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Thu Jun 12 22:07:40 PDT 2014

should be using as much of one language as possible.  mod_perl would be my
choice - you'll have more flexibility with mod_perl because Apache is more
accessable overall to developers, IMHO.

> 
> The database question. The database is large, but entirely static.
> Would PostgreSQL be able to handle this comparably to Oracle? The 
> licenses for Oracle are not so very expensive anymore, but if we're
> going towards a farm of boxes, this will start to cumulate. Otoh,
> some Oracle stuff seems to be able to handle parallel databases
> natively. Hmm.

I think it might!  I'm working with PostgreSQL, and I'm seeing comparable
performance, but you'll need to do some benchmarking.  If it doesn't compare
now, it eventually will.  Watch out for using joins in PostgreSQL - they can
impact run times.

> 
> Sorry for the bunch of clueless questions, but I'm not exactly a
> computer person, nor is the company extremely competent in technical
> questions (they're all a bunch of chemists, which just have been
> working with computers for a long time). The budget for hardware seems
> to be there, but I'm a new guy, and I can't afford buying a bunch
> of expensive crap which will just sit there gathering dust.

You're not clueless 'cause you're asking the right questions - this is the
same type of thing directors and managers must contend with.  You have a
chance to sell beowulf to your higher-ups.  Go for it!

> 
> I would also welcome some pointers towards lists where questions
> such as these are handled holistically. I'd settle for a bunch
> of dedicated lists too, though.

> 
> <off-topic/>
> 
> _______________________________________________
> Beowulf mailing list, Beowulf at beowulf.org
> To change your subscription (digest mode or unsubscribe) 
> visit http://www.beowulf.org/mailman/listinfo/beowulf
> 

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<TITLE>RE: phasing out Solaris/Oracle/Netscape with =
Linux/PostgreSQL/Apache</TITLE>
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Let me know if I can help beyond what I write =
below.  Additional comments from the crowd welcome.  See =
below . . .

> -----Original Message-----
 > From: Eugene.Leitl at lrz.uni-muenchen.de
 > [<A =
HREF=3D"mailto:Eugene.Leitl at lrz.uni-muenchen.de">mailto:Eugene.Leitl at lrz=
.uni-muenchen.de</A>]
 > Sent: Thursday, February 08, 2001 10:43 =
PM
 > To: linux-elitists at zgp.org; =
pigdog-l at bearfountain.com;
 > beowulf at beowulf.org
 > Subject: phasing out Solaris/Oracle/Netscape =
with
 > Linux/PostgreSQL/Apache
 > 
 > 
 > 
 > This is somewhat off-topic, so bear with =
me.
 > 
 > Um, I need some advice. The company I'm with =
has a Solaris Sun with
 > Netscape Enterprise Server. It is running a mix =
of C, Perl, Oracle
 > and Daylight. The latter beast currently =
requires 1.5 GByte RAM,
 > but is still creaking at all seams. We're going =
to kick Daylight 
 > sooner or later, so the memory footprint will =
drop, possibly a lot.
 > 
 > I don't yet understand the architecture of the =
chemical database
 > we're running, so I don't know where the =
bottlenecks are, but I need
 > to build a Linux machine which could outperform =
the Sun at a fraction
 > of the price. I will set it up locally, and =
hammer it with queries,
 > doing measurements, stability tests, =
etc.

<P><FONT SIZE=3D2>This could get you.  Critical to understand some =
basic things about the existing application.  Exporting data, etc =
is your first concern - you need to know how to do that.  That =
could very well set the pace of a conversion.</FONT></P>

> 
 > I would rather like to use Athlons, especially =
recent DDR 
 > Dual Athlons,
 > but this doesn't seem to go too well with =
required stability. This
 > means I should use a dual Pentium III =
motherboard, right? Does Linux
 > handle these well? I heard these can take up to =
8 GByte RAM, I think 
 > I should start with 2 GBytes. I don't think the =
application is CPU 
 > bound, but I don't know for sure yet. It =
certainly seems to exercise 
 > disks strongly, so here is another =
question:

<P><FONT SIZE=3D2>Linux does handle them well, but I'm impartial to =
FreeBSD.  Since you're using Sun OS already, you could continue =
with Sun X86 version without making the big switch all at once - it's =
free and a works well enough.  It would make a fine part of a =
beowulf, and allow you to get used to Linux over a longer period of =
time.  If you can make the transition in baby steps, it's =
better.</FONT></P>

> 
 > do I absolutely, positively need SCSI? I was =
thinking about putting a
 > second 100 EIDE host adapter in, and run disk =
striping plus mirroring
 > over 4 EIDE hard drives (the better models from =
IBM). Or should I
 > use a Dual-Pentium mumboard with onboard SCSI, =
and buy several fast,
 > hot & noisy scuzzys, soft-RAIDing them? =
Perhaps even harware RAID?
 > I don't think the disks need to be very large, =
but they 
 > better be fast.
 >

<P><FONT SIZE=3D2>SCSI is GREAT, and you should set up redundant hot =
swaps so if you crash, you insert a new disk, type "boot", =
and you're back online with a node.  I think Sun stations =
outperform the Intel boards on disk throughput, but you could =
check.</FONT></P>

> I would like to use Reiser FS, so this only =
allows me RAID 0/1, right?
 > Higher stability, lack of fscking delay in case =
machine needs to be
 > rebooted and no 2 GByte file size limit would =
seem to be needed.
 > Since this is ReiserFS, I should obviously go =
with the latest stable
 > kernel. I've been using Mandrake for my desktop =
and small 
 > time testing, 
 > but for this application this is probably not =
the way to go. Which 
 > distro should I choose? Debian?

<P><FONT SIZE=3D2>Not sure on this one.  Not enough exposure with =
all of those filesystems.  I know, use MFS, and load up machines =
with 2GB of ram!  Just kidding.</FONT></P>

> 
 > We seem to be moving towards an architecture =
consisting of a bunch 
 > of Perl programs (it's not settled, but the few =
routines we have are
 > in Perl) communicating via sockets. (Right now =
it's a mix of C and 
 > Perl, talking via named pipes). The queries (a =
chemical structure 
 > drawn within a browser, using a Java applet or =
a plug-in) are 
 > handled with a dispatcher (a cgi-bin Perl =
thing). Sooner or 
 > later we will spread the query to a farm of =
boxes, each containing 
 > a database, or segmenting a database across =
several, cheap, redundant 
 > boxes. (But where not there yet). There's no =
alternative to sockets, 
 > right?

<P><FONT SIZE=3D2>You'll take a big performace hit running perl too =
much - it's interpreted.  I know it's popular but with a big =
project, you should get the training required to do it in a compiled =
language, like C/C++.  If you insist on an interpreted language, =
use Java - it's a 'cleaner' language to manage on a large scale.  =
For socket work I would definitely stick with C - and create a library =
specific to your needs that your perl programs could call.</FONT></P>

> 
 > Right now a query can take up to minutes, so I =
don't think mod_perl
 > is needed. We don't get a lot of query hits, at =
least not yet. Should 
 > I try using Apache mod_perl instead of the =
Netscape Server 
 > nevertheless?

<P><FONT SIZE=3D2>How much data does the longer queries access?  =
If you're seeing less than sub-minute response times, it's a red =
flag.  That's just a rule of  thumb I use.  I've seen =
five second return times on several gigs of data with a Sun and =
Oracle.  </FONT></P>

<P><FONT SIZE=3D2>From the standpoint of managing the code, regardless =
of what you use, you should be using as much of one language as =
possible.  mod_perl would be my choice - you'll have more =
flexibility with mod_perl because Apache is more accessable overall to =
developers, IMHO.</FONT></P>

> 
 > The database question. The database is large, =
but entirely static.
 > Would PostgreSQL be able to handle this =
comparably to Oracle? The 
 > licenses for Oracle are not so very expensive =
anymore, but if we're
 > going towards a farm of boxes, this will start =
to cumulate. Otoh,
 > some Oracle stuff seems to be able to handle =
parallel databases
 > natively. Hmm.

<P><FONT SIZE=3D2>I think it might!  I'm working with PostgreSQL, =
and I'm seeing comparable performance, but you'll need to do some =
benchmarking.  If it doesn't compare now, it eventually =
will.  Watch out for using joins in PostgreSQL - they can impact =
run times.</FONT></P>

> 
 > Sorry for the bunch of clueless questions, but =
I'm not exactly a
 > computer person, nor is the company extremely =
competent in technical
 > questions (they're all a bunch of chemists, =
which just have been
 > working with computers for a long time). The =
budget for hardware seems
 > to be there, but I'm a new guy, and I can't =
afford buying a bunch
 > of expensive crap which will just sit there =
gathering dust.

<P><FONT SIZE=3D2>You're not clueless 'cause you're asking the right =
questions - this is the same type of thing directors and managers must =
contend with.  You have a chance to sell beowulf to your =
higher-ups.  Go for it!</FONT></P>
<BR>
<BR>

> 
 > I would also welcome some pointers towards =
lists where questions
 > such as these are handled holistically. I'd =
settle for a bunch
 > of dedicated lists too, though.

<P><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> <off-topic/></FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>> =
_______________________________________________</FONT>
<BR><FONT SIZE=3D2>> Beowulf mailing list, =
Beowulf at beowulf.org</FONT>
<BR><FONT SIZE=3D2>> To change your subscription (digest mode or =
unsubscribe) </FONT>
<BR><FONT SIZE=3D2>> visit <A =
HREF=3D"http://www.beowulf.org/mailman/listinfo/beowulf" =
TARGET=3D"_blank">http://www.beowulf.org/mailman/listinfo/beowulf</A></F=
ONT>
<BR><FONT SIZE=3D2>> </FONT>
</P>

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