From chemistry-request@ccl.net Thu Oct 14 01:51:49 2004 Received: from mailhub1.uq.edu.au (mailhub1.uq.edu.au [130.102.148.128]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9E6pldH030669 for ; Thu, 14 Oct 2004 01:51:48 -0500 Received: from smtp2.uq.edu.au (smtp2.uq.edu.au [130.102.5.53]) by mailhub1.uq.edu.au (8.12.11/8.12.11) with ESMTP id i9E73YjF028625 for ; Thu, 14 Oct 2004 17:03:34 +1000 (EST) Received: from uq.edu.au (gonzo.soe.uq.edu.au [130.102.5.131]) by smtp2.uq.edu.au (8.12.10/8.12.10) with ESMTP id i9E73Y1U017716 for ; Thu, 14 Oct 2004 17:03:34 +1000 (EST) Received: from [152.98.207.35] by msg2b.soe.uq.edu.au (mshttpd); Thu, 14 Oct 2004 17:03:34 +1000 From: Dr Seth Carlton OLSEN To: chemistry~at~ccl.net Message-ID: <5a17585a1c46.5a1c465a1758~at~uq.edu.au> Date: Thu, 14 Oct 2004 17:03:34 +1000 X-Mailer: iPlanet Messenger Express 5.2 HotFix 1.21 (built Sep 8 2003) MIME-Version: 1.0 Content-Language: en Subject: compiling G03 on opteron-64bit for use on Xeon-32bit X-Accept-Language: en Priority: normal Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 7bit X-Scanned-By: MIMEDefang 2.43 on UQ Mailhub Hi all, I've been having trouble with a Gaussian03 excecutable which was compiled using the Portland Compiler package on an 64 bit opteron system for use on a 32 bit Xeon system (both running linux). The excecutable was compiled with the 32bit flags. The excecutable works fine on the opteron, and it starts on the Xeon, but it stops quickly because it fails to expand the size of the read-write (*.rwf) file. Does anyone have any experience cross-compiling gaussian in this fashion? Is there any insight out there on what I may have missed? An alternative would be to use the intel compiler package to build the excecutable on the Xeon, but Gaussian doesn't support this option. Does anyone have experience compiling Gaussian03 with the intel compiler package on a Xeon 32bit machine? Cheers, Seth ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms Dr Seth Olsen, PhD Postdoctoral Fellow, Computational Systems Biology Group Centre for Computational Molecular Science Chemistry Building, The University of Queensland Qld 4072, Brisbane, Australia tel (617) 33653732 fax (617) 33654623 email: s.olsen1~at~uq.edu.au Web: www.ccms.uq.edu.au ccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccmsccms From chemistry-request@ccl.net Thu Oct 14 08:11:43 2004 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i9EDBXtT031460 for ; Thu, 14 Oct 2004 08:11:41 -0500 Received: (qmail 19833 invoked by uid 111); 14 Oct 2004 13:23:22 -0000 Received: from garoufal_at_physics.upatras.gr by nic.upatras.gr by uid 103 with qmail-scanner-1.22 (clamdscan: 0.71. Clear:RC:1(150.140.159.71):. Processed in 0.081693 secs); 14 Oct 2004 13:23:22 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 14 Oct 2004 13:23:22 -0000 Received: (qmail 30923 invoked from network); 14 Oct 2004 13:20:50 -0000 Received: from qchem-w03.physics.upatras.gr (HELO qchemw03) (150.140.159.226) by pythagoras.physics.upatras.gr with SMTP; 14 Oct 2004 13:20:50 -0000 Message-ID: <002e01c4b1f0$fa46ae20$e29f8c96@qchemw03> From: "Christos Garoufalis" To: Cc: Subject: parallel nwchem problem Date: Thu, 14 Oct 2004 16:23:22 +0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_002B_01C4B20A.1F8ABE60" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_20_30,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_002B_01C4B20A.1F8ABE60 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Dear nwchem users I am trying to run nwchem in parallel in a linux cluster without any = success I have installed the binary distribution which runs fine on a single=20 processor. when I try to use the parallel program (i.e. parallel nwchem test.nw) with nwchem.p file as described in the manual, i get the error message. Creating: host=3Dmol, user=3Dqchem, file=3D/home/qchem/NWCHEM/bin/nwchem, port=3D33133 2: interrupt(1) when I try to run it using mpirun (i.e. mpirun -np 8 nwchem test.nw) the program runs but when I look into the log file I see that it has used only one processor (nproc=3D1) The mpi and ssh are configured in the linux cluster work fine with=20 other programs. Any suggestions? Please reply directly to my email. Thanks in advance=20 Christos S. Garoufalis ------=_NextPart_000_002B_01C4B20A.1F8ABE60 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
Dear nwchem=20 users

I am trying to run nwchem in parallel in a linux cluster = without=20 any success
I have installed the binary distribution which runs fine = on a=20 single
processor.

when I try to use the parallel program = (i.e.=20 parallel nwchem test.nw)
with nwchem.p file as described in the = manual, i get=20 the error message.

Creating: host=3Dmol,=20 user=3Dqchem,
         &n= bsp;=20 file=3D/home/qchem/NWCHEM/bin/nwchem, port=3D33133
  2:=20 interrupt(1)

when I try to run it using mpirun (i.e. mpirun -np 8 = nwchem=20 test.nw)
the program runs but when I look into the log file I see = that
it=20 has used only one processor (nproc=3D1)
The mpi and ssh are = configured in the=20 linux cluster work fine with
other programs.

Any=20 suggestions?

Please reply directly to my email.
Thanks in = advance=20

Christos S. Garoufalis
------=_NextPart_000_002B_01C4B20A.1F8ABE60-- From chemistry-request@ccl.net Wed Oct 13 12:02:12 2004 Received: from lulu.it.northwestern.edu (lulu.it.northwestern.edu [129.105.16.54]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9DH2BLQ030625 for ; Wed, 13 Oct 2004 12:02:11 -0500 Received: (from mailnull@localhost) by lulu.it.northwestern.edu (8.12.10/8.12.10) id i9DHDvoJ000991 for ; Wed, 13 Oct 2004 12:13:57 -0500 (CDT) Received: from chunhui (cheme-86.chem-eng.northwestern.edu [129.105.205.86]) by lulu.it.northwestern.edu via smap (V2.0) id xma000577; Wed, 13 Oct 04 12:13:46 -0500 From: "chunhui" To: Subject: database for biochemical property through ab initio calculation? Date: Wed, 13 Oct 2004 12:13:32 -0500 Message-ID: <000001c4b147$f912cdd0$56cd6981@chunhui> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C4B11E.103E4C70" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, hits=0.0 required=7.5 tests=HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C4B11E.103E4C70 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear All, Could anybody tell me if there is a database which contains property for biochemical reactants and reactions through ab initio calculation? Or any literature regarding to this would be very helpful too. Thanks a lot, Chunhui ------=_NextPart_000_0001_01C4B11E.103E4C70 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear All,

 

Could anybody tell me if there is a database which = contains property for biochemical reactants and reactions through ab initio calculation? Or any literature regarding to = this would be very helpful too.

 

Thanks a lot,

 

Chunhui

 

------=_NextPart_000_0001_01C4B11E.103E4C70-- From chemistry-request@ccl.net Wed Oct 13 12:34:48 2004 Received: from lulu.it.northwestern.edu (lulu.it.northwestern.edu [129.105.16.54]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9DHYmLQ001677 for ; Wed, 13 Oct 2004 12:34:48 -0500 Received: (from mailnull@localhost) by lulu.it.northwestern.edu (8.12.10/8.12.10) id i9DHkYEH013876 for ; Wed, 13 Oct 2004 12:46:34 -0500 (CDT) Received: from chunhui (cheme-86.chem-eng.northwestern.edu [129.105.205.86]) by lulu.it.northwestern.edu via smap (V2.0) id xma013525; Wed, 13 Oct 04 12:46:25 -0500 From: "chunhui" To: Subject: any protein modeling workshop? Date: Wed, 13 Oct 2004 12:46:18 -0500 Message-ID: <000001c4b14c$8e822060$56cd6981@chunhui> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C4B122.A5AD9F00" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C4B122.A5AD9F00 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi, Is there any protein modeling workshop coming? Prefer in USA. Thanks a lot, Chunhui c-li:at:northwestern.edu ------=_NextPart_000_0001_01C4B122.A5AD9F00 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

 

Is there any protein modeling workshop coming? Prefer = in USA.

 

Thanks a lot,

 

Chunhui

c-li:at:northwestern.edu

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