From owner-chemistry@ccl.net Fri Aug 1 04:29:02 2008 From: "may abdelghani may01dz|a|yahoo.fr" To: CCL Subject: CCL:G: Re : CCL:G: Duel cords processors and parallel calculations Message-Id: <-37473-080801041807-19065-mQgbazzxsHxkiqSAsLLzkw#,#server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-297812393-1217578665=:67095" Date: Fri, 1 Aug 2008 08:17:45 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz|yahoo.fr] --0-297812393-1217578665=:67095 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable sir, This a small description on the code that I want to used in my calculation: =E2=80=9CStarting from ADF2007.01, the Windows version of ADF comes bundled with the HP-MPI runtime environment. This means that y= ou can run parallel ADF jobs on your brand new multi-core Windows machine. By default, if the NSCM environment variable is not defined, ADF will use all logical processors present in the system. To avoid this, you need to set NS= CM to 1. You can do this permanently by adding NSCM with the value 1 to the li= st of environment variables or on the per-queue basis putting "export NSCM=3D1" (without quotes) in the prolog field of the corresponding queue i= n ADFjobs. Moreover, you can define two local queues in ADFjobs: one for seri= al and one for parallel jobs. The queues may be called, for example, serial an= d parallel. You would then need to change the prolog value for the serial que= ue only=E2=80=9D --- En date de : Jeu 31.7.08, Herbert Fruchtl herbert.fruchtl^st-andrews.ac= .uk a =C3=A9crit : De: Herbert Fruchtl herbert.fruchtl^st-andrews.ac.uk Objet: CCL:G: Duel cords processors and parallel calculations =C3=80: "Abdelghani, May " Date: Jeudi 31 Juillet 2008, 11h54 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl#,#st-andrews.ac.uk] It would help to know WHAT you want to do in parallel. To use several=20 cores at the same time, you need to 1) Write the program for parallel execution 2) Compile the program for parallel execution 3) Run it in parallel. If you have a parallel executable, i.e. 1) and 2) are taken care of,=20 this leaves you with 3), which depends on the parallelization method=20 (and the operating system). - If it's Gaussian, you need %NProcShared=3D2 in the input. - If it's another OpenMP program, you have to set the environment=20 variable OMP_NUM_THREADS (it depends on the OS how you do that). - If it's an MPI program, you need to run it via a parallel startup=20 program (in most implementations this is called mpirun, but the syntax=20 may vary. RTFM!). - If it's yet another parallelization method (PVM, GA, ...), RTFM! But=20 since anybody who can't be bothered to mention his program is using=20 Gaussian anyway... Herbert may abdelghani may01dz*|*yahoo.fr wrote: > dear CCLers, > In any calculations, a duel core processors, using only one core for=20 > this calculation, whereas the second rest inactive. I ask if it is any=20 > possibility to help the tow cores of my processor to sharing a one=20 > calculation, like what we do in the parallel calculations (both cores do= =20 > a one task in the same time). > Thanks > =20 >=20 >=20 >=20 >=20 >=20 >=20 >=20 > ------------------------------------------------------------------------ > Envoy=C3=A9 avec Yahoo! Mail=20 > . > Une boite mail plus intelligente. --=20 Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt=0A=0A=0A ___= __________________________________________________________________________ = =0AEnvoyez avec Yahoo! Mail. Une boite mail plus intelligente http://mail.y= ahoo.fr --0-297812393-1217578665=:67095 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

sir, This a small description on the code that I want to used in my calculation:=


<= /span>

=E2=80=9CStarting from ADF2007.0= 1, the Windows version of ADF comes bundled with the HP-MPI runtime environment. This means that y= ou can run parallel ADF jobs on your brand new multi-core Windows machine. By default, if the NSCM environment variable is not defined, ADF will use all logical processors present in the system. To avoid this, you need to set NS= CM to 1. You can do this permanently by adding NSCM with the value 1 to the li= st of environment variables or on the per-queue basis putting "export NSCM=3D1" (without quotes) in the prolog field of the corresponding queue i= n ADFjobs. Moreover, you can define two local queues in ADFjobs: one for seri= al and one for parallel jobs. The queues may be called, for example, serial an= d parallel. You would then need to change the prolog value for the serial que= ue only=E2=80=9D



--- En date de : Jeu 31.7.08, Herbert Fruchtl herbert.fruchtl^= st-andrews.ac.uk <owner-chemistry],[ccl.net> a =C3=A9crit :<= br>
De: Herbert Fruchtl herbert.fruchtl^st-andrews.= ac.uk <owner-chemistry],[ccl.net>
Objet: CCL:G: Duel cords processor= s and parallel calculations
=C3=80: "Abdelghani, May " <may01= dz],[yahoo.fr>
Date: Jeudi 31 Juillet 2008, 11h54

Sent to C=
CL by: Herbert Fruchtl [herbert.fruchtl#,#st-andrews.ac.uk]
It would hel=
p to know WHAT you want to do in parallel. To use several 
cores at the =
same time, you need to
1) Write the program for parallel execution
2)=
 Compile the program for parallel execution
3) Run it in parallel.
If you have a parallel executable, i.e. 1) and 2) are taken care of, 
=
this
 leaves you with 3), which depends on the parallelization method 
(and t=
he operating system).
- If it's Gaussian, you need %NProcShared=3D2 in t=
he input.
- If it's another OpenMP program, you have to set the environm=
ent 
variable OMP_NUM_THREADS (it depends on the OS how you do that).- If it's an MPI program, you need to run it via a parallel startup 
pr=
ogram (in most implementations this is called mpirun, but the syntax 
ma=
y vary. RTFM!).
- If it's yet another parallelization method (PVM, GA, .=
..), RTFM! But 
since anybody who can't be bothered to mention his progr=
am is using 
Gaussian anyway...

   Herbert

may abdelghani =
may01dz*|*yahoo.fr wrote:
> dear CCLers,
> In any calculations,=
 a duel core processors, using only one core for 
> this calculation,=
 whereas the second rest inactive. I ask if it is any 
> possibility =
to help the tow cores of my processor to sharing a one 
>
 calculation, like what we do in the parallel calculations (both cores do <=
br>> a one task in the same time).
> Thanks
>  
> 
=
> 
> 
> 
> 
> 
> 
> ----------------=
--------------------------------------------------------
> Envoy=C3=
=A9 avec Yahoo! Mail 
>
<http://us.rd.yahoo.com/mailuk/taglines=
/isp/control/*http://us.rd.yahoo.com/evt=3D52423/*http://fr.docs.yahoo.com/=
mail/overview/index.html>.
> Une boite mail plus intelligente.
=

-- 
Herbert Fruchtl
EaStCHEM Fellow
School of Chemistry
Uni=
versity of St Andrews
--
The University of St Andrews is a charity re=
gistered in Scotland:
No SC013532



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=0A=0A=0A =
=0AEnvoy=C3=A9 avec Yahoo! Mail.
Une boite mail plus= intelligente. --0-297812393-1217578665=:67095-- From owner-chemistry@ccl.net Fri Aug 1 07:55:01 2008 From: "Sue Lam chsue2004===yahoo.com" To: CCL Subject: CCL:G: Locating a broken-symmetry singlet state in Gaussian Message-Id: <-37474-080801074355-2531-O/wVR6CrGwGKKkil4cTyoQ],[server.ccl.net> X-Original-From: Sue Lam Content-Type: multipart/alternative; boundary="0-1888444919-1217587423=:31238" Date: Fri, 1 Aug 2008 03:43:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004]![yahoo.com] --0-1888444919-1217587423=:31238 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Mariusz, =A0 Thank you for your reply. I am trying to locate a open-shell singlet=A0tran= sition state by using UDFT.=A0 What else that I need to check in order to c= onfirm that it is the=A0correct broken symmetry singlet state, other than t= he =A0correct occupation of singly alpha and beta orbitals and the=A0 non-z= ero vaule. =A0 Thanks a=A0 lot =A0 Sue --- On Thu, 7/31/08, Mariusz Radon mariusz.radon-,-gmail.com wrote: > From: Mariusz Radon mariusz.radon-,-gmail.com Subject: CCL:G: Locating a broken-symmetry singlet state in Gaussian To: "L, Sue " Date: Thursday, July 31, 2008, 5:16 PM Sent to CCL by: Mariusz Radon [mariusz.radon~~gmail.com] Sue L chsue2004:yahoo.com wrote: > Is it necessary to put a keyword guess=3Dmix, in order to locate a > broken-symmetry singlet state in Gaussian? If the molecule contains a > symmetry, in which the singly occupied alpha and beta orbitals are in > different symmetry, there is no need to put that keyword? >=20 Hi Sue, Is it enough or not, I think, it depends on particular case... You=20 always need to check whether you really have converged to a=20 broken-symmetry solution or not; AFAIK, even "guess=3Dmix" keyword doesn't=20 guarantee this. So, you need to inspect the molecular orbitals and/or=20 value after the calculations are finished. In such a case, that alpha and beta singly occupied orbitals belong to=20 different symmetries, a nice way to produce the broken symmetry solution=20 might be to manually permute the relevant orbitals (e.g. "guess=3Dalter")=20 and (probably) to use "scf=3Dsymm". best wishes, Mariusz Radon -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt=0A=0A=0A --0-1888444919-1217587423=:31238 Content-Type: text/html; charset=us-ascii

Dear Mariusz,

 

Thank you for your reply. I am trying to locate a open-shell singlet transition state by using UDFT.  What else that I need to check in order to confirm that it is the correct broken symmetry singlet state, other than the  correct occupation of singly alpha and beta orbitals and the  non-zero <S**2> vaule.

 

Thanks a  lot

 

Sue

--- On Thu, 7/31/08, Mariusz Radon mariusz.radon-,-gmail.com <owner-chemistry-$-ccl.net> wrote:

From: Mariusz Radon mariusz.radon-,-gmail.com <owner-chemistry-$-ccl.net>
Subject: CCL:G: Locating a broken-symmetry singlet state in Gaussian
To: "L, Sue " <chsue2004-$-yahoo.com>
Date: Thursday, July 31, 2008, 5:16 PM

Sent to CCL by: Mariusz Radon [mariusz.radon~~gmail.com]
Sue L chsue2004:yahoo.com wrote:
> Is it necessary to put a keyword guess=mix, in order to locate a
> broken-symmetry singlet state in Gaussian? If the molecule contains a
> symmetry, in which the singly occupied alpha and beta orbitals are in
> different symmetry, there is no need to put that keyword?
> 

Hi Sue,

Is it enough or not, I think, it depends on particular case... You 
always need to check whether you really have converged to a 
broken-symmetry solution or not; AFAIK, even "guess=mix" keyword
doesn't 
guarantee this. So, you need to inspect the molecular orbitals and/or 
<S**2> value after the calculations are finished.

In such a case, that alpha and beta singly occupied orbitals belong to 
different symmetries, a nice way to produce the broken symmetry solution 
might be to manually permute the relevant orbitals (e.g.
"guess=alter") 
and (probably) to use "scf=symm".

best wishes,
Mariusz Radonhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

--0-1888444919-1217587423=:31238-- From owner-chemistry@ccl.net Fri Aug 1 09:52:01 2008 From: "Siamkhanthang Neihsial sktn06 . gmail.com" To: CCL Subject: CCL:G: ESP-derived-charge error messages Message-Id: <-37475-080801092315-23997-d4VFz3aT1mc2f941Lp5Nog]^[server.ccl.net> X-Original-From: "Siamkhanthang Neihsial" Date: Fri, 1 Aug 2008 09:23:11 -0400 Sent to CCL by: "Siamkhanthang Neihsial" [sktn06*gmail.com] Dear all, I was trying to run an ESP-derived charge calculation in Gaussian 03 for my sytem at single point calculation at MP2/6-311++G(d,p) pop=mk iop(6/33=2) iop(6/42=6)level on the optimized geometry calculated at the level of B3LYP/6-31g(d,p). My system is a novel base-pair consisting of 85 atoms, including six N atoms, four P atoms,twenty three O atoms. The sugar is a D-allopyranose .I got the following error messages--, " Erroneous write: write -1 instead of 4096, fd=4, orig len=4096 left=4096, g-write, " Can any one tell me the significance of this messages and how to solve it ? . Ofcourse, when I used B3LYP/6-311++G(d,p) the job terminated normally. Thanks in advance, Siamkhanthang Neihsial, Deptt. of Chemistry, NEHU, Shillong(India) sktn06##gmail.com From owner-chemistry@ccl.net Fri Aug 1 12:16:00 2008 From: "Close, David M. CLOSED%%mail.etsu.edu" To: CCL Subject: CCL:G: ESP-derived-charge error messages Message-Id: <-37476-080801114623-31105-DMaBY7VuaJZ0VAMhiq/Tog ~~ server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Fri, 1 Aug 2008 10:23:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED]_[mail.etsu.edu] Siamkhanthang: The problem is that you have tried to write information to the disk, and have exceeded the limitations in Gaussian. If you are using a 32 bit machine, the program limits you to writing 16Gbytes of space on the hard drive. MP2 uses a lot more disk space than B3LYP. The Gaussian manual shows you how to save .rwf files in 2 GByte segments. Do what the manual says, and then watch the rwf.a, rwf.b, files fill up. If you get to the limit you will have to do the problem over on a 64 bit machine. -----Original Message----- > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net]=20 Sent: Friday, August 01, 2008 9:23 AM To: Close, David M. Subject: CCL:G: ESP-derived-charge error messages Sent to CCL by: "Siamkhanthang Neihsial" [sktn06*gmail.com] Dear all, I was trying to run an ESP-derived charge calculation in Gaussian 03 for my sytem at single point calculation at MP2/6-311++G(d,p) pop=3Dmk iop(6/33=3D2) iop(6/42=3D6)level on the optimized geometry calculated at = the level of B3LYP/6-31g(d,p). My system is a novel base-pair consisting of 85 atoms, including six N atoms, four P atoms,twenty three O atoms. The sugar is a D-allopyranose .I got the following error messages--, " Erroneous write: write -1 instead of 4096, fd=3D4, orig len=3D4096 left=3D4096, g-write, " Can any one tell me the significance of this messages and how to solve it ? . Ofcourse, when I used B3LYP/6-311++G(d,p) the job terminated normally. Thanks in advance, Siamkhanthang Neihsial, Deptt. of Chemistry, NEHU, Shillong(India) sktn06-x-gmail.com -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt