From owner-chemistry@ccl.net Fri Jul 16 00:14:01 2010 From: "RITESH RUHELA riteshruhela**gmail.com" To: CCL Subject: CCL:G: Use of memory in Gaussian G09 A.01 Message-Id: <-42295-100716001020-22537-iO8cLnG6ux/9JuowSpJXoQ**server.ccl.net> X-Original-From: RITESH RUHELA Content-Type: multipart/alternative; boundary=000e0cd33196239806048b796570 Date: Fri, 16 Jul 2010 09:40:10 +0530 MIME-Version: 1.0 Sent to CCL by: RITESH RUHELA [riteshruhela++gmail.com] --000e0cd33196239806048b796570 Content-Type: text/plain; charset=ISO-8859-1 Dear Sir, Thanks for your prompt reply I have tried with lesser memory also like %mem=1GB but again the programme is using only 98MB memory Please advice Also someone adviced me to permanently add memory and processor usage in default.route file Please suggest how i can do that whether i have to create a file called default.route or it somewhere located and i have to manage it through command I am using suse 11.2 Than you with regards On 7/16/10, Jamin Krinsky jamink]|[berkeley.edu wrote: > > In Gaussian the mem keyword specifies the total for the job, NOT per cpu > (if running network parallel with LINDA than it is the memory for each > node). Also, if you specify more memory than exists and the job asks for the > specified amount of memory the job will die, it won't revert to the default. > Jamin > > > 2010/7/15 Serdar Bado?lu sbadoglu(_)gazi.edu.tr > > >> >> Sent to CCL by: "Serdar Bado?lu" [sbadoglu[]gazi.edu.tr] >> Dear Ritesh, >> >> I'm using Gaussian 03 not 09, but I suppose settings are the same. Now if >> I'm not wrong, %mem stands for the memory per core. Because %nproc=2 in >> your case, Gaussian looks for 2 x 3 GB = 6 GB of memory, but your total >> physical memory is 4 GB. So, that's why it used only 98-100 MB (default >> memory setting is 6 MW which is roughly equal to 96 MB). Try %mem=1500MB, >> this should work. With %nproc=2, this means that Gaussian will use 3GB of >> memory. Also, try not to spend all of the memory for Gaussian, keep some >> for the operating system and other stuff. >> >> Regards >> >> >> -- >> Serdar BADOGLU >> Gazi University >> Department of Physics>> E-mail to subscribers: CHEMISTRY-#-ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use>> >> >> > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink-#-berkeley.edu, 510-643-0616 > > http://glab.cchem.berkeley.edu > > -- Ritesh Ruhela --000e0cd33196239806048b796570 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Sir,
=A0
Thanks for your prompt reply
I have tried with lesser memory also like %mem=3D1GB
but again the programme is using only 98MB memory
Please advice
Also someone adviced me to permanently add memory and processor usage = in default.route file
Please suggest how i can do that
whether i have to create a file called default.route
or it somewhere located and i have to manage it through command
I am using suse 11.2
=A0
Than you with regards


=A0
On 7/16/10, = Jamin Krinsky jamink]|[berkeley.edu= <owner-chemistry-.-ccl.net= > wrote:
In Gaussian the mem keyword spec= ifies the total for the job, NOT per cpu (if running network parallel with = LINDA than it is the memory for each node). Also, if you specify more memor= y than exists and the job asks for the specified amount of memory the job w= ill die, it won't revert to the default.
Jamin


2010/7/15 Serdar Bado?lu sbadoglu(_)gazi.edu.tr <owner-chemistry-#-ccl.net>
Sent to CCL by: "Serdar Bado?lu" [sbadoglu[]gazi.edu.tr]
Dear Ritesh,

I'm using Gaussian 03 not 09, but I suppose setting= s are the same. Now if
I'm not wrong, %mem stands for the memory per= core. Because %nproc=3D2 in
your case, Gaussian looks for 2 x 3 GB =3D = 6 GB of memory, but your total
physical memory is 4 GB. So, that's why it used only 98-100 MB (default=
memory setting is 6 MW which is roughly equal to 96 MB). Try %mem=3D150= 0MB,
this should work. With %nproc=3D2, this means that Gaussian will us= e 3GB of
memory. Also, try not to spend all of the memory for Gaussian, keep somefor the operating system and other stuff.

Regards


--
= Serdar BADOGLU
Gazi University
Department of Physics



-=3D This is automatically added to each message b= y the mailing script =3D-
E-mail to subscribers: CHEMISTRY-#-ccl.net or use: =A0 =A0 =A0http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to adm= inistrators: CHEMISTRY-REQUE= ST-#-ccl.net or use
=A0 =A0 =A0http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscrib= e:
=A0 =A0 =A0h= ttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: htt= p://www.ccl.net

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Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
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RTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/


<= /blockquote>



--
Jamin L Krinsky, P= h.D.
Molecular Graphics and Computation Facility
175 Tan Hall, Univer= sity of California, Berkeley, CA 94720
jamink-#-berkeley.edu, 510-643-0616=20



--
Ritesh Ruhela=20 --000e0cd33196239806048b796570-- From owner-chemistry@ccl.net Fri Jul 16 03:07:00 2010 From: "Chris Swain swain]~[mac.com" To: CCL Subject: CCL: Safari Extensions Message-Id: <-42296-100716030549-21212-4hPUVTgXOF6FXrfBj3gHyA*o*server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Fri, 16 Jul 2010 08:05:02 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain[*]mac.com] Hi, Any Mac users might be interested to hear I've written a few extensions to Safari that might be of interest to chemists. http://homepage.mac.com/swain/Macinchem/Extensions/Extensions.html Cheers Chris From owner-chemistry@ccl.net Fri Jul 16 08:43:00 2010 From: "Sagarika Dev sagarika.dev]*[gmail.com" To: CCL Subject: CCL: delocalisation indices Message-Id: <-42297-100716065616-5242-qwC6cT1GXHL44L9zY69Sig_+_server.ccl.net> X-Original-From: "Sagarika Dev" Date: Fri, 16 Jul 2010 06:56:15 -0400 Sent to CCL by: "Sagarika Dev" [sagarika.dev||gmail.com] Hi, I am anew user of AIM2000. I wish to calculate multicentre delocalisation indices, as a measuremnet of charge transfer in stacking interaction by AIM2000. Can anybody suggest me the detailed steps to do this? sagarika From owner-chemistry@ccl.net Fri Jul 16 13:16:00 2010 From: "Alex Allardyce aa(!)chemaxon.hu" To: CCL Subject: CCL: Repost: Program announcement and call for participants: ChemAxon's US UGM: September 14-15, Boston, MA Message-Id: <-42298-100716110206-21306-3Nj2zZwvCfCCfgRczsR8PQ#server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------060304010508040801030907" Date: Fri, 16 Jul 2010 17:01:48 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa%chemaxon.hu] This is a multi-part message in MIME format. --------------060304010508040801030907 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit My apologies, I must re-post this, there were errors in some links. ************ The program is now available for ChemAxon's 2010 US User Group Meeting which will be held on Tuesday and Wednesday September 14-15 at the Omni Parker House, Downtown Boston. The meeting will preceded by a end user & developer training day on September 13th and followed by a Markush Forum on the morning of September 16th. Program: http://www.chemaxon.com/events/2010-us-ugm/#program The meeting will feature presentations from ChemAxon users, introduce a focus session on SharePoint, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments. Preceding the meeting will be a dual track developer and end user Training Day on May 18th. To see the topics and schedule visit: * Developer Training Day: http://www.chemaxon.com/events/2010-us-ugm/#training--developer * End user: Application Focus Training Day: http://www.chemaxon.com/events/2010-us-ugm/#training--application-focus Following the UGM we have the first meeting of the Markush Forum, an open morning for interested organizations (users and content developers) to participate in the further development of ChemAxon's tools for Markush structure enumeration and search. More information here: http://www.chemaxon.com/events/2010-us-ugm/#markush-forum To find out more about the meeting , register or submit a poster abstract (open until September 6th) and view the program, please visit: http://www.chemaxon.com/events/2010-us-ugm/. To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Yvonne Martin and Wendy Warr visit: http://www.chemaxon.com/library/ugm-presentations/. Yvonne Martin's meeting report from San Diego 2009 is here: http://www.chemaxon.com/library/ugm-presentations/2009-us/#2 We hope you can join us for a very interesting event. BR Alex Selected user presentations: * Evaluation of pKa Estimation Methods on 211 Druglike Compounds. Joann Prescott Roy, AstraZeneca * A Robotic Chemistry System for the Discovery of Cancer-Specific Targeting Ligands. John Frangioni, Harvard Medical School * Migrating Chemical Toolkits. Dan Durkin, Broad Institute * 2004-2010 - 6 years of using ChemAxon tools at Evotec. Ian Berry, Evotec (UK) Ltd * Chemical-text hybrid search engines. Yingyao Zhou, GNF * Implementation of ChemAxon in a SOA environment, Brett Hiemenz, GlaxoSmithKline * Helium: An EXCEL based User Tool for SAR analysis. Charles Wilkins, GlaxoSmithKline * Using J Chem Base - in a Db 2 environment & no chemical cartridge. Stephen Boyer, IBM Research * logD comparison with in-house data. Yvonne Martin, Martin Associates * Structure-based approaches to the indexing and retrieval of patent chemistry. Don Walter, Thomson Reuters * Fast flexible search in ZINC. John Irwin, University of California San Francisco ChemAxon Partners participants (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html ************* *Alex Allardyce* Marketing Dir. *ChemAxon* *Ltd*. Maramaros koz 3/A, Budapest, 1037, Hungary Tel: +361 453 0435 skype: alex_allardyce --------------060304010508040801030907 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit My apologies, I must re-post this, there were errors in some links.

************

The program is now available for ChemAxon's 2010 US User Group Meeting which will be held on Tuesday and Wednesday September 14-15 at the Omni Parker House, Downtown Boston. The meeting will preceded by a end user & developer training day on September 13th and followed by a Markush Forum on the morning of September 16th.

Program: http://www.chemaxon.com/events/2010-us-ugm/#program

The meeting will feature presentations from ChemAxon users, introduce a focus session on SharePoint, lightning presentations/exhibition from ChemAxon Partners and the latest updates on product developments.

Preceding the meeting will be a dual track developer and end user Training Day on May 18th. To see the topics and schedule visit:

    * Developer Training Day: http://www.chemaxon.com/events/2010-us-ugm/#training--developer
    * End user: Application Focus Training Day: http://www.chemaxon.com/events/2010-us-ugm/#training--application-focus

Following the UGM we have the first meeting of the Markush Forum, an open morning for interested organizations (users and content developers) to participate in the further development of ChemAxon’s tools for Markush structure enumeration and search. More information here: http://www.chemaxon.com/events/2010-us-ugm/#markush-forum

To find out more about the meeting , register or submit a poster abstract (open until September 6th) and view the program, please visit: http://www.chemaxon.com/events/2010-us-ugm/. To review the archives of previous meetings, including original presentations (slides and video) and meeting reports from Yvonne Martin and Wendy Warr visit: http://www.chemaxon.com/library/ugm-presentations/. Yvonne Martin's meeting report from San Diego 2009 is here: http://www.chemaxon.com/library/ugm-presentations/2009-us/#2

We hope you can join us for a very interesting event.

BR
Alex

Selected user presentations:

    * Evaluation of pKa Estimation Methods on 211 Druglike Compounds.   Joann Prescott Roy, AstraZeneca
    * A Robotic Chemistry System for the Discovery of Cancer-Specific Targeting Ligands. John Frangioni, Harvard Medical School
    * Migrating Chemical Toolkits. Dan Durkin, Broad Institute
    * 2004-2010 - 6 years of using ChemAxon tools at Evotec. Ian Berry, Evotec (UK) Ltd
    * Chemical-text hybrid search engines. Yingyao Zhou, GNF
    * Implementation of ChemAxon in a SOA environment, Brett Hiemenz, GlaxoSmithKline
    * Helium: An EXCEL based User Tool for SAR analysis. Charles Wilkins, GlaxoSmithKline
    * Using J Chem Base - in a  Db 2  environment & no chemical cartridge. Stephen Boyer, IBM Research
    * logD comparison with in-house data. Yvonne Martin, Martin Associates
    * Structure-based approaches to the indexing and retrieval of patent chemistry. Don Walter, Thomson Reuters
    * Fast flexible search in ZINC. John Irwin, University of California San Francisco

ChemAxon Partners participants (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html

*************
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037, Hungary
Tel: +361 453 0435
skype: alex_allardyce

--------------060304010508040801030907-- From owner-chemistry@ccl.net Fri Jul 16 16:24:00 2010 From: "Jamin Krinsky jamink^-^berkeley.edu" To: CCL Subject: CCL:G: Use of memory in Gaussian G09 A.01 Message-Id: <-42299-100716162215-6881-wqbBvo1KvyyKDN6vxFYqyQ . server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=00c09f905e9ffebe94048b86f8dc Date: Fri, 16 Jul 2010 13:22:05 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink[a]berkeley.edu] --00c09f905e9ffebe94048b86f8dc Content-Type: text/plain; charset=ISO-8859-1 Ritesh, You make a file called Default.Route (I think it IS case-sensitive, and make sure whatever account owns G09 has read permission for it) and put it in the gaussian root directory (the directory with the g09 executable and all of the l###.exe instances). If you want to specify 2GB of memory and 100GB of scratch disk, the contents of the file would be: {blank line} -M- 3GB -#- MaxDisk=100GB {blank line} Did you try my suggestion of running a frequency calculation on a large molecule and still got only 98MB of memory used? If so than a Default.Route file is not going to help you, there is something wrong with your system setup. Jamin PS: A clarification, the default memory usage I quoted of 256MB assumes you are running the 64-bit version of G09. This is not the same default as G03 (the 32-bit versions, at any rate). On Thu, Jul 15, 2010 at 9:10 PM, RITESH RUHELA riteshruhela**gmail.com < owner-chemistry[A]ccl.net> wrote: > Dear Sir, > > Thanks for your prompt reply > I have tried with lesser memory also like %mem=1GB > but again the programme is using only 98MB memory > Please advice > Also someone adviced me to permanently add memory and processor usage in > default.route file > Please suggest how i can do that > whether i have to create a file called default.route > or it somewhere located and i have to manage it through command > I am using suse 11.2 > > Than you with regards > > > > On 7/16/10, Jamin Krinsky jamink]|[berkeley.edu > > wrote: >> >> In Gaussian the mem keyword specifies the total for the job, NOT per cpu >> (if running network parallel with LINDA than it is the memory for each >> node). Also, if you specify more memory than exists and the job asks for the >> specified amount of memory the job will die, it won't revert to the default. >> Jamin >> >> >> 2010/7/15 Serdar Bado?lu sbadoglu(_)gazi.edu.tr < >> owner-chemistry-#-ccl.net> >> >>> >>> Sent to CCL by: "Serdar Bado?lu" [sbadoglu[]gazi.edu.tr] >>> Dear Ritesh, >>> >>> I'm using Gaussian 03 not 09, but I suppose settings are the same. Now if >>> I'm not wrong, %mem stands for the memory per core. Because %nproc=2 in >>> your case, Gaussian looks for 2 x 3 GB = 6 GB of memory, but your total >>> physical memory is 4 GB. So, that's why it used only 98-100 MB (default >>> memory setting is 6 MW which is roughly equal to 96 MB). Try %mem=1500MB, >>> this should work. With %nproc=2, this means that Gaussian will use 3GB of >>> memory. Also, try not to spend all of the memory for Gaussian, keep some >>> for the operating system and other stuff. >>> >>> Regards >>> >>> >>> -- >>> Serdar BADOGLU >>> Gazi University >>> Department of Physics>>> E-mail to subscribers: CHEMISTRY-#-ccl.net or use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use>>> >>> >>> >> >> >> -- >> Jamin L Krinsky, Ph.D. >> Molecular Graphics and Computation Facility >> 175 Tan Hall, University of California, Berkeley, CA 94720 >> jamink-#-berkeley.edu, 510-643-0616 >> >> http://glab.cchem.berkeley.edu >> >> > > > -- > Ritesh Ruhela -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink[A]berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --00c09f905e9ffebe94048b86f8dc Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Ritesh,

You make a file called Default.Route (I think it IS case-sen= sitive, and make sure whatever account owns G09 has read permission for it)= and put it in the gaussian root directory (the directory with the g09 exec= utable and all of the l###.exe instances). If you want to specify 2GB of me= mory and 100GB of scratch disk, the contents of the file would be:

{blank line}
-M- 3GB
-#- MaxDisk=3D100GB
{blank line}

D= id you try my suggestion of running a frequency calculation on a large mole= cule and still got only 98MB of memory used? If so than a Default.Route fil= e is not going to help you, there is something wrong with your system setup= .

Jamin

PS: A clarification, the default memory usage I quoted of = 256MB assumes you are running the 64-bit version of G09. This is not the sa= me default as G03 (the 32-bit versions, at any rate).



On Thu, Jul 15, 2010 at 9:10 PM, RITESH RUHELA riteshruhela**gmail.com <owner-chemistry[A]ccl.net> wrote:
Dear Sir,
=A0
Thanks for your prompt reply
I have tried with lesser memory also like %mem=3D1GB
but again the programme is using only 98MB memory
Please advice
Also someone adviced me to permanently add memory and processor usage = in default.route file
Please suggest how i can do that
whether i have to create a file called default.route
or it somewhere located and i have to manage it through command
I am using suse 11.2
=A0
Than you with regards


=A0
On 7/16/10, = Jamin Krinsky jamink]|[be= rkeley.edu <owner-chemistry() ccl.net> wrote:
In Gaussian the m= em keyword specifies the total for the job, NOT per cpu (if running network= parallel with LINDA than it is the memory for each node). Also, if you spe= cify more memory than exists and the job asks for the specified amount of m= emory the job will die, it won't revert to the default.
Jamin


2010/7/15 Serdar Bado?lu sbadoglu(_)gazi.edu.tr <= ;owner-chemi= stry-#-ccl.net>

Sent to= CCL by: "Serdar Bado?lu" [sbadoglu[]gazi.edu.tr]
Dear Ritesh,

I'm using Gaussian 03 not 09, but I suppose setting= s are the same. Now if
I'm not wrong, %mem stands for the memory per= core. Because %nproc=3D2 in
your case, Gaussian looks for 2 x 3 GB =3D = 6 GB of memory, but your total
physical memory is 4 GB. So, that's why it used only 98-100 MB (default=
memory setting is 6 MW which is roughly equal to 96 MB). Try %mem=3D150= 0MB,
this should work. With %nproc=3D2, this means that Gaussian will us= e 3GB of
memory. Also, try not to spend all of the memory for Gaussian, keep somefor the operating system and other stuff.

Regards


--
= Serdar BADOGLU
Gazi University
Department of Physics



-=3D This is automatically added to each mes= sage by the mailing script =3D-
E-mail t= o subscribers: CHE= MISTRY-#-ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use

=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Su= bscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.s= html

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/




--
Jamin L Krinsky, Ph.D.
Mole= cular Graphics and Computation Facility
175 Tan Hall, University of Cali= fornia, Berkeley, CA 94720
jamink-#-berkeley.edu, 510-643-0616=20



--
Ritesh Ruhela=20



--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink[A]berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--00c09f905e9ffebe94048b86f8dc--