From daizadeh@indigo.ucdavis.edu Thu Jul 31 03:14:36 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id DAA01363; Thu, 31 Jul 1997 03:14:25 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id AAA07593; Thu, 31 Jul 1997 00:23:45 -0700 From: "Iraj Daizadeh" Message-Id: <9707310023.ZM7591@indigo.ucdavis.edu> Date: Thu, 31 Jul 1997 00:23:30 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: daizadeh@indigo.ucdavis.edu, roberts@indigo.ucdavis.edu, bashore@indigo.ucdavis.edu, chemistry@www.ccl.net, fink@indigo.ucdavis.edu, goodyear@indigo.ucdavis.edu, heifets@indigo.ucdavis.edu, stuchebr@indigo.ucdavis.edu Subject: Multi-Language Programming on SGI Cc: schlyer@indigo.ucdavis.edu, tucker@indigo.ucdavis.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. The conversation on the CCL concerning OO led very nicely into a discussion of mixing programming languages (for an incomplete summary, please see below). This methodology should merit considerable thought by the computational chemistry society since it combines aspects in computational efficiency and modern coding practices (viz., raw speed, dynamic memory allocation, and object oriented design) with that of using old routines that are still very functional. How to implement these ideas in a pragmatic manner, however, has not been well-documented within these discussions bombarding our email terminals. We have been using multi-language programming ever since I began my computational career here at UC Davis under the watchful eye of Prof. Stuchebrukhov (circa. 3 academic years ago). Thus, I thought it might be useful to describe in detail a (probably) complicated procedure (for the novice) which would allow the generation of an executable from a C code calling a Fortran routine. Generalization of the ideas presented (briefly) below should suffice to enable any programmer using an SGI running IRIX 5.2 or above (up to 6.2) (at least what we have used) to be able to create an executable from C/Fortran (Fortran/C, Fortran/Pascal, etc.. (<-in a similar manner->) ) code. An outline of this procedure follows: (The methodology was suggested to us when we first started in this direction ( see Fortran/C Interface in the Fortran 77 Programmer's Guide on the insight pages by SGI (5.2) )... 1. Here is an example C code: #include extern double add_(double *,double *); void main() { double x,y; x=y=10.0; printf("%f %f %f\n", x, y, add_(&x,&y)); } /* end main */ This very easy program takes two doubles x,y and adds their assigned values. There exist a couple of items within the C code that are of particular interest to us. First, we have used an external function called add. Add is the fortran function (returns a value). The fortran call must by followed by an UNDERSCORE. Next notice that we have parameterized this function with pointers and sent the addresses of our variables to the fortran routine (This is essential since fortran uses implicitly pointers (no more on this)). That is all there is to it. 2. Next follows the fortran function: function add(x,y) double precision add,x,y add = x+y return end Notice there is no underscore after the add function. This is an intact code without any changes (YEA!). 3. Compile as follows: cc -c main.c # main.c is the file that contains the c code f77 -c add.f # add.f is the file that contains the fortran code cc -o add main.o add.o # now link them with the compiler that contains main You are done!!! A couple of notes: a. Remember: c is case-sensitive, fortran is not. What c does is convert the fortran statement to lowercase: [function statement(arg-list) or subroutine name(arg-list)] Thus, the following are equivalent to the c call above: function ADD() subroutine ADD() function Add() subroutine Add() function add() or subroutine add function AdD() subroutine AdD() ...etc... b. Watch your datatype! c. For a fortran routine calling a C function a similar procedure works. But keep in mind whichever code contains main should be the compiler that links all the object codes; e.g. if fortran code contained main use: cc -c add.c f77 -c main.f f77 -o add add.o main.o d. There are some minor details for sending arrays and structures but trial and error will allow you to figure this out on your own. e. remember it may be necessary to use the -lftn extension when there exist some unresolved errors. I would appreciate it if there were others in the field with this type of programming experience would kindly send me their explicit methodologies for muli-language implementations on other platforms. We are in the process of re-evaluating our computational hardware and are considering acquiring a Dec \alpha or HP. I will summarize all of them as is customary. Any comments, concerns or questions, please do not hesitate to email. If I am too busy, I will say so. Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Alex Turner Ultimately, most folks are more concerned with optimizing their time > use than the computer's :-) . In my opinion, this is the reason _to_ use mixed language programming. If I wanted to write a robust input parser for a large chemistry software package, I'm sure I could write it in Fortran, but it would take a lot of work. These days, there are tools to do this quite easily in C (lex, yacc, etc.). For many people, the time required to write the parser in C _and_ the time to sort out the interface to Fortran would be shorter than writing it in scratch from Fortran. And the C-Fortran interfacing skills learned during the exercise could easily be reused for other projects. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > Some things, like mixed Fortran77 and C, are now so common that there > is a community of people out there who understand pretty well how to > >Are you offering your services? :-) Perhaps it's not as bad as it >looks from my end, but if I had to rely on the kindness of unpaid [...snip ...] Hmm. How about mixed tcl/C ? The tcl interpreter is done in C, so rebuilding the interpreter is not mixed-language. But the result would be -- use tcl (slow as molasses, but lots of high level constructs like hashes, regular expressions, flow control) for the putting-together-the-tools part, and let C (or fortran) do the heavy lifting. Someone could provide a toolkit of tcl commands written in C, and anyone could put the tools together in new ways using a highlevel scripting language. I think perl and python would also work as scripting languages here. This is not just object-oriented (for the programmer) but also somewhat component-oriented (for the application builder or end user). bobg ---------------------------------------------------------------------------------------------------------------------------------------------------------------- David E. Bernholdt: > It idea of mixed language programming is to use languages most > appropriate for the task at hand, not just for speed, but for ease of > implementation. Such decisions are usually fairly coarse-grained. Exactly! > > Ultimately, most folks are more concerned with optimizing their time > > use than the computer's :-) . > > In my opinion, this is the reason _to_ use mixed language > programming. If I wanted to write a robust input parser for a large I couldn't agree more! > One can DESIGN software based on these principles (OOD) regardless of > what language the software is to be implemented in. Right. But implementing an OO design in a non-OO language requires a lot of experience and discipline - to be expected of a professional programmer, but not of a programming scientist. Of course the more basic problem is that scientists tend to skip the design phase altogether. Which is why big projects ought to be started in collaboration with software engineering experts. > I disagree with the person who proposed C++ is "the" langauge for > future work because it is an OOL. There are a lot of other > considerations that (should) factor into the decision of which > language to use. However I think that ALL projects should consider > object-oriented DESIGN regardless of implementation language. Again I agree completely. -------------------------------------------------- Lestaw K. Bieniasz: > If you need a program for individual purpose, use Fortran if you like it. Of course. However, don't do one of the following: 1) Force your students and postdocs to use Fortran even if they know and prefer something else. 2) Teach your students nothing but Fortran. Unfortunately, both are standard practice today. -------------------------------------------------- OK, that's it, sorry for the long post, and back to work... -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu From pbrown@prodigy.com Thu Jul 31 04:14:36 1997 Received: from p3.net for pbrown@prodigy.com by www.ccl.net (8.8.3/950822.1) id DAA01480; Thu, 31 Jul 1997 03:32:43 -0400 (EDT) From: Received: from prodigy.com (xykpa21.p3.net [207.76.249.60]) by p3.net (8.6.12/8.6.12) with SMTP id VAA12000; Wed, 30 Jul 1997 21:10:11 -0400 Date: Wed, 30 Jul 1997 21:10:11 -0400 Message-Id: <199707310110.VAA12000@p3.net> To: pbrown@prodigy.com Subject: Greetings! /////////////////////////////////////////////////////////////////////////////// If you wish to be removed from this advertiser's future mailings, please reply with the subject "Remove" and this software will automatically block you from their future mailings. //////////////////////////////////////////////////////////////////////////////// *** MAKE $36,000 in 14 WEEKS *** *** Just what you needed, just when you needed it! *** The main reason for this letter is to convince you that this system is honest, lawful, extremely profitable, and is a way to get a large amount of money in a short time. 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From chan@uni-muenster.de Thu Jul 31 06:22:14 1997 Received: from asterix.uni-muenster.de for chan@uni-muenster.de by www.ccl.net (8.8.3/950822.1) id FAA01768; Thu, 31 Jul 1997 05:44:06 -0400 (EDT) Received: from localhost (chan@localhost) by asterix.uni-muenster.de (8.7.5/8.7.5) with SMTP id LAA90970 for ; Thu, 31 Jul 1997 11:44:07 +0200 X-Authentication-Warning: asterix.uni-muenster.de: chan owned process doing -bs Date: Thu, 31 Jul 1997 11:44:07 +0200 (MES) From: "Jerry C.C. Chan" To: chemistry@www.ccl.net Subject: Diffuse and Polarization functions for TZV basis set (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers, We are working on DFT calculations of molecules containing C, F, etc, using TZVP basis set (UniChem_basis). Could anyone please tell us where we can get some appropriate diffuse and polarization functions for the first two row elements? I will summarize. Many thanks, Jerry ****************************************************************** * Jerry Chun Chung CHAN chan@moorea.uni-muenster.de * * * * Universitaet Muenster phone: 0049-251-83-29156 * * Institut fuer Physikalische Chemie fax: 0049-251-83-29159 * * Schlossplatz 4-7 * * D-48149 Muenster * * Germany * ****************************************************************** From bradley@mail.enterprise.net Thu Jul 31 08:22:00 1997 Received: from dns0.enterprise.net for bradley@mail.enterprise.net by www.ccl.net (8.8.3/950822.1) id HAA02114; Thu, 31 Jul 1997 07:44:24 -0400 (EDT) Received: from dbradley (ppp407.enterprise.net [194.72.196.153]) by dns0.enterprise.net (8.8.5/8.7.3) with SMTP id MAA14389 for ; Thu, 31 Jul 1997 12:44:04 +0100 (BST) Message-Id: <199707311144.MAA14389@dns0.enterprise.net> Comments: Authenticated sender is From: "David Bradley Science Writer" To: chemistry@www.ccl.net Date: Thu, 31 Jul 1997 12:45:30 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: ChemOffice Reply-to: Bradley@enterprise.net Priority: urgent In-reply-to: <199707310520.BAA00933@www.ccl.net> X-mailer: Pegasus Mail for Win32 (v2.54) How do the molecular modelling aspects of ChemOffice Ultra (v 4) from CambridgeSoft Corp, which includes various optimisation engines such as MOPAC93 compare with standalone units. Anyone willing to discuss their experiences of this package please feel free to get in touch Thanks in advance Dave Bradley -------------------------------------------------------- | David Bradley Science Writer | | Bradley@enterprise.net | | Tel/Fax +44 1223 440834 (Intl) | | Tel/Fax 01223 440834 (UK) | | | | http://homepages.enterprise.net/bradley/bradhome.html | -------------------------------------------------------- From daizadeh@indigo.ucdavis.edu Thu Jul 31 13:14:40 1997 Received: from indigo.ucdavis.edu for daizadeh@indigo.ucdavis.edu by www.ccl.net (8.8.3/950822.1) id MAA04268; Thu, 31 Jul 1997 12:37:14 -0400 (EDT) Received: by indigo.ucdavis.edu (940816.SGI.8.6.9/940406.SGI.AUTO) id JAA02048; Thu, 31 Jul 1997 09:46:45 -0700 From: "Iraj Daizadeh" Message-Id: <9707310946.ZM2046@indigo.ucdavis.edu> Date: Thu, 31 Jul 1997 09:46:31 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry-request@www.ccl.net, chemistry@www.ccl.net, daizadeh@indigo.ucdavis.edu, jkl@ccl.net Subject: (Fwd) Multi-Language Programming on SGI Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. There was a problem sending the message below to be posted on the CCl. Would you mind ensuring this. Thanks. Iraj. -------------------------------------------------------------------------------- Hello. The conversation on the CCL concerning OO led very nicely into a discussion of mixing programming languages (for an incomplete summary, please see below). This methodology should merit considerable thought by the computational chemistry society since it combines aspects in computational efficiency and modern coding practices (viz., raw speed, dynamic memory allocation, and object oriented design) with that of using old routines that are still very functional. How to implement these ideas in a pragmatic manner, however, has not been well-documented within these discussions bombarding our email terminals. We have been using multi-language programming ever since I began my computational career here at UC Davis under the watchful eye of Prof. Stuchebrukhov (circa. 3 academic years ago). Thus, I thought it might be useful to describe in detail a (probably) complicated procedure (for the novice) which would allow the generation of an executable from a C code calling a Fortran routine. Generalization of the ideas presented (briefly) below should suffice to enable any programmer using an SGI running IRIX 5.2 or above (up to 6.2) (at least what we have used) to be able to create an executable from C/Fortran (Fortran/C, Fortran/Pascal, etc.. (<-in a similar manner->) ) code. An outline of this procedure follows: (The methodology was suggested to us when we first started in this direction ( see Fortran/C Interface in the Fortran 77 Programmer's Guide on the insight pages by SGI (5.2) )... 1. Here is an example C code: #include extern double add_(double *,double *); void main() { double x,y; x=y=10.0; printf("%f %f %f\n", x, y, add_(&x,&y)); } /* end main */ This very easy program takes two doubles x,y and adds their assigned values. There exist a couple of items within the C code that are of particular interest to us. First, we have used an external function called add. Add is the fortran function (returns a value). The fortran call must by followed by an UNDERSCORE. Next notice that we have parameterized this function with pointers and sent the addresses of our variables to the fortran routine (This is essential since fortran uses implicitly pointers (no more on this)). That is all there is to it. 2. Next follows the fortran function: function add(x,y) double precision add,x,y add = x+y return end Notice there is no underscore after the add function. This is an intact code without any changes (YEA!). 3. Compile as follows: cc -c main.c # main.c is the file that contains the c code f77 -c add.f # add.f is the file that contains the fortran code cc -o add main.o add.o # now link them with the compiler that contains main You are done!!! A couple of notes: a. Remember: c is case-sensitive, fortran is not. What c does is convert the fortran statement to lowercase: [function statement(arg-list) or subroutine name(arg-list)] Thus, the following are equivalent to the c call above: function ADD() subroutine ADD() function Add() subroutine Add() function add() or subroutine add function AdD() subroutine AdD() ...etc... b. Watch your datatype! c. For a fortran routine calling a C function a similar procedure works. But keep in mind whichever code contains main should be the compiler that links all the object codes; e.g. if fortran code contained main use: cc -c add.c f77 -c main.f f77 -o add add.o main.o d. There are some minor details for sending arrays and structures but trial and error will allow you to figure this out on your own. e. remember it may be necessary to use the -lftn extension when there exist some unresolved errors. I would appreciate it if there were others in the field with this type of programming experience would kindly send me their explicit methodologies for muli-language implementations on other platforms. We are in the process of re-evaluating our computational hardware and are considering acquiring a Dec \alpha or HP. I will summarize all of them as is customary. Any comments, concerns or questions, please do not hesitate to email. If I am too busy, I will say so. Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Alex Turner Ultimately, most folks are more concerned with optimizing their time > use than the computer's :-) . In my opinion, this is the reason _to_ use mixed language programming. If I wanted to write a robust input parser for a large chemistry software package, I'm sure I could write it in Fortran, but it would take a lot of work. These days, there are tools to do this quite easily in C (lex, yacc, etc.). For many people, the time required to write the parser in C _and_ the time to sort out the interface to Fortran would be shorter than writing it in scratch from Fortran. And the C-Fortran interfacing skills learned during the exercise could easily be reused for other projects. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > Some things, like mixed Fortran77 and C, are now so common that there > is a community of people out there who understand pretty well how to > >Are you offering your services? :-) Perhaps it's not as bad as it >looks from my end, but if I had to rely on the kindness of unpaid [...snip ...] Hmm. How about mixed tcl/C ? The tcl interpreter is done in C, so rebuilding the interpreter is not mixed-language. But the result would be -- use tcl (slow as molasses, but lots of high level constructs like hashes, regular expressions, flow control) for the putting-together-the-tools part, and let C (or fortran) do the heavy lifting. Someone could provide a toolkit of tcl commands written in C, and anyone could put the tools together in new ways using a highlevel scripting language. I think perl and python would also work as scripting languages here. This is not just object-oriented (for the programmer) but also somewhat component-oriented (for the application builder or end user). bobg ---------------------------------------------------------------------------------------------------------------------------------------------------------------- David E. Bernholdt: > It idea of mixed language programming is to use languages most > appropriate for the task at hand, not just for speed, but for ease of > implementation. Such decisions are usually fairly coarse-grained. Exactly! > > Ultimately, most folks are more concerned with optimizing their time > > use than the computer's :-) . > > In my opinion, this is the reason _to_ use mixed language > programming. If I wanted to write a robust input parser for a large I couldn't agree more! > One can DESIGN software based on these principles (OOD) regardless of > what language the software is to be implemented in. Right. But implementing an OO design in a non-OO language requires a lot of experience and discipline - to be expected of a professional programmer, but not of a programming scientist. Of course the more basic problem is that scientists tend to skip the design phase altogether. Which is why big projects ought to be started in collaboration with software engineering experts. > I disagree with the person who proposed C++ is "the" langauge for > future work because it is an OOL. There are a lot of other > considerations that (should) factor into the decision of which > language to use. However I think that ALL projects should consider > object-oriented DESIGN regardless of implementation language. Again I agree completely. -------------------------------------------------- Lestaw K. Bieniasz: > If you need a program for individual purpose, use Fortran if you like it. Of course. However, don't do one of the following: 1) Force your students and postdocs to use Fortran even if they know and prefer something else. 2) Teach your students nothing but Fortran. Unfortunately, both are standard practice today. -------------------------------------------------- OK, that's it, sorry for the long post, and back to work... -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@ibs.ibs.fr Laboratoire de Dynamique Moleculaire | Tel.: +33-4.76.88.99.28 Institut de Biologie Structurale | Fax: +33-4.76.88.54.94 41, av. des Martyrs | Deutsch/Esperanto/English/ 38027 Grenoble Cedex 1, France | Nederlands/Francais ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 916.754.8695 Fax: 916.752.8995 email: daizadeh@indigo.ucdavis.edu