becomes white. Secondly, i would suggest to put the Ensemble's E! on the right
hand side corner/bottom left on the viewer pages, othewise it appears that its
not Gramene but E! is the actual insigna for us.

Steven Schmidt wrote:

> Hi Ken,
>
> I got rid of the  background="" .
> Does it make a difference?
>
> What about the pages on brie2 (and brie)?
> http://brie2.cshl.org:8082/
> also has    background="" in  <body>
>
> -Steve
>
>
> "Ken Y. Clark" wrote:
>
>> On Thu, 25 Oct 2001, Steven Schmidt wrote:
>>
>> > Date: Thu, 25 Oct 2001 18:53:54 -0400
>> > From: Steven Schmidt <schmidt at brie.cshl.org>
>> > Reply-To: gramene at brie.cshl.org
>> > To: gramene at brie.cshl.org
>> > Subject: Appearance of Gramene Ensembl pages
>> >
>> > The gramene banner has been fixed and navigation bar added for some
>> > pages generated on chevre.
>> >
>> > Examples:
>> >
>> > http://brie2.cshl.org:8082/perl/unisearch
>> > http://brie2.cshl.org:8082/perl/contigview?clone=AP002743
>> > http://brie2.cshl.org:8082/perl/protview?peptide=Transc4261
>>
>> I checked out the above three examples using Konqueror (on my iBook
>> running YellowDog Linux 2.0), and the background comes up as black.  I
>> see in the source that the <BODY>'s background attribute is set to the
>> empty string ("").  In Netscape and Mozilla, it displays as a white
>> background.  Perhaps the value should be stated absolutely.
>>
>> ky
>>
>> --
>> # -----------------------------
>> # k e n            Ken Y. Clark
>> # r   y      kclark at logsoft.com
>> # a l c            972-542-7923
>> # -----------------------------
>
> --
> Steven Schmidt
> snp.cshl.org     www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977
>
>

--

**************************************************************
Pankaj Jaiswal, Ph.D.
Postdoctoral Associate
Dept. of plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   http://ars-genome.cornell.edu/rice
**************************************************************




From schmidt at stein.cshl.org  Mon Oct 29 16:48:18 2001
From: schmidt at stein.cshl.org (Steven Schmidt)
Date: Mon, 29 Oct 2001 16:48:18 -0500
Subject: Connections from Brie to Oracle DBs on chevre and gruyere
References: <Pine.GSO.4.05.10110261303540.4256-100000@phage.cshl.org>
Message-ID: <3BDDCEA2.7E05842D@cshl.org>

Hi Xiaokang,

I was able to fetch sequences from the DNA table on chevre on both
brie2 and brie.
This was somewhat slow.
http://brie2:8082/gramene/seq/foo.pl
http://www.gramene.org/gramene/seq/foo.pl

It seems that most of the slowness is due to chevre:
http://chevre/perl/foo.pl
vs.
http://gruyere/perl/foo.pl

-Steve

Xiaokang Pan wrote:

>     The port for firewall exceptions was opened from Brie to chevre and
> gruyere. An Oracle client and DBD have also installed on Brie. So, after
> setting the environmental variable ORACLE_HOME to /usr/local/oracle/home,
> you can connect to the Oracle databases on chevre and gruyere separately
> from Brie.
>
>     Xiaokang

--
Steven Schmidt
snp.cshl.org     www.gramene.org
Cold Spring Harbor Laboratory
516-367-6977





From pan at stein.cshl.org  Mon Oct 29 17:09:35 2001
From: pan at stein.cshl.org (Xiaokang Pan)
Date: Mon, 29 Oct 2001 17:09:35 -0500 (EST)
Subject: Connections from Brie to Oracle DBs on chevre and gruyere
In-Reply-To: <3BDDCEA2.7E05842D@cshl.org>
Message-ID: <Pine.GSO.4.05.10110291700140.14873-100000@phage.cshl.org>


    Please notice, currently, there are 9 people working on chevre but
only 1 people working on gruyere. I think the work load is one of the main
reasons which make it much slower when fetching from chevre than from
gruyere. 

    Xiaokang


On Mon, 29 Oct 2001, Steven Schmidt wrote:

> Hi Xiaokang,
> 
> I was able to fetch sequences from the DNA table on chevre on both
> brie2 and brie.
> This was somewhat slow.
> http://brie2:8082/gramene/seq/foo.pl
> http://www.gramene.org/gramene/seq/foo.pl
> 
> It seems that most of the slowness is due to chevre:
> http://chevre/perl/foo.pl
> vs.
> http://gruyere/perl/foo.pl
> 
> -Steve
> 
> Xiaokang Pan wrote:
> 
> >     The port for firewall exceptions was opened from Brie to chevre and
> > gruyere. An Oracle client and DBD have also installed on Brie. So, after
> > setting the environmental variable ORACLE_HOME to /usr/local/oracle/home,
> > you can connect to the Oracle databases on chevre and gruyere separately
> > from Brie.
> >
> >     Xiaokang
> 
> --
> Steven Schmidt
> snp.cshl.org     www.gramene.org
> Cold Spring Harbor Laboratory
> 516-367-6977
> 
> 
> 
> 



From kclark at logsoft.com  Mon Oct 29 17:17:00 2001
From: kclark at logsoft.com (Ken Y. Clark)
Date: Mon, 29 Oct 2001 17:17:00 -0500 (EST)
Subject: Connections from Brie to Oracle DBs on chevre and gruyere
In-Reply-To: <Pine.GSO.4.05.10110291700140.14873-100000@phage.cshl.org>
Message-ID: <Pine.LNX.4.33.0110291712050.19407-100000@brahman.logsoft.com>

On Mon, 29 Oct 2001, Xiaokang Pan wrote:

> Date: Mon, 29 Oct 2001 17:09:35 -0500 (EST)
> From: Xiaokang Pan <pan at brie.cshl.org>
> Reply-To: gramene at brie.cshl.org
> To: gramene at brie.cshl.org
> Subject: Re: Connections from Brie to Oracle DBs on chevre and gruyere
>
>
>     Please notice, currently, there are 9 people working on chevre but
> only 1 people working on gruyere. I think the work load is one of the main
> reasons which make it much slower when fetching from chevre than from
> gruyere.
>
>     Xiaokang

Absolutely!  Just look at the load average on chevre:

[chevre@~:]$ uptime
  5:12pm  up 35 day(s),  3:25,  16 users,  load average: 1.93, 1.91, 1.74

top points out some more interesting info:

last pid:  1660;  load averages:  2.03,  1.97,  1.80 17:15:40
128 processes: 125 sleeping, 1 running, 2 on cpu
CPU states:  4.3% idle, 88.7% user,  7.1% kernel,  0.0% iowait,  0.0% swap
Memory: 2048M real, 1342M free, 43M swap in use, 2007M swap free

  PID USERNAME THR PRI NICE  SIZE   RES STATE   TIME    CPU COMMAND
20206 groracle   1  10    0   12M 3560K cpu3   99.4H 48.47% tnslsnr
 1588 x-pan      1  10    0   38M   36M run    21:46 43.22% perl
[snip]

Wow.  Just those two processes seem to be eating most of the cycles.

Chevre is obviously much overworked.  I notice a *huge* difference
moving from my little Intel-based, single-processor server to the Sun
box.  I think we have a lot more progress to make on balancing the
various loads asked of our hardware.  Probably our Oracle box should
be very beefy and should not be asked to do much else.

ky

-- 
# -----------------------------
# k e n            Ken Y. Clark
# r   y      kclark at logsoft.com
# a l c            972-542-7923
# -----------------------------



