From owner-chemistry@ccl.net Mon Nov 2 04:06:01 2009 From: "Stan van Gisbergen vangisbergen%a%scm.com" To: CCL Subject: CCL: ADF and SGE(Grid Engine) : How To ? Message-Id: <-40587-091102040332-7866-qjY9DWTj4Oo28uXrBihlZg|server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-357--327522336 Date: Mon, 2 Nov 2009 10:02:31 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Stan van Gisbergen [vangisbergen[*]scm.com] --Apple-Mail-357--327522336 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Surasjajwej, This type of technical ADF question, is perhaps more suitable for the ADF forum: http://www.scm.com/forums/ or to send directly to our support E-mail address (support [at] scm.com). I will now forward this message to support, so you will receive instructions from one of my colleagues. Other than the generic recommendation to install the latest release ADF2009, I can only tell you now that the ADFjobs command center in the ADF-GUI includes SGE support. The GUI installation manual gives examples on how to set up a new SGE queue within ADFjobs: http://www.scm.com/Doc/Doc2009.01/Install/GUI/page1.html http://www.scm.com/Doc/Doc2009.01/Install/GUI/page9.html This allows ADF users to submit parallel ADF jobs to a remote cluster directly from the ADF-GUI on their desktop. This works in a transparent way and affords local visualization of the results. Best regards, Stan van Gisbergen On Oct 30, 2009, at 10:03 PM, Sudarshan Wadkar wadkar^_^gmail.com wrote: > Dear CCL subscribers, > I have few queries regarding Grid Engine's queue system and ADF > (2008.01e). > First a little background : > I have a 4 node mini-cluster(4 x Core 2 Quad) using Rocks 5.1/ > CentOS 5, where I have managed to install and run ADF2008.01e in > parallel. The important file for parallel execution, ".machine" or > the "machinefile" is working properly. It's contents are -- > > compute-0-0 4 > compute-0-1 4 > compute-0-2 4 > > I am confused about 3 things > 1. ADF uses its own HP-MPI library ($ADFHOME/bin/hpmpi) how do I > configure SGE so that it uses that HP-MPI library and not the > system MPI ? > 2. When I run ADF in interactive mode from ADF-GUI, I know I can > change the .machinefile to control behaviour of ADF in a prallel > run. How do I manage that using SGE? To put it in another way, how > do I use SGE to determine which nodes are free and ADF should start > as and when it gets, say 8 processors (i.e. 2 nodes) free? How to > tell ADF to run only on those specific nodes? > 3. How to create a parallel run shell script (which would interact > with "qsub" command) from an ADf ".job" file? > > Thank you :) > > > -Surasjajwej > ~$udhi > "Success is getting what you want. Happiness is wanting what you get." > - Dale Carnegie > "There is only one success - to be able to spend your life in your > own way." > - Christopher Morley Dr. S.J.A. van Gisbergen Chief Executive Officer Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen * scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-357--327522336 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=US-ASCII Dear Surasjajwej, 

This type of technical ADF = question, is perhaps more suitable for the ADF forum: http://www.scm.com/forums/
or to send directly to our support E-mail address (support [at] = scm.com). 

I will now forward this message = to support, so you will receive instructions from one of my = colleagues. 
Other than the generic recommendation to = install the latest release ADF2009, I can only tell you now that the = ADFjobs
command center in the ADF-GUI includes SGE = support.

The GUI installation manual gives = examples on how to set up a new SGE queue within = ADFjobs: 
http://w= ww.scm.com/Doc/Doc2009.01/Install/GUI/page1.html
http://w= ww.scm.com/Doc/Doc2009.01/Install/GUI/page9.html

<= div>This allows ADF users to submit parallel ADF jobs to a remote = cluster directly from the ADF-GUI on their desktop. 
This = works in a transparent way and affords local visualization of the = results. 

Best regards,
Stan van = Gisbergen 

On Oct 30, 2009, at 10:03 PM, = Sudarshan Wadkar wadkar^_^gmail.com wrote:

Dear CCL = subscribers,
I have few queries regarding Grid Engine's queue system = and ADF (2008.01e).
First a little background :
I have a 4 node = mini-cluster(4 x Core 2 Quad) using Rocks 5.1/CentOS 5, where I have = managed to install and run ADF2008.01e in parallel. The important file = for parallel execution, ".machine" or the "machinefile" is working = properly. It's contents are --

compute-0-0 4
compute-0-1 = 4
compute-0-2 4

I am confused about 3 = things
1. ADF uses its own HP-MPI library ($ADFHOME/bin/hpmpi) how do = I configure SGE so that it uses that HP-MPI library and not the system = MPI ?
2. When I run ADF in interactive mode from ADF-GUI, I know I = can change the .machinefile to control behaviour of ADF in a prallel = run. How do I manage that using SGE? To put it in another way, how do I = use SGE to determine which nodes are free and ADF should start as and = when it gets, say 8 processors (i.e. 2 nodes) free? How to tell ADF to = run only on those specific nodes?
3. How to create a parallel run = shell script (which would interact with "qsub" command) from an ADf = ".job" file?

Thank you = :)


-Surasjajwej
~$udhi
"Success is getting what you = want. Happiness is wanting what you get."
- Dale Carnegie
"There = is only one success - to be able to spend your life in your own = way."
- Christopher Morley

Dr. S.J.A. van Gisbergen
Chief Executive Officer
De = Boelelaan 1083
1081 HV Amsterdam
The Netherlands         =                     =    
T: +31-20-5987626    
F: +31-20-5987629

= --Apple-Mail-357--327522336-- From owner-chemistry@ccl.net Mon Nov 2 06:05:01 2009 From: "Roger Kevin Robinson scu98rkr/a\gmail.com" To: CCL Subject: CCL:G: Sun Grid Engine or General Cluster Management Message-Id: <-40588-091102060315-15792-cj9X1MRkMVAZGFxIFBODbw/a\server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 02 Nov 2009 11:07:50 +0000 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [scu98rkr..gmail.com] Dear All, We have a 64 node cluster consisting of 32 dual node machines. There are about 3 users. 2 of the users run single processor jobs that usually last between 7 hours and 1-2 days and they tend to queue up a batch of test cases ie up 70 jobs each. Im running Gaussian and run many different types of jobs 1-2 hours or composite calculations several days. Recently I've started running dual processor open mp2 jobs. I tend to just run a few jobs at a time. Although I occasionally will run batches. We've never really come to a satisfactory conclusion of how to manage the resources most efficiently. Quite often 1-2 users will not be using the node so I want the all of the resources open to every one. I've set up the share policy to 33% each so Queued jobs will be order according to how much computing power each user is using on the cluster. Which is good but it still means the user with the least jobs has to wait till the previous jobs have finished until their (possibly 1 hour job) will run. Also as I mentioned earlier I've started running dual processor jobs. I've just come back over the weekend to find none of my jobs have ran even after being at the front of the queue because at no point have 2 nodes on the same machine been free ( rather unsurprisingly)(I can pretend the jobs only uses 1 processor but I've noticed if you specify 2 processors and some one else starts a job on the same machine the computation time become much slower than if you'd specified 1 processor) What I really need SGE to do is monitor the usage of each user check if any user is using more than 33% of the cluster. If there are currently any other jobs queued it needs to suspend the user over 33% jobs and replace them with the queued jobs. SGE doesnt seem to have any problem suspending jobs so can it running other jobs in that suspended space. I dont want limit peoples access to queues because I want the whole cluster available to 1 user if there is space. Thanks Roger From owner-chemistry@ccl.net Mon Nov 2 06:40:01 2009 From: "kave h kaveh01-.-yahoo.com" To: CCL Subject: CCL:G: Mo and basis set in chk file Message-Id: <-40589-091102054234-13929-C8g0CzEvj1la+nnHCuT/uQ[a]server.ccl.net> X-Original-From: "kave h" Date: Mon, 2 Nov 2009 05:42:30 -0500 Sent to CCL by: "kave h" [kaveh01**yahoo.com] Dear all is there any way to put just basis set and Mo in chk file ( gaussian 09 ) ? actually finaly I want a formated checkpoint file with g03 format.in gaussian 03 I do this easily by this line in input file "# formcheck=(mo,basis) " but in g09 the output of above line is different. I want to put Mo and basis set in chk file and convert it to g03 format using "formchk -2" Thank you From owner-chemistry@ccl.net Mon Nov 2 11:11:00 2009 From: "Zsolt Zsoldos zsolt]-[simbiosys.ca" To: CCL Subject: CCL:G: Be a bit cautious... Message-Id: <-40590-091102110413-16152-3hD+M80JwIAeAqR5tbLDBA/a\server.ccl.net> X-Original-From: Zsolt Zsoldos Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 2 Nov 2009 11:04:27 -0400 MIME-Version: 1.0 Sent to CCL by: Zsolt Zsoldos [zsolt|simbiosys.ca] This is a serious problem that I have also been fighting for years -- so far without any general silver-bullet solution. There is a very simple example code to demonstrate how horrible the problem is on my earlier blog post I made as response to a similar emal on this list: http://www.simbiosys.ca/blog/2008/05/28/floating-point-errors/ If you compile that sample code on different platform, different optimization options, you get different cases giving the wrong result, but what is common to all platforms and option is that you have a very significant portion of the tested cases fail. Which means, floating point errors can wrack havoc on our calculations even at single decimal digit precisions! ZZ On Fri, Oct 30, 2009 at 6:04 PM, John McKelvey jmmckel^^^gmail.com wrote: > Folks, > > I have a dilemma: Significantly results depending on the compiler. > > All copies of source are identical and compiled for real*8 (double precision > for 32 bits), and all answers are independent of optimization level. The > gfortran is the latest available download version. ( I chose it because it > is available across several OS's) The g77 came with RHEL. > > The calculation involved reading output from a G03 log file where Mulliken > populations were computed from selected printed open shell MO's and printed > AO overlaps. [log file numbers had 5-6 significant figuresafter decimal] > Again, all calculations done in the special program were done in real*8, and > results are independent of optimization level. > Compiler Answer Hardware, OS > 1) Linux Intel compiler (ifort) ~16 AMD64 opteron RHEL4 > (~=Centos 4) > 2) Linux g77 compiler ~10 " > 3) Windows Digital Corp compiler ~16 Intel P4 Windows2000 > 4) Windows gfortran compiler ~10 " > 5) Linux gfortran " ~10 Xeon Centos 5.3 > (~= RHEL5.3) > > Thoughts? > > Thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel%a%gmail.com > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel%a%gmail.com > -- Zsolt Zsoldos From owner-chemistry@ccl.net Mon Nov 2 13:20:01 2009 From: "Stephen Todd stodd\a/accelrys.com" To: CCL Subject: CCL: Announcement: Materials Studio 5.0 Release Message-Id: <-40591-091102131653-25373-jShlJeYtnjKXGtLCg6zBpQ**server.ccl.net> X-Original-From: "Stephen Todd" Date: Mon, 2 Nov 2009 13:16:50 -0500 Sent to CCL by: "Stephen Todd" [stodd[A]accelrys.com] I am pleased to announce the release of Materials Studio 5.0. New functionality in this release includes: * Parallelized versions of Forcite Plus and Mesocite for classical simulations of atoms and beads * Mesocite now includes a parallel implementation of dissipative particle dynamics for simulations of soft matter * A new Amorphous Cell which enables building of any type of amorphous structure, including the capabilities to constrain packing to defined volumes and improved treatment of flexible torsions and ring spearing. * CASTEP, our plane-wave DFT code, can now compute Raman intensities, has improved spectra display for core level spectra, and includes the new PBEsol gradient corrected density functional. * Improved forcefield support, periodic QMPot, and vibrational frequencies for QM/MM calculations using QMERA * Extensions to the AM1* semi-empirical hamiltonian in VAMP * Much much more... Interested in finding out more? Attend one of our webinars: http://accelrys.com/events/webinars/materials-studio-50/index.html Best regards, Stephen Todd, Senior Product Manager, Materials Studio From owner-chemistry@ccl.net Mon Nov 2 14:01:00 2009 From: "dewdew zhou dewdew,126.com" To: CCL Subject: CCL:G: The l502 error in CBS-QB3 calculation Message-Id: <-40592-091102135821-13543-FWjdbGifqUiGdJ3XTbRuVA,server.ccl.net> X-Original-From: "dewdew zhou" Date: Mon, 2 Nov 2009 13:58:17 -0500 Sent to CCL by: "dewdew zhou" [dewdew|,|126.com] Dear all, I have used the B3lyp/cbsb7 method to calculate the geometry of a very loose complex, and it is termined well. Based on this geometry i used the CBS/QB3 method to calculate the single point energy, and it always shows the following error: >>>>>>>>>> Convergence criterion not met. SCF Done: E(UHF) = -267.358083472 A.U. after 129 cycles Convg = 0.4652D-04 -V/T = 2.0021 = 0.0000 = 0.0000 = 0.5000 = 0.7554 S= 0.5027 = 0.000000000000E+00 Annihilation of the first spin contaminant: S**2 before annihilation 0.7554, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in /ichec/packages/gaussian/09a02/l502.exe at Tue Oct 20 10:27:32 2009. Job cpu time: 0 days 0 hours 1 minutes 49.3 seconds. File lengths (MBytes): RWF= 48 Int= 0 D2E= 0 Chk= 3 Scr= 1 Do you know how to fix it? If you know, please tell me, i will very appreciate that. Thanks a lot!