From owner-chemistry@ccl.net Thu Dec 9 08:10:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek:+:few.vu.nl" To: CCL Subject: CCL:G: Help for cluster Message-Id: <-43310-101209033728-13983-50YMMFyCrIh58EcG9s23UQ===server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 9 Dec 2010 09:37:22 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek]-[few.vu.nl] On Wed, Dec 8, 2010 at 5:48 PM, Utpal Sarkar utpalchemiitkgp[-]gmail.com wrote: > Dear CCL users, >                                We are planning to purchase a 16 node (or > even 32 node depending upon the price needed) cluser in which we will run > softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly give > your valuable suggestion about: > a) which type of specification is better ? Exactly what kind of jobs will you run? This is important since it will tell us how much memory, network bandwidth and disk performance you need. > b) How much does it cost (we can spent upto $10K to $11K) ? > c) does the company/ provider (ie, HP, Dell, SGI ets) will install the > cluster in the lab or we have to install ourself? They will install an operating system for you if you pay, however the operating system is usually very easy to install, the applications are more difficult. > We are starting  from the begining and have no idel of purchasing clusters, > so asking so many questions. Will you maintain this machine yourself? Generally if you have a good/cheap administrator you can buy components of lower quality, and in some sense get more for your money. You cluster will be so small that you perhaps won't need a very expensive file server, for example. However, if you have to pay for maintenance when something breaks you really should consider some fancier hardware. Regards, Ulf Ekstrom From owner-chemistry@ccl.net Thu Dec 9 08:45:00 2010 From: "Herbert Fruchtl herbert.fruchtl],[st-andrews.ac.uk" To: CCL Subject: CCL:G: Help for cluster Message-Id: <-43311-101209050455-19492-uC+My5p0mkFBfqLaE1BjrQ/a\server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 09 Dec 2010 10:04:29 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl-x-st-andrews.ac.uk] Very general questions. The answers depend on your mix of applications, budget and level of expertise. I'll try to address a few points. Utpal Sarkar utpalchemiitkgp[-]gmail.com wrote: > Dear CCL users, > We are planning to purchase a 16 node (or > even 32 node depending upon the price needed) cluser in which we will > run softwares like Gaussian, VASP, DLPOLY . So may I request you to > kindly give your valuable suggestion about: > a) which type of specification is better ? That's where the type of applications comes in: If it's mainly Gaussian, and mainly DFT calculations, get fast processors. DFT doesn't need much memory (2GB/core is plenty), and most people run only the SMP parallel version, so you don't need a fast network. If it's post-HF calculations (MP2, CCSD, ...) you're after, get more memory. And if it's beyond MP2, get a different program :-). If you want big VASP calculations (and they quickly get big), you need a fast network (Infiniband) and possibly more memory. In a small cluster like yours, you may get away with Gigabit Ethernet, but talk to somebody who has tried it first. For force-field MD, you get incredible performance for little money from GPUs, but it's still a bit experimental. Make sure the program you use supports your hardware. There's a project under way for DL_POLY, but I don't know if it's already available. > b) How much does it cost (we can spent upto $10K to $11K) ? Clusters are modular. You buy as many nodes as you can afford. Don't forget storage. > c) does the company/ provider (ie, HP, Dell, SGI ets) will install the > cluster in the lab or we have to install ourself? > You get what you pay for. They all sell turnkey solutions (i.e. fully configured and installed). Buying just hardware and slapping ROCKS (or something similar) on it is cheaper, but may cost you months of configuring. If you're lucky it works immediately, but I have seen other cases... Hope this helps, Herbert -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Thu Dec 9 10:16:00 2010 From: "Andras Borosy andras.borosy:-:givaudan.com" To: CCL Subject: CCL:G: Help for cluster Message-Id: <-43312-101209093813-22001-PkAWw4B4jCRhVRzVEDNddQ a server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 005060FDC12577F4_=" Date: Thu, 9 Dec 2010 15:37:51 +0100 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy\a/givaudan.com] This is a multipart message in MIME format. --=_alternative 005060FDC12577F4_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable I would use pqs (instead of Gaussian) at a PQS cluster: http://www.pqs-chem.com/ Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Ulf Ekstr=F6m ulfek:+:few.vu.nl" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com _ ccl.net 09.12.2010 09:37 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL:G: Help for cluster Sent to CCL by: =3D?ISO-8859-1?Q?Ulf=5FEkstr=3DF6m?=3D [ulfek]-[few.vu.nl] On Wed, Dec 8, 2010 at 5:48 PM, Utpal Sarkar utpalchemiitkgp[-]gmail.com wrote: > Dear CCL users, > We are planning to purchase a 16 node (or > even 32 node depending upon the price needed) cluser in which we will=20 run > softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly=20 give > your valuable suggestion about: > a) which type of specification is better ? Exactly what kind of jobs will you run? This is important since it will tell us how much memory, network bandwidth and disk performance you need. > b) How much does it cost (we can spent upto $10K to $11K) ? > c) does the company/ provider (ie, HP, Dell, SGI ets) will install the > cluster in the lab or we have to install ourself? They will install an operating system for you if you pay, however the operating system is usually very easy to install, the applications are more difficult. > We are starting from the begining and have no idel of purchasing=20 clusters, > so asking so many questions. Will you maintain this machine yourself? Generally if you have a good/cheap administrator you can buy components of lower quality, and in some sense get more for your money. You cluster will be so small that you perhaps won't need a very expensive file server, for example. However, if you have to pay for maintenance when something breaks you really should consider some fancier hardware. Regards, Ulf Ekstrom -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 005060FDC12577F4_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
I would use pqs (instead of Gaussian) at a  PQS cluster:

http://www.pqs-chem.com/

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com




"Ulf Ekstr=F6m u= lfek:+:few.vu.nl" <owner-chemistry _ ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com _ ccl.net

09.12.2010 09:37
Please respond to
"CCL Subscribers" <chemistry _ ccl.net>

To
"Borosy, Andras " <andras.borosy _ givaudan.com>
cc
Subject
CCL:G: Help for cluster





Sent to CCL by: =3D?ISO-8859-1?Q?Ulf=5FEkstr=3DF6m?=3D [ulfek]-[few.vu.nl]<= br> On Wed, Dec 8, 2010 at 5:48 PM, Utpal Sarkar
utpalchemiitkgp[-]gmail.com <owner-chemistry]^[ccl.net> wrote:
> Dear CCL users,
>            &nbs= p;            &= nbsp;      We are planning to purchase a 16 node (or
> even 32 node depending upon the price needed) cluser in which we will run
> softwares like Gaussian, VASP, DLPOLY . So may I request you to kindly give
> your valuable suggestion about:
> a) which type of specification is better ?

Exactly what kind of jobs will you run? This is important since it
will tell us how much memory, network bandwidth and disk performance
you need.

> b) How much does it cost (we can spent upto $10K to $11K) ?
> c) does the company/ provider (ie, HP, Dell, SGI ets) will install the
> cluster in the lab or we have to install ourself?

They will install an operating system for you if you pay, however the
operating system is usually very easy to install, the applications are
more difficult.

> We are starting  from the begining and have no idel of purchasing clusters,
> so asking so many questions.

Will you maintain this machine yourself? Generally if you have a
good/cheap administrator you can buy components of lower quality, and
in some sense get more for your money. You cluster will be so small
that you perhaps won't need a very expensive file server, for example.
However, if you have to pay for maintenance when something breaks you
really should consider some fancier hardware.

Regards,
Ulf Ekstrom



-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
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--=_alternative 005060FDC12577F4_=-- From owner-chemistry@ccl.net Thu Dec 9 11:13:01 2010 From: "Sidney Ramos Santana santanasidney ~~ quimica.ufpb.br" To: CCL Subject: CCL:G: G09 PBC Errors in Opt and Freq Calculations of Metal Oxides surfaces Message-Id: <-43313-101209101908-7347-Kgag8lIxvL3+EqNaX/G/SA.@.server.ccl.net> X-Original-From: "Sidney Ramos Santana" Date: Thu, 9 Dec 2010 10:19:05 -0500 Sent to CCL by: "Sidney Ramos Santana" [santanasidney*quimica.ufpb.br] Dear CCL users, I am trying to study adsorption of thiophene and benzothiophene on some metal oxide surfaces focusing its hydrodesulphurization reactions with G09 Revision A.02. I build my input from the CIF files. I has been choosen a minor number of coordenates to simulate the unit cell generating the G09 inputs from CIF files using Gaussview. I running Periodic Boundary Condition (PBC) calculations, with Translation Vectors, and using Fast Multipole Method in a DFT funcionals. Initally my choise was MoO3 and my goals are: Step 1) Geometry optimization of that Unit cell. Step 2) Frequency, and thermoynamics properties of that Unit cell. Step 3) Expand the optimized geometry with Gaussview to build a supercell and to define the adsorption surface to represent some adsorption plane (0,1,0), or, (1,0,0), ... Step 4) Geometry optimization of this supercell. Step 2) Frequency, and thermoynamics properties of that Unit cell. I have three kind of computer: ========== Computer 1: ========== Motherboard: Intel DP45SG Processor: Intel Core2 Quad CPU Q9550 2.83GHz No of Core: 8 L1 cache: 32KB L2 cache: 6MB Memory: 8GB Hard disk: 1TB OS: Ubuntu 9.10 Filesystem type: reiserfs ========== Computer 2: (Beowulf Cluster with two this below PC) ========== Motherboard: Intel S5000VSA Processor: (Dual) Intel Xeon CPU E5420 2.50GHz No of Core: 8 L1 cache: 128KB L2 cache: 12MB Memory: 16GB Hard disk: 1TB OS: Ubuntu 10.04 Filesystem type: reiserfs ========== Computer 3: ========== Motherboard: Intel S5520HC Processor: (Dual) Intel Xeon CPU E5520 2.27GHz No of Core: 16 L1 cache: 32KB L2 cache: 256KB L3 cache: 8MB Memory: 24GB Hard disk: 1TB OS: Ubuntu 10.04 Filesystem type: reiserfs The Geometry optimization of the unit cell is runnig well. However it is creating a huge output with 2.8 to 3.0 GB. With this optimized geometry I try to run the Frequency calculation and independent what the computer has been choosen it always stop in the l1110.exe link printing the error below: NB too large for integers on this machine. Error termination via Lnk1e in /programs/g09/l1110.exe Beside, if I get the unit cell optimized geometry and build a supercell input growing three unit in the directions x and y, to create a surface, the calculation always stop in the l502.exe link printing the error below: DSDGMF failed for ItDFit. Error termination via Lnk1e in /programs/g09/l502.exe So please, I would appreciate if anyone answer the following questions: Please anybody know what is going on? Please anybody know what can I do to solve this problem ? Please anybody know what am I doing wrong ? Unfortunately the g09 doesn't seem the best choice, does it? Please could anyone suggest some other program to study surfaces and, pay attention, not cristals ? Thanks for any help. Best Regards. Sidney R. Santana Computational Quantum Chemistry Lab. (LQQC) Chemistry Department (DQ) Federal University of Paraiba (UFPB) Joo Pessoa - PB - Brazil e-mail: santanasidney_at_quimica.ufpb.br or santanasidney_at_yahoo.com.br Please see below details of inputs and outputs files: ====================================================== The Geometry Optimization of the Unit Cell: ====================================================== %chk=Lanl2dz_Opt_PBC_MoO3_half_Fixed_2D.chk %mem=7500MB %nprocshared=8 # pbepbe/gen/auto pbc pop=full gfinput fmm iop(5/13=1,5/33=1) # pseudo=read opt=(maxcycles=10000) scf=(maxcycles=10000) 2 Tv's - basis: LANL2DZ - Surface Unit Cell Tv(axis B)=(0.0,6.73134090,0.0) 0 1 Mo 0.69682403 0.83161011 0.50000000 O 2.61486763 0.81634772 0.50000000 O 0.45112423 2.59649739 0.50000000 O 0.47490163 0.50000000 2.35350000 Mo 2.67827403 4.89973079 2.35350000 O 0.63341763 4.91499318 2.35350000 O 2.43257423 3.13484351 2.35350000 O 2.29783563 5.23134090 0.50000000 Tv 3.96290000 0.00000000 0.00000000 Tv 0.00000000 0.00000000 3.70700000 Mo 0 lanl2dz **** O 0 lanl2dz **** Mo 0 lanl2dz The system have: 98 basis functions, 248 primitive gaussians, 102 cartesian basis functions Job cpu time: 34 days 8 hours 46 minutes 52.8 seconds. File lengths (MBytes): RWF= 1911 Int= 0 D2E= 0 Chk= 175 Scr= 1 Normal termination of Gaussian 09 at Fri Nov 5 00:27:42 2010. The log file size was: sidney!^!eniac:~/work2/PBC/LANL2DZ$ ls -lah total 3,0G drwxr-xr-x 6 sidney users 464 2010-12-03 06:45 . drwxr-xr-x 3 sidney users 248 2010-11-03 04:27 .. -rw-r--r-- 1 sidney users 237M 2010-12-03 05:57 Lanl2dz_Opt_PBC_MoO3_half_Fixed_2D.chk -rw-r--r-- 1 sidney users 904 2010-11-05 02:38 Lanl2dz_Opt_PBC_MoO3_half_Fixed_2D.gjf -rw-r--r-- 1 sidney users 2,8G 2010-11-05 02:42 Lanl2dz_Opt_PBC_MoO3_half_Fixed_2D.log ========================================== The Frequency calculation of the Unit Cell ========================================== The frequency calculation route section was: # pbepbe/gen/auto pbc pop=full gfinput fmm iop(5/13=1,5/33=1) # pseudo=read freq scf=(maxcycles=10000) =========== Computer 1: =========== ==> Lanl2dz_Freq_PBC_MoO3_half_Fixed_2Da.log <== ECPInt: NShTT= 1081 NPrTT= 7944 LenC2= 1049 LenP2D= 5317. LDataN: DoStor=T MaxTD1= 6 Len= 172 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 9 centers at a time, making 1 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3507 FMM=T I1Cent= 4 AccDes= 0.00D+00. NB too large for integers on this machine. Error termination via Lnk1e in /programs/g09/l1110.exe at Fri Dec 3 04:26:33 2010. Job cpu time: 0 days 12 hours 23 minutes 31.0 seconds. File lengths (MBytes): RWF= 1489 Int= 0 D2E= 0 Chk= 45 Scr= 1 =========== Computer 2: =========== ==> Lanl2dz_Freq_PBC_MoO3_half_Fixed_2Db.log <== LDataN: DoStor=T MaxTD1= 6 Len= 172 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 9 centers at a time, making 1 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3507 FMM=T I1Cent= 4 AccDes= 0.00D+00. NB too large for integers on this machine. Error termination via Lnk1e in /programs/g09/linda-exe/l1110.exel at Sat Dec 4 10:30:39 2010. Job cpu time: 0 days 0 hours 0 minutes 0.9 seconds. File lengths (MBytes): RWF= 1489 Int= 0 D2E= 0 Chk= 45 Scr= 1 failed to open execfile =========== Computer 3: =========== ==> Lanl2dz_Freq_PBC_MoO3_half_Fixed_2Dc.log <== ECPInt: NShTT= 1081 NPrTT= 7944 LenC2= 1049 LenP2D= 5317. LDataN: DoStor=T MaxTD1= 6 Len= 172 Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 9 centers at a time, making 1 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3507 FMM=T I1Cent= 4 AccDes= 0.00D+00. NB too large for integers on this machine. Error termination via Lnk1e in /programs/g09/l1110.exe at Wed Dec 8 17:32:58 2010. Job cpu time: 0 days 11 hours 37 minutes 28.6 seconds. File lengths (MBytes): RWF= 1489 Int= 0 D2E= 0 Chk= 45 Scr= 1 ============================================== The Geometry Optimization of a Supercell (3x3) =============================================== I am using exactly the same options in the route section of unit cell input above. Independent what kind of computer has been choosen, in the end of the output files we can see this error: IPart= 3 NShTot= 4143150 NShNF= 4143150 NShFF= 0 NBatch= 3120 AvBLen= 1327.9 IPart= 5 NShTot= 4143150 NShNF= 4143150 NShFF= 0 NBatch= 3120 AvBLen= 1327.9 IPart= 2 NShTot= 4143150 NShNF= 4143150 NShFF= 0 NBatch= 3120 AvBLen= 1327.9 FoFCou EC= 10.5228030956 ENF= 10.5486106028 ISDGMR: 7000 0.5494798D-07 0.5494798D-07 IErr= 2 Err= 5.49D-08 NSaved= 2 NIter= 7000 NITot= 7001. DSDGMF failed for ItDFit. Error termination via Lnk1e in /programs/g09/l502.exe at Fri Dec 3 13:13:23 2010. Job cpu time: 2 days 4 hours 3 minutes 13.3 seconds. File lengths (MBytes): RWF= 7240 Int= 0 D2E= 0 Chk= 548 Scr= 1 From owner-chemistry@ccl.net Thu Dec 9 12:43:00 2010 From: "Nuno A. G. Bandeira nuno.bandeira**ist.utl.pt" To: CCL Subject: CCL:G: G09 PBC Errors in Opt and Freq Calculations of Metal Oxides surfaces Message-Id: <-43314-101209122152-6365-ARmof1Uer7tYW3WEbq6v/g+/-server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Date: Thu, 9 Dec 2010 18:21:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira()ist.utl.pt] To my knowledge Gaussian does not do frequency calculations in PBC. Their manual says nothing about this and I found that out when their support staff told me. I would recommend using either Crystal (Gamma Point freqs only) or VASP if you've got access to those codes. Or else there's always PWSCF or Abinit which do have that capability. Best, Nuno -- Nuno A. G. Bandeira, AMRSC Departamento de Química Física i Inorgánica Despatx 207, N4 - Universitat Rovira i Virgili Campus Sescelades, Carrer Marcel.lí Domingo 43007 Tarragona - SPAIN http://cqb.fc.ul.pt/intheochem/nuno/ -- From owner-chemistry@ccl.net Thu Dec 9 20:03:00 2010 From: "Joe Leonard jleonard42+/-gmail.com" To: CCL Subject: CCL: MBA/printing problem resolved Message-Id: <-43315-101209195833-27749-tzrnmJSEzRnRMJhx/8BwIA**server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary=Apple-Mail-2-102877907 Date: Thu, 9 Dec 2010 19:58:10 -0500 Mime-Version: 1.0 (Apple Message framework v1082) Sent to CCL by: Joe Leonard [jleonard42:_:gmail.com] --Apple-Mail-2-102877907 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Folks, thought I'd pass along what worked to get printing going: 1) Turn off the maximum firewall setting (uncheck Block all incoming = connections) 2) Configure the Airport Express, or merely connect to an existing one 3) Create the new printer, served by the Airport Express 4) Check that printing occurs (it did) and restore the Firewall = settings. It's possible that I had to do this several years ago when I got my last = Mac. It's also possible that there has been some kind of security = change that requires contact through the Firewall to finish setup on = printers or Expresses. It seems Canon printers required more changes = during their setup process, which brought the firewall issue to the = fore. FYI Joe Leonard jleonard42|-|gmail.com -- "This isn't right. This isn't even wrong." -- Wolfgang Pauli --Apple-Mail-2-102877907 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii jleonard42|-|gmail.com
--
"This isn't right.  This isn't = even wrong."
  -- Wolfgang = Pauli

<= /div>
=


= --Apple-Mail-2-102877907-- From owner-chemistry@ccl.net Thu Dec 9 21:17:00 2010 From: "rkdelisle^gmail.com" To: CCL Subject: CCL: Running GAMESS on ROCKS using SGE Message-Id: <-43316-101209180030-21594-BcdEKFoDuHzNaMyqVsNQCg^-^server.ccl.net> X-Original-From: rkdelisle*|*gmail.com Content-Type: multipart/alternative; boundary=90e6ba61543c000d590497023480 Date: Thu, 09 Dec 2010 23:00:24 +0000 MIME-Version: 1.0 Sent to CCL by: rkdelisle+*+gmail.com --90e6ba61543c000d590497023480 Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes I'm struggling to get GAMESS to run within a ROCKS cluster using SGE. Working through the sge-gms and rungms scripts is a very convoluted process. Has anyone implemented something similar? I'll hold off on further details/questions until I hear back. -Kirk --90e6ba61543c000d590497023480 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I'm struggling to get GAMESS to run within a ROCKS cluster using SGE. = Working through the sge-gms and rungms scripts is a very convoluted process= . Has anyone implemented something similar? I'll hold off on further = details/questions until I hear back.

-Kirk --90e6ba61543c000d590497023480--