From owner-chemistry@ccl.net Mon Oct 17 03:19:00 2005 From: "=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= FB153746[A]ATIL.CEA.FR" To: CCL Subject: CCL: RE : Compilation troubles Message-Id: <-29628-051017031708-25288-4rueGL44kDMmBcaj4lb2XA(a)server.ccl.net> X-Original-From: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 17 Oct 2005 09:16:50 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= [FB153746..ATIL.CEA.FR] Dear All, and Dear Perry, Here, you will find the errors returned by ifort, the intel fortran compiler (v. 8.0). It was linked with the MKL libraries. This is only at the end that these errors were produced ... 80 .exe were build instead ... See below .... Between == == Changing the compiler, ifort by g77, the errors are not the same : ___________________ with g77 ___________________________________________ chkmove.f: In subroutine `ckcon': chkmove.f:419: Subroutine ChkWRI(DoWrt,IFormU,IA,Len) 1 chkmove.f:761: (continued): Call ChkWRI(ToFmt,IFormU,V(INBond),NAtoms) 2 Argument #3 of `chkwri' is one type at (2) but is some other type at (1) [info -f g77 M GLOBALS] chkmove.f:419: Subroutine ChkWRI(DoWrt,IFormU,IA,Len) 1 chkmove.f:762: (continued): Call ChkWRI(ToFmt,IFormU,V(IIBond),NAtoms*MxBond) 2 Argument #3 of `chkwri' is one type at (2) but is some other type at (1) [info -f g77 M GLOBALS] make: *** [chkmove.o] Error 1 ____________________________________________________________________________ ________ Well, is there only a global variable to change in order to run g77, or is it more complicated ? Or, how to overcome the errors made by ifort ? I am looking forward to reading from you and any tips that could help me. Regards, Frédéric ====================== BEGIN OF MADNESS AND INSANE TALK (ifort)============================= newzmat.a(newzmt.o)(.text+0xa3d): In function `newzmt_': : r: référence indéfinie vers « roundz_ : référence indéfinie vers « roundz_ » newzmat.a(newzmt.o)(.text+0xef6): In function `newzmt_': : référence indéfinie vers « symavg_ référence indéfinie vers « symavg_ » newzmat.a(newzmt.o)(.text+0x28ba): In function `newzmt_': : référence indéfinie vers « wcache_ » newzmat.a(newzmt.o)(.text+0x3775): In function `newzmt_': : référence indéfinie vers « wxyz_ » newzmat.a(newzmt.o)(.text+0x37d8): In function `newzmt_': : référence indéfinie vers « wpcmod_ » newzmat.a(newzmt.o)(.text+0x382e): In function `newzmt_': : référence indéfinie vers « wfrag_ » newzmat.a(newzmt.o)(.text+0x3884): In function `newzmt_': : référence indéfinie vers « wmodel_ » newzmat.a(newzmt.o)(.text+0x39a4): In function `newzmt_': : référence indéfinie vers « wppp_ » newzmat.a(newzmt.o)(.text+0x39f0): In function `newzmt_': : référence indéfinie vers « wzindo_ » newzmat.a(newzmt.o)(.text+0x3a39): In function `newzmt_': : référence indéfinie vers « wcon_ » newzmat.a(newzmt.o)(.text+0x3a9c): In function `newzmt_': : référence indéfinie vers « wmcmod_ » newzmat.a(newzmt.o)(.text+0x3b12): In function `newzmt_': : référence indéfinie vers « wmopac_ » newzmat.a(newzmt.o)(.text+0x4a1e): In function `newzmt_': : référence indéfinie vers « rdxyz_ » newzmat.a(newzmt.o)(.text+0x5a2e): In function `newzmt_': : référence indéfinie vers « rdpcmz_ » newzmat.a(newzmt.o)(.text+0x5e5c): In function `newzmt_': : référence indéfinie vers « rmopac_ » newzmat.a(rdmm2z.o)(.text+0x6a): In function `rdmm2z_': : référence indéfinie vers « readmm_ » newzmat.a(bondtb.o)(.text+0xf8): In function `bondtb_': : référence indéfinie vers « unpka_ » newzmat.a(bondtb.o)(.text+0x130): In function `bondtb_': : référence indéfinie vers « unpkb_ » ============================================================================ ================== -----Message d'origine----- De : owner-chemistry=ccl.net [mailto:owner-chemistry=ccl.net] Envoyé : jeudi 13 octobre 2005 00:02 À : B, F Objet : CCL: Compilation troubles Sent to CCL by: "Perry E. Metzger" [perry++piermont.com] > Did anyone compile gaussian03 with g77 ? I have only the first > executable, but all the .exe are not build, because of some undefined > references. I try to compile the source code on a PC Xeon with redhat > 9. Many thanks in advance for any kind of hep and any tip that could > help me (makefile and flags to share). Hi! In general, undefined references are caused by a failure in the link command line to refer to all needed pieces of software, but without the actual error information it is difficult to answer in your specific case. In order to make it easier to help with answering questions like this, it is helpful if you post a transcript (or an edited transcript) of the compile, and if you give us information on the versions of the software you are trying to use. To produce an accurate transcript, I suggest you either redirect both stdout and stderr to a file, like this: make >make.out 2>&1 This will produce a full transcript of the compile, called "make.out" (You can learn more about redirection commands in the man page for the standard linux shell, via "man bash"). BTW, that works for any command, not just "make". Alternatively, you can use the "script" command ("man script" for details). "script" is especially helpful if you are posting about problems with an interactive command. Versions of all the things you are using can, as I said, be helpful. Most of the gcc based compile tools on Linux will tell you their version numbers if you ask like this: g77 --version or gcc --version The version of the software you are compiling is also often quite important, as well as how you set it up to compile. By the way, on linux, you don't generally think of it as a ".EXE" file since linux does not use the Microsoft .EXE convention. It is better to call your .o files "object files" or ".o files", and your final liked executable simply "the executable". Perryhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Oct 17 10:56:00 2005 From: "Steve Bowlus chezbowlus[*]goldrush.com" To: CCL Subject: CCL: Where can you publish articles on software? Message-Id: <-29629-051017095905-12473-ngohC6k91GvMtBQWpl00pQ/./server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 17 Oct 2005 06:57:45 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus_+_goldrush.com] $0.02 from a (grateful) enduser (who can't spell "C") of everyone else's code: At one time, the CompChem community had its own vehicle for this purpose. It was (and still is) called the "Quantum Chemistry Program Exchange." For nominal cost (basically then media costs), academics and industry could get access to cutting edge programming. As QCPE matured in the mid- to late '80's, there was published (again, at modest cost) the quarterly "QCPE Bulletin," in which contributors could (as my memory serves me) publish exactly the kind of information being debated in this thread. Descriptions of new contributions were made in every issue by the director/editor (Richard Counts/Peggy Edwards). A uniform mechanism was provided for citation of contributions. I would suggest it is time to re-examine the utility of such a repository, and revive it along the lines envisioned by Counts. I don't know how IU currently supports QCPE (AFAIK, its capabilities are considerably curtailed); Jan's experience in obtaining funding for CCL does not bode well for the venture. But perhaps someone knowledgeable in these areas might inquire. Cheers, Steve From owner-chemistry@ccl.net Mon Oct 17 11:30:00 2005 From: "Rick Venable rvenable===pollux.cber.nih.gov" To: CCL Subject: CCL: Cremer & Pople Fortran source Message-Id: <-29630-051017110023-18740-5yEiJFSpWRD6xA5X8eka8w|-|server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 17 Oct 2005 10:57:24 -0400 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable]=[pollux.cber.nih.gov] On Sat, 15 Oct 2005, Tell Tuttle tell.tuttle*gmx.net wrote: > The program RING, written by Cremer, can be downloaded from the QCPE. > It can do what you need. It turns out that while the original RING program QCPE288 is no longer available thru QCPE, a Fortran77 "PC" version (?) is available under another entry number, QCMP110. I was confused by the way QCPE lists items in their catalog, and the lack of cross referencing. It's a real shame that a lot of this code isn't available as open source at this point; one needs a credit card, etc. for this download. ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- www.redcross.org From owner-chemistry@ccl.net Mon Oct 17 12:05:00 2005 From: "Noel O Boyle no228*o*cam.ac.uk" To: CCL Subject: CCL: Where can you publish articles on software? Message-Id: <-29631-051017113422-13476-lzOJtoF4iRhZqf0/fNliOA:-:server.ccl.net> X-Original-From: "Noel O'Boyle" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 17 Oct 2005 16:34:12 +0100 Mime-Version: 1.0 Sent to CCL by: "Noel O'Boyle" [no228{}cam.ac.uk] On Mon, 2005-10-17 at 06:57 -0700, Steve Bowlus chezbowlus[*]goldrush.com wrote: > Sent to CCL by: Steve Bowlus [chezbowlus_+_goldrush.com] > $0.02 from a (grateful) enduser (who can't spell "C") of everyone else's > code: > > At one time, the CompChem community had its own vehicle for this > purpose. It was (and still is) called the "Quantum Chemistry Program > Exchange." For nominal cost (basically then media costs), academics and > industry could get access to cutting edge programming. Things have improved in this regard since the 80s. The facilities provided by open-source repositories such as SourceForge (http://www.sf.net) are light-years beyond simple dump-it-and-leave-it-there type repositories. For example, SourceForge provides, for each program, a web site, a CVS repository (this is for coordinated the work of several developers), mailing lists, forums, bug trackers and feature requests. Whether one uses these or not is up to the individual developer(s). And it's cheaper than the QCPE - it's free for users *and* developers! > As QCPE matured > in the mid- to late '80's, there was published (again, at modest cost) > the quarterly "QCPE Bulletin," in which contributors could (as my memory > serves me) publish exactly the kind of information being debated in this > thread. Descriptions of new contributions were made in every issue by > the director/editor (Richard Counts/Peggy Edwards). A uniform mechanism > was provided for citation of contributions. Anything that provides a mechanism for developers to tell users about their software, as well as providing an encouragement for people to share code openly, sounds good to me. I would prefer though a more formal publication procedure with a peer review process, examples of which have been mentioned in both Physics and Bioinformatics. Dropping the Q in QCPE might also be a good idea; and it would encourage people to share code in the wider chemistry community. Regards, Noel From owner-chemistry@ccl.net Mon Oct 17 21:39:00 2005 From: "Schrodinger Announcements announce * schrodinger.com" To: CCL Subject: CCL: Schrodinger Fall Webinars Message-Id: <-29632-051017213234-31890-ZEtApOORuJwEnBkHTw+nog*server.ccl.net> X-Original-From: Schrodinger Announcements Date: Mon, 17 Oct 2005 21:30:42 -0400 Sent to CCL by: Schrodinger Announcements [announce ~~ schrodinger.com] Schrodinger is pleased to announce a new series of webcast seminars for fall 2005. With featured speakers that include noted researchers as well as Schrodinger product managers and applications scientists, the seminars will cover a wide variety of topics including software development, methodology, applications, and usage. The schedule for the first half of the seminar series is given below. To learn more, and to see the full abstracts, please visit our website at: http://www.schrodinger.com/SeminarCenter.php?mID=8&sID=53&cID=0 Date/Time Seminar --------- ------------------------------------------------------- 10/20/2005 Combining quantum chemistry and classical physics 1 PM EDT modeling: Using mixed QM/MM methods to obtain an atomically detailed view of biological processes Presented by Professor Victor Guallar Washington University at St. Louis 10/27/2005 Induced Fit models of hERG channel blockage 1 PM EDT Presented by Jason K. Perry, Ph.D. Schrodinger Applications Scientist 11/3/2005 Schrodinger Induced Fit Docking: 1 PM EST Methodology and results Presented by Woody Sherman, Ph.D. Schrodinger Applications Scientist 11/10/2005 Structure-based strategies: 1 PM EST Getting started with Maestro and Glide Presented by Hege Beard, Ph.D. Schrodinger Applications Scientist The seminars will run for approximately one hour, including time for questions and answers. The number of connections is limited, so please register early at http://www.schrodinger.com/Fall2005Webinars.html to ensure your participation. Sincerely, Mike Campbell Schrodinger Seminar Coordinator From owner-chemistry@ccl.net Mon Oct 17 22:21:00 2005 From: "Wright, Terry (MDL US) T.Wright,mdl.com" To: CCL Subject: CCL: FW: Call for Papers: CINF symposium on Advances in Reaction infor matics - ACS Atlanta, March 26-30 Message-Id: <-29633-051017203501-20320-hcPqbV79cPh3z0/Y+NdjRg%x%server.ccl.net> X-Original-From: "Wright, Terry (MDL US)" Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5D373.C44D8D66" Date: Tue, 18 Oct 2005 00:37:41 +0100 MIME-Version: 1.0 Sent to CCL by: "Wright, Terry (MDL US)" [T.Wright() mdl.com] This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C5D373.C44D8D66 Content-Type: text/plain Dear Colleagues: You are invited to participate in the following symposium for the Atlanta ACS, March 26-30: Advances in Reaction informatics - New Tools and Technologies to Improve Synthesis Planning This symposium will cover all aspects of reaction database technologies, including: New tools for searching and manipulation of reaction results Technologies for linking, integration of reaction information from disparate sources Faster and more efficient search applications New methods of database design and construction Reaction registration systems Reaction prediction and synthetic route building applications Integrating in-house data with commercial data sources Integration of reaction databases with reporting tools and other external applications. If you are interested in being a speaker for this symposium, please submit an abstract via the ACS OASYS system. A direct link to the CINF sessions is below: http://oasys.acs.org/acs/231nm/cinf/papers/index.cgi The deadline for abstract submission is November 23. Please contact me if you have any questions. Thank you. Terry Terry Wright MDL Information Systems 14600 Catalina Street San Leandro, CA 94577 Phone: 510-357-2222 ext. 1392 Email: terryw,;,mdli.com ------_=_NextPart_001_01C5D373.C44D8D66 Content-Type: text/html

Dear Colleagues:

 

You are invited to participate in the following symposium for the Atlanta ACS, March 26-30:

 

 

Advances in Reaction informatics - New Tools and Technologies to Improve Synthesis Planning

 

This symposium will cover all aspects of reaction database technologies, including:

 

New tools for searching and manipulation of reaction results

 

Technologies for linking, integration of reaction information from disparate sources

 

Faster and more efficient search applications

 

New methods of database design and construction

 

Reaction registration systems

 

Reaction prediction and synthetic route building applications

 

Integrating in-house data with commercial data sources

 

Integration of reaction databases with reporting tools and other external applications.

 

If you are interested in being a speaker for this symposium, please submit an abstract via the ACS OASYS system. A direct link to the CINF sessions is below:

 

http://oasys.acs.org/acs/231nm/cinf/papers/index.cgi

 

The deadline for abstract submission is November 23. Please contact me if you have any questions.

 

Thank you.

 

Terry

 

 

Terry Wright

MDL Information Systems

14600 Catalina Street

San Leandro, CA 94577

 

Phone: 510-357-2222 ext. 1392

Email: terryw,;,mdli.com

 

------_=_NextPart_001_01C5D373.C44D8D66--