From owner-chemistry@ccl.net Thu Jul 28 08:18:01 2011 From: "Andras Borosy andras.borosy-,-givaudan.com" To: CCL Subject: CCL: Reg: Configuration of a group of computers for Speeding up calculations Message-Id: <-45161-110728043327-32453-UNx87URgxW7cVfCZQnK2iA*_*server.ccl.net> X-Original-From: Andras Borosy Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Date: Thu, 28 Jul 2011 10:33:13 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy\a/givaudan.com] Dear Colleagues, I share the opinion of Mr. Kieffer. I add one more thing: much time (which means money) can be saved by purchasing dedicated software with the hardware! I have good experiences with PQS: http://www.pqs-chem.com/ Best wishes, Dr. András Péter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - Dübendorf - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com > From: "Jerome Kieffer Jerome.Kieffer/a\terre-adelie.org" To: "Borosy, Andras " Date: 27.07.2011 19:51 Subject: CCL: Reg: Configuration of a group of computers for Speeding up calculations Sent by: owner-chemistry+andras.borosy==givaudan.com###ccl.net Sent to CCL by: Jerome Kieffer [Jerome.Kieffer#%#terre-adelie.org] Hi all, I would like to feed back some experience I had 3 years ago from such "idea" which I implemented and run for a year: desktop computer are not designed to do calculation (and it is probably even worth with laptop computer): Computation chemistry software make heavy use of CPU (and RAM resources). Unlike most desktop program, they run for ages (hours to days or even month) at full power causing a lot of heat to be generated and subsequently exhausted by the cooling system. Surprisingly most of the failure I noticed were from premature death of hard-drives because the whole case became too hot (whereas the CPUs, generating this heat were fine). Later on I bought a small cluster (20 dual CPU, 4core each) that surprised the admin of the "datacenter" as they were consuming 8x more than "standard servers" (they were kicked out of the UPS). This was not due to the hardware but to the type of processing done on the type of programs running: Computation chemistry software are not like web-servers. Conclusion: Buy dedicated hardware !!! -- Jerome Kieffer . PS: I tested the intel "sandy-bridge" (latest i7) and it rocks really for not that expensive: 500€ mobo+proc, RAM is cheap at the moment, take a lot!!!. The server version which is arriving is likely to be great for computational chemistry.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jul 28 08:53:00 2011 From: "=?utf-8?B?bHl6aGFv?= lyzhao:zjnu.cn" To: CCL Subject: CCL: =?utf-8?B?bWFrZSBhIHByb2dyYW0gdG8gcnVuIGEgY291cGxlZC1jbHVzdGVyKENDKSBjYWxjdWxhdGlvbg==?= Message-Id: <-45162-110728044853-2753-95JepoXYlM8UaMVAoewMww{=}server.ccl.net> X-Original-From: "=?utf-8?B?bHl6aGFv?=" Content-Type: multipart/alternative; boundary="=====003_Dragon680118057285_=====" Date: Thu, 28 Jul 2011 16:48:43 +0800 Mime-Version: 1.0 Sent to CCL by: "=?utf-8?B?bHl6aGFv?=" [lyzhao[a]zjnu.cn] This is a multi-part message in MIME format. --=====003_Dragon680118057285_===== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 7bit Dear all, I want to make a program to run a coupled-cluster(CC) calculation. Could you tell me the best algorithm I should use to solve the CC equation? Any references are welcome. Note that I have finished the HF and MP2 codes and the atomic and molecular orbitals based integrals can be obtained freely. Any help will be appreciated. 2011-07-28 --=====003_Dragon680118057285_===== Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 77u/PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9u YWwvL0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgY29udGVudD0idGV4dC9odG1sOyBjaGFyc2V0 PXV0Zi04IiBodHRwLWVxdWl2PUNvbnRlbnQtVHlwZT4NCjxNRVRBIG5hbWU9R0VORVJBVE9SIGNv bnRlbnQ9Ik1TSFRNTCA4LjAwLjYwMDEuMTkwODgiPjxMSU5LIHJlbD1zdHlsZXNoZWV0IA0KaHJl Zj0iQkxPQ0tRVU9URXttYXJnaW4tVG9wOiAwcHg7IG1hcmdpbi1Cb3R0b206IDBweDsgbWFyZ2lu LUxlZnQ6IDJlbX0iPjwvSEVBRD4NCjxCT0RZIA0Kc3R5bGU9Ik1BUkdJTi1UT1A6IDEwcHg7IEZP TlQtRkFNSUxZOiBWZXJkYW5hOyBDT0xPUjogIzAwMDAwMDsgTUFSR0lOLUxFRlQ6IDEwcHg7IEZP TlQtU0laRTogMTBwdDsgTUFSR0lOLVJJR0hUOiAxMHB4Ij4NCjxESVY+RGVhciZuYnNwO2FsbCw8 L0RJVj4NCjxESVY+Jm5ic3A7Jm5ic3A7SSZuYnNwO3dhbnQmbmJzcDt0byZuYnNwO21ha2UmbmJz cDthJm5ic3A7cHJvZ3JhbSZuYnNwO3RvJm5ic3A7cnVuJm5ic3A7YSZuYnNwO2NvdXBsZWQtY2x1 c3RlcihDQykmbmJzcDtjYWxjdWxhdGlvbi48L0RJVj4NCjxESVY+Jm5ic3A7Jm5ic3A7Q291bGQm bmJzcDt5b3UmbmJzcDt0ZWxsJm5ic3A7bWUmbmJzcDt0aGUmbmJzcDtiZXN0Jm5ic3A7YWxnb3Jp dGhtJm5ic3A7SSZuYnNwO3Nob3VsZCZuYnNwO3VzZSZuYnNwO3RvJm5ic3A7c29sdmUmbmJzcDt0 aGUmbmJzcDtDQyZuYnNwO2VxdWF0aW9uPyZuYnNwO0FueSZuYnNwO3JlZmVyZW5jZXMmbmJzcDth cmUmbmJzcDt3ZWxjb21lLjwvRElWPg0KPERJVj4mbmJzcDsmbmJzcDtOb3RlJm5ic3A7dGhhdCZu YnNwO0kmbmJzcDtoYXZlJm5ic3A7ZmluaXNoZWQmbmJzcDt0aGUmbmJzcDtIRiZuYnNwO2FuZCZu YnNwO01QMiZuYnNwO2NvZGVzJm5ic3A7YW5kJm5ic3A7dGhlJm5ic3A7YXRvbWljJm5ic3A7YW5k Jm5ic3A7bW9sZWN1bGFyJm5ic3A7b3JiaXRhbHMmbmJzcDtiYXNlZCZuYnNwO2ludGVncmFscyZu YnNwO2NhbiZuYnNwO2JlJm5ic3A7b2J0YWluZWQmbmJzcDtmcmVlbHkuJm5ic3A7PC9ESVY+DQo8 RElWPiZuYnNwOyZuYnNwOzwvRElWPg0KPERJVj4mbmJzcDsmbmJzcDtBbnkmbmJzcDtoZWxwJm5i c3A7d2lsbCZuYnNwO2JlJm5ic3A7YXBwcmVjaWF0ZWQuPC9ESVY+DQo8RElWPjwvRElWPg0KPERJ Vj48L0RJVj4NCjxESVY+MjAxMS0wNy0yODwvRElWPjwvQk9EWT48L0hUTUw+DQo= --=====003_Dragon680118057285_=====-- From owner-chemistry@ccl.net Thu Jul 28 10:08:01 2011 From: "Saman Mandegar mandegar_saman=yahoo.com" To: CCL Subject: CCL: G09: transition dipole moment in g09 Message-Id: <-45163-110728100735-28023-5w+s0xifrfNnE3Dm1cPUYw*server.ccl.net> X-Original-From: "Saman Mandegar" Date: Thu, 28 Jul 2011 10:07:31 -0400 Sent to CCL by: "Saman Mandegar" [mandegar_saman%%yahoo.com] Dear All, I am using G09 to calculate transition dipole moment for ground and excited state using TDDFT. 1-Which part of out I can find the transition dipole moment (TDM) in TD-DFT? 2-How can I find and visualize the dipole derivatives with respect to the x, y, and z components of the different normal modes? I mean (du/dQ) where Q is normal coordinate. 3-I need the dipole derivatives . However, as you know normal mode analysis in excited states is computationally too demanding. Is there any trick in G09 to do normal analysis in parallel? As far as I understand, the G09 calculates the du/dQ one-by-one. Can we use any keyword or modify the source code in a way that we could send any derivative to one node? I was thinking of finding normal mode and then building a multistep job including a job for each normal mode. Any help is greatly appreciated. Kind wishes, Saman From owner-chemistry@ccl.net Thu Jul 28 10:43:00 2011 From: "lyzhao lyzhao~!~zjnu.cn" To: CCL Subject: CCL: Please ignore the message "make a program to run ..." Message-Id: <-45164-110728100747-28104-C3FziTqo1U+7nPBTpmCRXg*|*server.ccl.net> X-Original-From: "lyzhao" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Thu, 28 Jul 2011 22:07:34 +0800 Mime-Version: 1.0 Sent to CCL by: "lyzhao" [lyzhao-x-zjnu.cn] Dear All, I am sorry for pressing the wrong button to submit the message of "make a program to run a coupled-cluster(CC) calculation". Please ignore it if you received. Lan 2011-07-28 From owner-chemistry@ccl.net Thu Jul 28 11:28:01 2011 From: "rocky walden rocky.walden19[#]gmail.com" To: CCL Subject: CCL: Reg: Configuration of a group of computers for Speeding up calculations Message-Id: <-45165-110728112128-4554-+WuMetM5vo1ev41fxcB33A(0)server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=90e6ba3097ca69ae8804a922b776 Date: Thu, 28 Jul 2011 20:51:17 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19[]gmail.com] --90e6ba3097ca69ae8804a922b776 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear All, Thank you for your valuable suggestions. I managed to get a licensed RHLE 5.0 , now i am planning to boot my machine= s with RHLE , so this makes me to easy in setting up network and i have a Internet connection with pretty good speed (10 Mbs) this is generally used for browsing and stuff ( hope this should be used) . Any furthur inputs ( which machine like core i7 or core i5 is to be made as server so that jobs run , and can be launched from other machines.) Thanks Rocky On Wed, Jul 27, 2011 at 8:11 PM, Jerome Kieffer Jerome.Kieffer/ aterre-adelie.org wrote: > > Sent to CCL by: Jerome Kieffer [Jerome.Kieffer#%#terre-adelie.org] > Hi all, > > I would like to feed back some experience I had 3 years ago from such > "idea" which I implemented and run for a year: desktop computer are not > designed to do calculation (and it is probably even worth with laptop > computer): > > Computation chemistry software make heavy use of CPU (and RAM resources). > Unlike most desktop program, they run for ages (hours to days or even mon= th) > at full power causing a lot of heat to be generated and subsequently > exhausted by the cooling system. Surprisingly most of the failure I notic= ed > were from premature death of hard-drives because the whole case became to= o > hot (whereas the CPUs, generating this heat were fine). > > Later on I bought a small cluster (20 dual CPU, 4core each) that surprise= d > the admin of the "datacenter" as they were consuming 8x more than "standa= rd > servers" (they were kicked out of the UPS). This was not due to the hardw= are > but to the type of processing done on the type of programs running: > Computation chemistry software are not like web-servers. > > Conclusion: Buy dedicated hardware !!! > -- > Jerome Kieffer . > > PS: > I tested the intel "sandy-bridge" (latest i7) and it rocks really for not > that expensive: 500=80 mobo+proc, RAM is cheap at the moment, take a lot!= !!. > The server version which is arriving is likely to be great for > computational chemistry. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --90e6ba3097ca69ae8804a922b776 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear All,

Thank you for your valuable suggestions.
I managed to g= et a licensed RHLE 5.0 , now i am planning to boot my machines with RHLE , = so this makes me to easy in setting up network and i have a Internet connec= tion with pretty good speed (10 Mbs) this is generally used for browsing an= d stuff ( hope this should be used) .

Any furthur inputs ( which machine like core i7 or core i5 is to be mad= e as server so that jobs run , and can be launched from other machines.)
Thanks
Rocky

On Wed, Jul 27, 2011= at 8:11 PM, Jerome Kieffer Jerome.Kieffer/aterre-adelie.org <owner-chemistry#ccl.net> wrote:

Sent to CCL by: Jerome Kieffer [Jerome.Kieffer#%#terre-adelie.org]
Hi all,

I would like to feed back some experience I had 3 years ago from such "= ;idea" which I implemented and run for a year: desktop computer are no= t designed to do calculation (and it is probably even worth with laptop com= puter):

Computation chemistry software make heavy use of CPU (and RAM resources). U= nlike most desktop program, they run for ages (hours to days or even month)= at full power causing a lot of heat to be generated and subsequently exhau= sted by the cooling system. Surprisingly most of the failure I noticed were= from premature death of hard-drives because the whole case became too hot = (whereas the CPUs, generating this heat were fine).

Later on I bought a small cluster (20 dual CPU, 4core each) that surprised = the admin of the "datacenter" as they were consuming 8x more than= "standard servers" (they were kicked out of the UPS). This was n= ot due to the hardware but to the type of processing done on the type of pr= ograms running: Computation chemistry software are not like web-servers.
Conclusion: Buy dedicated hardware !!!
--
Jerome Kieffer <Jerome.Kieffer a terre-adelie.org>.

PS:
I tested the intel "sandy-bridge" (latest i7) and it rocks really= for not that expensive: 500=80 mobo+proc, RAM is cheap at the moment, take= a lot!!!.
The server version which is arriving is likely to be great for computationa= l chemistry.



-=3D This is automatically added to each message by the mailing script =3D-=
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--90e6ba3097ca69ae8804a922b776-- From owner-chemistry@ccl.net Thu Jul 28 14:41:01 2011 From: "Tymofii Nikolaienko tim_mail]_[ukr.net" To: CCL Subject: CCL: BSSE for MP2 Message-Id: <-45166-110728143711-4482-JFyKs65igYhOLBw3p6ydlQ,,server.ccl.net> X-Original-From: "Tymofii Nikolaienko" Date: Thu, 28 Jul 2011 14:37:07 -0400 Sent to CCL by: "Tymofii Nikolaienko" [tim_mail(_)ukr.net] Dear Adel! Please find detailed description of sample calculation at http://timn.ho.ua/ccs/bsse.htm Best regards Tymofii >Dear Nikolaienko, > >Really thanks for your e-mail and help as I am confused of how to calculate >the binding energy at the MP2 level. I think it would be a lot better for >me if you show me how to calculate the binding energy at the MP2 level for, >e.g., of the H2O-Na+ complex calculated in the attached file. > >Thanking you in advance for your cooperation. > >Best regards, >Adel El-Azhary From owner-chemistry@ccl.net Thu Jul 28 15:15:01 2011 From: "Frank Neese neese : thch.uni-bonn.de" To: CCL Subject: CCL: make a program to run a coupled-cluster(CC) calculation Message-Id: <-45167-110728143731-4728-a30U/1Kgv52VGUT1SV7jBQ_+_server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 28 Jul 2011 20:37:06 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Frank Neese [neese],[thch.uni-bonn.de] A very nice formulation of the closed shell CCSD equations that is also entirely correct can for example be found in Scuseria, G.E.; Janssen, C.L.; Schaefer II, H.F. J. Chem. Phys., 1988, 89, 7382 Our take on the intermediates and how to calculate them is described in: Neese, F.; Wennmohs, F.; Hansen, A. (2009) Efficient and accurate local approximations to coupled electron pair approaches. An attempt to revive the pair-natural orbital method J. Chem. Phys., 130, 114108 Wennmohs, F.; Neese, F. (2008) A Comparative Study of Single Reference Correlation Methods of the Coupled-Pair Type, Chem. Phys., 343, 217-230 Good luck, Frank Neese Am 28.07.2011 um 10:48 schrieb lyzhao lyzhao:zjnu.cn: > Dear all, > I want to make a program to run a coupled-cluster(CC) calculation. > Could you tell me the best algorithm I should use to solve the CC equation? Any references are welcome. > Note that I have finished the HF and MP2 codes and the atomic and molecular orbitals based integrals can be obtained freely. > > Any help will be appreciated. > 2011-07-28 ------------------------------------------------------------------------- ++++ NOTE CHANGE OF ADDRESS ON 1.7.2011 ++++ Prof. Dr. Frank Neese Max-Planck Institut für Bioanorganische Chemie Stiftstr. 34-36 D-45470 Mülheim an der Ruhr Germany E-Mail: neese%mpi-muelheim.mpg.de ------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Jul 28 20:14:01 2011 From: "Jun Zhang coolrainbow!^!yahoo.cn" To: CCL Subject: CCL: Reg: Configuration of a group of computers for Speeding up calculations Message-Id: <-45168-110728201005-31165-fNepvFDDrYlCO3lYNImSxg() server.ccl.net> X-Original-From: Jun Zhang Content-Type: multipart/alternative; boundary="0-203150160-1311898189=:43584" Date: Fri, 29 Jul 2011 08:09:49 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: Jun Zhang [coolrainbow()yahoo.cn] --0-203150160-1311898189=:43584 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Hello Rocky:=0A=C2=A0=0AFor your hardware, it is OK. Although not impossibl= e, however, to construct a cluster by Windows is very awkward, and it is re= ccommended to use Linux.=0A=0A---------------------------------------------= -------------------=0AJun Zhang (coolrainbow*o*yahoo.ch)=0AComputational Chem= istry Group=0ANo.94, Weijinlu=0ANankai University =0ATianjin, China=0A=0A= =E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A rocky walden rocky.walden19-.-gmail.co= m =0A=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, = Jun " =0A=E5=8F=91=E9=80=81=E6=97=A5=E6=9C=9F= =EF=BC=9A 2011=E5=B9=B47=E6=9C=8827=E6=97=A5, =E6=98=9F=E6=9C=9F=E4=B8=89, = =E4=B8=8A=E5=8D=88 1:49=0A=E4=B8=BB=E9=A2=98: CCL: Reg: Configuration of a = group of computers for Speeding up calculations=0A=0A=0ADear CCL folks,=0A= =0A=C2=A0=C2=A0=C2=A0 I have 3 Laptop machines which operate 24X7 , so i am= planning to group them together and try to make a small group so that i ca= n use them for exhaustive calculations.=0A=0AMy lappy configuration.=0AInte= l Dualcore 1.86 GHz,160GB HDD,1GB RAM=0AIntel Corei7, (quad core) 1.60Ghz, = 6GB RAM, 650 GBHDD, 1 GB=C2=A0 Graphics ATI Mobil radon=0AIntel Corei5=C2= =A0 4GB RAM 350GB,HDD, 512 ATI Radon.=0A=0AAll these lappys have windows 7 = Ultimate OS=0A=0AI have license versions of various computational chemistry= (DESMOND,GROMACS, ABINTIO, )suites, can i set up a home cluster ? =0ACan a= ny one give me some ideas =0A=0A=0AThanks=0ARocky --0-203150160-1311898189=:43584 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
Hello Rock= y:
 
For your hardware, = it is OK. Although not impossible, however, to construct a cluster by Windo= ws is very awkward, and it is reccommended to use Linux.
<= /div>
 
------------------------------------------------= ----------------
Jun Zhang (coolrainbow*o*yahoo.ch)
Computational Chemi= stry Group
No.94, Weijinlu
Nankai University
Tianjin, China
=E5=8F=91=E4= =BB=B6=E4=BA=BA=EF=BC=9A rocky walden rocky.walden19-.-gmail.com= <owner-chemistry*o*ccl.net>
= =E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun " <c= oolrainbow*o*yahoo.cn>
=E5=8F=91= =E9=80=81=E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B47=E6=9C=8827= =E6=97=A5, =E6=98=9F=E6=9C=9F=E4=B8=89, =E4=B8=8A=E5=8D=88 1:49
=E4=B8=BB=E9=A2=98: CCL: Reg: Conf= iguration of a group of computers for Speeding up calculations
Dear CCL folks,

    I have= 3 Laptop machines which operate 24X7 , so i am planning to group them toge= ther and try to make a small group so that i can use them for exhaustive ca= lculations.

My lappy configuration.
=0AIntel Dualcore 1.86 GHz,16= 0GB HDD,1GB RAM
Intel Corei7, (quad core) 1.60Ghz, 6GB RAM, 650 GBHDD, 1= GB  Graphics ATI Mobil radon
Intel Corei5  4GB RAM 350GB,HDD,= 512 ATI Radon.

All these lappys have windows 7 Ultimate OS
=0AI have license versions of various computational chemistry (DESMOND,GROMA= CS, ABINTIO, )suites, can i set up a home cluster ?
Can any one give me= some ideas


Thanks
Rocky
=0A


--0-203150160-1311898189=:43584--