From owner-chemistry@ccl.net Sat Jun 4 10:08:00 2011 From: "Jun Zhang coolrainbow\a/yahoo.cn" To: CCL Subject: CCL:G: How to build a linux cluster for computational chemistry purposes?, HELP Message-Id: <-44837-110604014506-30661-DyARyF9wu2A/rYqfyJCU/A%x%server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="0-1787980667-1307166294=:72047" Date: Sat, 4 Jun 2011 13:44:54 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow a yahoo.cn] --0-1787980667-1307166294=:72047 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello=C2=A0 Karen: =C2=A0 Thank you for your suggestions.=20 =C2=A0 The document is in fact a summary of my early works (2009~2010) when I star= ted to build clusters for my lab. After the cluster being stable and relati= vely=C2=A0good efficiency, I began to work in computational chemistry and s= ome programming, seldomly trying new techniques in clusters (such as Rocks,= Lustre, Slurm, etc).=20 =C2=A0 Since I am far from an "expert" in cluster building, my=C2=A0document has t= o wait for a long time before publishing until its author becoming more "pr= ofessional" in the field. Just a joke. If the needs=C2=A0are really high, I= will try to put it into English and be very happy to share it . =C2=A0 Cheers up! Jun Zhang Nankai University coolrainbow(_)yahoo.cn --- Karen.Green(_)sanofi-aventis.com =20 =C2=A0Karen.Green(_)sanofi-aventis.com Karen.Green(_)sanofi-aventis.com =C2=A0RE: G: How to build a linux cluster for computational chemistry purpo= ses?, HELP =C2=A0coolrainbow(_)yahoo.cn Dear Jun, =C2=A0 Have you ever considered translating it into English and publishing with a = technical/scientific publisher like McGraw-Hill? (It seems that your hard work could benefit others and also maybe yourself = financially.) =C2=A0 I recall in the past that a professor of mine had designed a course for upp= er-level undergraduates that had no textbook because he said that none addr= essed his needs. I asked him why he didn't publish it since he had already done the work.=C2= =A0 Now that book is a classic medicinal chemistry textbook (The Organic Ch= emistry of Drug Design and Drug Action). =C2=A0 I get the same feeling about your work referenced in your email. =C2=A0 Just a thought (although I am not a publisher but a fellow research scienti= st), Karen > From: owner-chemistry+karen.green=3D=3Dsanofi-aventis.com(_)ccl.net [mailto:o= wner-chemistry+karen.green=3D=3Dsanofi-aventis.com(_)ccl.net] On Behalf Of Ju= n Zhang coolrainbow]*[yahoo.cn Sent: Thursday, June 02, 2011 7:31 PM To: Green, Karen R&D/US Subject: CCL:G: How to build a linux cluster for computational chemistry pu= rposes?, HELP Hi Miguel Quiliano: =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0 I had ever written a very detailed document=C2=A0o= n cluster building, but it was written in Chinese rather than=C2=A0in Engli= sh so I don't know whether it can help you... If you need it, I can send yo= u by e-mail. =C2=A0 Good Luck! Jun Zhang Nankai University coolrainbow(_)yahoo.cn Dear community. After... talk.. and talk.. with my boss, I convinced him to build a linux c= luster for computational chemistry purposes, in other words... to use Gauss= ian03. So now I have 80 cores at my disposal. We also have TCP/LINDA. Could you please recommend me, one operative system and some online guide t= o build it or book? Personal experiences are welcome. Thanks in advance. Miguel Quiliano. --0-1787980667-1307166294=:72047 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hello  Karen:
 
Thank you for your suggestions.
 
The document is in fact a summary of my early works (2009~2010) when I= started to build clusters for my lab. After the cluster being stable and r= elatively good efficiency, I began to work in computational chemistry = and some programming, seldomly trying new techniques in clusters (such as R= ocks, Lustre, Slurm, etc).
 
Since I am far from an "expert" in cluster building, my document = has to wait for a long time before publishing until its author becoming more "professional" in the field. Just a joke= . If the needs are really high, I will try to put it into English and = be very happy to share it .
 
Cheers up!

Jun Zhang
Nankai University
coolrainbow(_)yahoo.cn

--- = Karen.Green(_)sanofi-ave= ntis.com <Karen.Green(_)sanofi-aventis.com>

 Karen.Green(_)sanofi-aventis.com Karen.Green(_)sanofi-aventis.com
 RE: G: How to = build a linux cluster for computational chemistry purposes?, HELP
 = coolrainbow(_)yahoo.cn

Dear Jun,
 
Have you ever considered transla= ting it into English and publishing with a technical/scientific publisher l= ike McGraw-Hill?
(It seems that your hard work co= uld benefit others and also maybe yourself financially.)
 
I recall in the past that a prof= essor of mine had designed a course for upper-level undergraduates that had= no textbook because he said that none addressed his needs.
<= FONT color=3D#0000ff size=3D2 face=3DArial>I asked him why he didn't publis= h it since he had already done the work.  Now that book is a classic m= edicinal chemistry textbook (The Organic Chemistry of Drug Design and Drug Action).
<= FONT color=3D#0000ff size=3D2 face=3DArial> 
<= FONT color=3D#0000ff size=3D2 face=3DArial>I get the same feeling about you= r work referenced in your email.
 
Just a thought (although I am not a publisher but a fel= low research scientist),
Karen

From: owner-chemistry+karen.green=3D=3D= sanofi-aventis.com(_)ccl.net [mailto:owner-chemistry+karen.green=3D=3Dsanofi-= aventis.com(_)ccl.net] On Behalf Of Jun Zhang coolrainbow]*[yahoo.cnSent: Thursday, June 02, 2011 7:31 PM
To: Green, Karen R= &D/US
Subject: CCL:G: How to build a linux cluster for comput= ational chemistry purposes?, HELP

Hi Miguel Quiliano:
 
     I had ever written a very detailed document&n= bsp;on cluster building, but it was written in Chinese rather than in = English so I don't know whether it can help you... If you need it, I can se= nd you by e-mail.
 
Good Luck!

Jun Zhang
Nankai University
coolrainbow(_)yaho= o.cn


Dear community.

After... talk.. and talk.. w= ith my boss, I convinced him to build a linux clust= er for computational chemistry purposes, in other words... to use Gaussian0= 3. So= now I have 80 cores at my disposal. We also have TCP/LINDA.

Could y= ou please recommend me, one operative system and some online guide to build= it or book? Personal experiences are welcome.

Thanks in advance.
Miguel Quiliano.
--0-1787980667-1307166294=:72047-- From owner-chemistry@ccl.net Sat Jun 4 17:56:00 2011 From: "Michael K Gilson mgilson]-[ucsd.edu" To: CCL Subject: CCL: Availability of compounds in BindingDB, via Zinc Message-Id: <-44838-110604175440-2155-C9CnzfAE9dRADnwXSDJZtA{:}server.ccl.net> X-Original-From: "Michael K Gilson" Date: Sat, 4 Jun 2011 17:54:31 -0400 Sent to CCL by: "Michael K Gilson" [mgilson- -ucsd.edu] BindingDB (www.bindingdb.org) now provides information on compound availability, via integration with and links to the Zinc compound database (zinc.docking.org). This is a new feature and could still have glitches. Please let me know if you have any problems with it. General comments and suggestions are also welcome! Regards, Mike P.S. Thanks to John Irwin at UCSF for making this possible.