From chemistry-request@server.ccl.net Fri Apr 20 11:17:40 2001 Received: from arianna.cineca.it ([130.186.1.53]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3KFHdI10957 for ; Fri, 20 Apr 2001 11:17:40 -0400 Received: from arianna.cineca.it (localhost [127.0.0.1]) by arianna.cineca.it (8.11.0.Beta1/8.11.0.Beta1/CINECA 4.0) with ESMTP id f3KFHYp17948 for ; Fri, 20 Apr 2001 17:17:34 +0200 (MET DST) Received: from pc-emerson.cineca.it (pc-emerson.cineca.it [130.186.6.89]) by arianna.cineca.it (8.11.0.Beta1/8.11.0.Beta1/CINECA 4.0) with ESMTP id f3KFHXF17944 for ; Fri, 20 Apr 2001 17:17:33 +0200 (MET DST) Message-Id: <5.0.2.1.0.20010420171142.00a8f0b0@arianna.cineca.it> X-Sender: aemerson@arianna.cineca.it X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Fri, 20 Apr 2001 17:16:37 +0200 To: chemistry@ccl.net From: Andrew Emerson Subject: Re: CCL:About the Fortran I/O. In-Reply-To: <20010420100456.17891.qmail@sina.com> Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f3KFHeI10958 Try using the flush(unit) subroutine just after the write. For example, call flush(6) best wishes Andy Emerson At 06:04 PM 4/20/01 +0800, you wrote: >Dear all. > >I am using the SGI IRIX system. The Fortran program might used the write >buffer. It will always write to disk at size of 4096 bytes once a time. > >Is there any method to force the program to write at once when required? > >Best regrads > >Chungen >______________________________________ >Chungen Liu, Dr. >Chemistry Department >Nanjing University >Nanjing, 210093 >China > >cgliu@sina.com > > >=================================================================== >新浪免费电子邮箱 (http://mail.sina.com.cn) >网里寻她千百度!没有"聊友速配",怎能"成双成对"? (http://newchat.sina.com.cn) > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net ------------------------ Dr Andrew Emerson CINECA (High Performance Systems) via Magnanelli, 6/3 40033 Casalecchio di Reno (BO)-ITALY tel: +39-051-6171653, fax: +39-051-6132198 e-mail: a.emerson@cineca.it From chemistry-request@server.ccl.net Fri Apr 20 11:15:01 2001 Received: from huygens.rijnh.nl ([192.42.124.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3KFF0I10940 for ; Fri, 20 Apr 2001 11:15:00 -0400 Received: from [192.42.124.250] (dhcp124-250.rijnh.nl [192.42.124.250]) by huygens.rijnh.nl (SGI-8.9.3/8.9.3) with ESMTP id RAA87849; Fri, 20 Apr 2001 17:14:11 +0200 (MET_DST) Mime-Version: 1.0 X-Sender: gertvh@huygens.rijnh.nl Message-Id: In-Reply-To: <20010420100456.17891.qmail@sina.com> References: <20010420100456.17891.qmail@sina.com> Date: Fri, 20 Apr 2001 17:12:39 +0200 To: cgliu , chemistry@ccl.net From: Gert von Helden Subject: Re: CCL:About the Fortran I/O. Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit Hi, You can do a "call flush(unit)". See the (short) man page on flush. Hope that helps, Gert At 6:04 PM +0800 4/20/01, cgliu wrote: >Dear all. > >I am using the SGI IRIX system. The Fortran program might used the >write buffer. It will always write to disk at size of 4096 bytes >once a time. > >Is there any method to force the program to write at once when required? > >Best regrads > >Chungen >______________________________________ >Chungen Liu, Dr. >Chemistry Department >Nanjing University >Nanjing, 210093 >China > >cgliu@sina.com > > >=================================================================== >-缊拝-盗""  (http://mail.sina.com.cn) >寨吭-兝洬邇崗!埅"-""-缻墧",'灍"剨来剨'"? (http://newchat.sina.com.cn) > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ******************************************************* Dr. Gert von Helden FOM Institute for Plasmaphysics Rijnhuizen Edisonbaan 14, 3439 MN Nieuwegein, The Netherlands http://www.rijnh.nl/ e-mail: gertvh@rijnh.nl phone: (+31) 30 6096999, fax: (+31) 30 6031204 From chemistry-request@server.ccl.net Fri Apr 20 18:09:32 2001 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3KM9VI12661 for ; Fri, 20 Apr 2001 18:09:32 -0400 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id SAA28727; Fri, 20 Apr 2001 18:03:49 -0400 (EDT) Date: Fri, 20 Apr 2001 18:03:49 -0400 From: Rick Venable To: Joerg Grunenberg cc: Christoph van =?iso-8859-1?Q?W=FCllen?= , Yubo Fan , chemistry@ccl.net Subject: Re: CCL:Linux on PowerPC In-Reply-To: <3ADED54D.EB2459A4@tu-bs.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id f3KM9WI12662 Perhaps there's a discrepancy, perhaps not; see the note below from Cristoph regarding compilers. The main problem with getting good performance under Linux for PPC has been that the GNU compilers (gcc, g77) were optimized for Intel, and produce code that runs very poorly under ppclinux or mklinux. Now that OSX has been formally released, one hopes that affordable, true native compilers might become available for Linux kernels on Mac PPC systems. If the SPEC benchmarks cited below were done with gcc, they do not indicate the machine speed as much as the lack of architecture dependent optimization in the GNU compilers. On Thu, 19 Apr 2001, Joerg Grunenberg wrote: > Here are some more benchmarks pointing to a discrepancy between reality > and advertisement: > > Processor SPECint95 SPECfp95 > PowerPC G3(450 MHz) 21.4 13.8 > PowerPC G4(450 MHz) 21.4 20.4 > (" ...processing speed of a supercomputer..." ; www.apple.com) > > Athlon (1.0GHz) 42.0 29.4 > Pentium III (1.0GHz) 46.8 32.2 > Alpha (833 MHz)21264A 49.4 95.6 > > -- > Dr. J鰎g Grunenberg, Org. Chemie, Hagenring 30, 38106 Braunschweig > email: Joerg.Grunenberg@tu-bs.de phone: +49 531 391 5252 > URL: http://www.tu-bs.de/institute/org-chem/grunenberg/grunenberg.html > > Yubo Fan wrote: > > >computers can run Linux OS. PowerPC processor is much more powerful than > > >PC chips in scientific calculations, at least Apple's ads said so. My > > >question is: Can G98 run on SuSe Linux-Apple combination? > > Christoph van W黮len: > > This depends on the quality of the compiler. My timings for a small > > TURBOMOLE test suite are > > > > Mac/g77 (29. 08. 99) 532 user 37 sys 0:10 real G3 400 MHz > > unibo13/g77 (22. 09. 99) 445 user 28 sys 0:41 real Piii 500 MHz > > CvW/PGI (28. 09. 99) 320 user 16 sys 0:06 real Piii 500 MHz > > Gadolinium (30. 03. 01) 178 user 29 sys 0:04 real Piii 850 MHz > > Achilleus/PGI (29. 03. 01) 161 user 11 sys 0:03 real Athlon 900 MHz > > > > That is, a G3 and Pentium-iii are similar at the same clock speed. The PGI > > compiler for pentium gives 30 percent, and modern PCs at 900 MHz outperform > > a G3-400 MHz by a factor of 3.3. Unless you have a FORTRAN compiler that > > exploits the new G4 architecture, I cannot see why a PowerPC should be faster > > than a Pentium. I love my Macintosh on my desk, but for doing computations.... > > > > -- > > +---------------------------------+-------------------------------------+ > > | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 | > > | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | > > | Strasse des 17. Juni 135 | eMail | > > | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | > > +---------------------------------+-------------------------------------+ =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Sat Apr 21 04:55:43 2001 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3L8thI14783 for ; Sat, 21 Apr 2001 04:55:43 -0400 Received: from [128.97.147.215] (ch-15.psnet.ucla.edu [128.97.147.215]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with ESMTP id BAA12844; Sat, 21 Apr 2001 01:55:38 -0700 (PDT) Mime-Version: 1.0 Message-Id: Date: Sat, 21 Apr 2001 01:55:36 -0700 To: philchem@vm.sc.edu From: Eric Scerri Subject: FOCH volume 3 new issue. Foundations of Chemistry Philosophical Historical, Educational and Interdisciplinary Studies of Chemistry Table of Contents Volume 3, Issue 1, 2001 Editorial 7 Eric R. Scerri pp. 1-5 Berzelian Formulas as Paper Tools in Early Nineteenth-Century Chemistry Ursula Klein pp. 7-32 Modeling Biological Systems: The Belousov-Zhabotinsky Reaction Niall Shanks pp. 33-53 From the Periphery: the genesis of Eugene P. Wigner's application of group theory to quantum mechanics Michael Chayut pp. 55-78 Book Review of A. Kukla's Studies in Scientific Realism Stathis Psillos pp. 79-86 The International Society for the Philosophy of Chemistry, Conference Announcement pp. 87-88 Instructions for Authors pp. 89-96 -------------------------------------------------------- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.wkap.nl/journalhome.htm/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Sat Apr 21 16:39:40 2001 Received: from postoffice.igalaxy.net ([64.160.104.184]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3LKdeI18460 for ; Sat, 21 Apr 2001 16:39:40 -0400 Received: from hpotter.vaughan.home [64.160.106.91] by postoffice.igalaxy.net with ESMTP (SMTPD32-6.04) id A56C535B0140; Sat, 21 Apr 2001 14:02:36 -0700 Received: from daddy by hpotter.vaughan.home with local (Exim 3.22 #1 (Debian)) id 14r3sr-0000KG-00 for ; Sat, 21 Apr 2001 13:21:33 -0700 Date: Sat, 21 Apr 2001 13:21:33 -0700 From: Kenward Vaughan To: chemistry@ccl.net Subject: Autodock 3.0.5 compile dies on Linux... ??? Message-ID: <20010421132133.A1220@hpotter.vaughan.home> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.15i Sender: Daddy Vaughan Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f3LKdeI18461 Hello, I've just tried compiling v. 3.0.5 on my Debian box (Athlon cpu, FWIW) and the linking stage died on me. My Makefile was a duplicate of the suggested Linux changes found on the site off of the Autodock page. I also tried compiling autogrid--it gets toasted too. (The _real_ problem is that I am not a programmer, so my efforts die there as well. :-( ) Has someone been through this and/or can help me with these things? I am very interested in using Autodock as a part of a demo to my community college administrators to support a grant request for computers in the department. It hopefully would become a staple of the independent study program I want to offer my advanced students, too. I have attached excerpts of the Makefile and compiling messages autodock. If this can be worked out I would like to try addressing the problem with autogrid as well, if the kind soul is willing. :) Thanks very much, Kenward Vaughan kaynjay@igalaxy.net (home) ---snippet of Makefile--- ... # # C++ compiler # # AutoDock 3.0 Makefile GNU Linux -- START CC = g++ LIB = -lm CSTD = -DHPPA $(PROF) $(DBUG) $(WARN) CFLAGS = $(OPT) OPTLEVEL = -O3 OPT = $(CSTD) $(OPTLEVEL) OLIMIT = $(OPT) LINKOPT = $(OPT) LINK = $(LINKOPT) LINT = lint LINTFLAGS = -DHPPA $(LIB) -c DBUG = -DNDEBUG # No debugging and no assert code PROF = # No profiling WARN = # Default warning level # AutoDock 3.0 Makefile GNU Linux -- END autodock3 : main.o $(ADLIB) ... ---errors in compiling messages---I don't believe the warnings are important? Sorry about the line wrap... ... g++ -DHPPA -DNDEBUG -O3 -c getpdbcrds.cc g++ -DHPPA -DNDEBUG -O3 -DCHECK_ISNAN -c gs.cc -o gs.o gs.cc: In method enetic_Algorithm::Genetic_Algorithm(EvalMode, Selection_Mode, Xover_Mode, Worst_Mode, int, float, float, int, unsigned int, unsigned int)': gs.cc:170: warning: assignment to nt' from ouble' gs.cc:170: warning: assignment to nt' from ouble' ... g++ -DHPPA -DNDEBUG -O3 -c ranlib.cc ranlib.cc: In function ourByteLong ignbin(long int, float)': ranlib.cc:766: warning: assignment to ourByteLong' from loat' ranlib.cc:791: warning: assignment to ourByteLong' from loat' ranlib.cc:801: warning: assignment to ourByteLong' from loat' ranlib.cc:808: warning: assignment to ourByteLong' from ouble' ranlib.cc:816: warning: assignment to ourByteLong' from ouble' ... g++ -DHPPA -DNDEBUG -O3 -c trilinterp.cc ar r libad.a analysis.o banner.o bestpdb.o call_glss.o call_gs.o call_ls.o changeState.o check_header_float.o check_header_int.o check_header_line.o cluster_analysis.o clmode.o cmdmode.o cnv_state_to_coords.o com.o stateLibrary.o readfield.o readmap.o readPDBQ.o dpftypes.o eval.o evaluate_energy.o gencau.o getrms.o get_atom_type.o getInitialState.o getpdbcrds.o gs.o initautodock.o input_state.o investigate.o linpack.o ls.o mapping.o minmeanmax.o mkNewState.o mkTorTree.o mkRandomState.o nonbonds.o openfile.o output_state.o parse_com_line.o parse_dpf_line.o parse_pdbq_line.o parse_trj_line.o print_2x.o print_atomic_energies.o print_avsfld.o writeMolAsPDBQ.o writePDBQ.o writePDBQState.o print_rem.o printdate.o printEnergies.o printhms.o prClusterHist.o prInitialState.o prTorConList.o qmultiply.o qtransform.o quicksort.o ranlib.o rep.o scauchy.o set_cmd_io_std.o setflags.o simanneal.o sort_enrg.o stop.o strindex.o success.o summarizegrids.o support.o swap.o timesys.o timesyshms.o torNorVec.o torsion.o usage.o weedbonds.o warn_bad_file.o eintcal.o eintcalPrint.o intnbtable.o nbe.o trilinterp.o echo . ' on 'ate', using 'ostname >> LATEST_MAKE echo 'Flags: 'g++ -DHPPA -DNDEBUG -O3 -DNOSQRT -L. -lad -lm >> LATEST_MAKE g++ -DHPPA -DNDEBUG -O3 -DNOSQRT -o autodock3 main.o -L. -lad -lm ./libad.a(clmode.o): In function lmode(char *, int, float, char *, long, tms, char, char *, float (*)[2], float *, char, char *)': clmode.o(.text+0x640): undefined reference to et_atom_type(char *, char *)' ./libad.a(cmdmode.o): In function mdmode(int, long, tms, float, float, float, float, float, float, float, float (*)[127][127][7], float (*)[5][5], float, float (*)[2], int (*)[2047], int, int, int (*)[1], char (*)[127], float (*)[2], char *, int *, float *, char, float *, char *, float, int)': cmdmode.o(.text+0x48f): undefined reference to et_atom_type(char *, char *)' ./libad.a(readPDBQ.o): In function eadPDBQ(char *, char *, int, int *, float (*)[2], float *, char *, int *, char (*)[4], char *, _ciT0T3T3T5T5T3T3PA2047_iT4 (*)[1], int *, int *, int (*)[1], long, tms, char *, int *)': readPDBQ.o(.text+0x465): undefined reference to et_atom_type(char *, char *)' collect2: ld returned 1 exit status make: *** [autodock3] Error 1 ---end of run--- -- .'^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Bakersfield College |,;| Bakersfield, CA 93305 / ', \ 661-395-4243 / o O \ kvaughan@bc.cc.ca.us (oOoOOoOo) ---========--- ???$$MM$$???