From owner-chemistry@ccl.net Sat Jul 17 06:27:01 2010 From: "RITESH RUHELA riteshruhela|gmail.com" To: CCL Subject: CCL:G: Use of memory in Gaussian G09 A.01 Message-Id: <-42300-100717042912-2435-R0uJMP4+b0vJ5UAmDkAhgw#server.ccl.net> X-Original-From: RITESH RUHELA Content-Type: multipart/alternative; boundary=000e0cd312fcce76f3048b911eb5 Date: Sat, 17 Jul 2010 13:58:30 +0530 MIME-Version: 1.0 Sent to CCL by: RITESH RUHELA [riteshruhela:_:gmail.com] --000e0cd312fcce76f3048b911eb5 Content-Type: text/plain; charset=ISO-8859-1 Dear Sir, As advices by you I run gaussian using large molecule also but again the memory used by the programme is 98MB. Also i have made a default.route file and put it in gaussian root directroy. when I run gaussian the memory used is still 98MB inspite of the fact that i have assigned more memory in the dafault.route file. you have told that there may be problem with system setup How can I identify and rectify the problem with setup if any Please guide me thanks with regards On Sat, Jul 17, 2010 at 1:52 AM, Jamin Krinsky jamink^-^berkeley.edu < owner-chemistry(0)ccl.net> wrote: > 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 . 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 > ccl.net > 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 . berkeley.edu , 510-643-0616 > http://glab.cchem.berkeley.edu > > -- Ritesh Ruhela --000e0cd312fcce76f3048b911eb5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sir,

As advices by you I=A0 run gaussian using large molecule a= lso but again the memory used by the programme is 98MB. Also i have made a = default.route file and put it in gaussian root directroy. when I run gaussi= an the memory used is still 98MB inspite of the fact that i have assigned m= ore memory in the dafault.route file.
you have told that there may be problem with system setup
How can I iden= tify and rectify the problem with setup if any
Please guide me

th= anks with regards


On Sat, Jul 17, 201= 0 at 1:52 AM, Jamin Krinsky jamink^-^berkel= ey.edu <owner-chemistry(0)ccl.net> wrote:
Ritesh,

Yo= u 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 th= e 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=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 . = 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 message by the m= ailing script =3D-
E-mail to subscribers: CHEMISTRY-#-ccl.net or us= e:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

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



--
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.
Molecular Graphics and Computation Facility
1= 75 Tan Hall, University of California, Berkeley, CA 94720
jamink . berkeley.edu, 510= -643-0616
http://glab.cc= hem.berkeley.edu




--
Ritesh Ruhela --000e0cd312fcce76f3048b911eb5--