From chemistry-request@server.ccl.net Sat May 29 01:12:41 1999 Received: from emlab2.nmsu.edu (scastill@emlab2.NMSU.Edu [128.123.70.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA05739 for ; Sat, 29 May 1999 01:12:41 -0400 Received: from localhost (scastill@localhost) by emlab2.nmsu.edu (8.8.7/8.8.7) with ESMTP id WAA09959; Fri, 28 May 1999 22:49:44 -0600 X-Authentication-Warning: emlab2.nmsu.edu: scastill owned process doing -bs Date: Fri, 28 May 1999 22:49:44 -0600 (MDT) From: Steven Castillo To: Eugene.Leitl@lrz.de, eugene.leitl@lrz.uni-muenchen.de cc: Richard Gillilan , chemistry@server.ccl.net Subject: Re: CCL:DX goes open source In-Reply-To: <374D9DFB.636E7699@bioreason.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 27 May 1999 Eugene.Leitl@lrz.de wrote: > > From: Andrew Dalke > > Richard Gillilan said: > > The IBM Data Explorer visualization software that we have used > > for a number of years has officially gone open source and can > > be obtained free from the web site (OpenDX.org). > > And if anyone is interested, here are instructions for getting > the source to compile on IRIX 6.5 using the 7.2 C/C++ compiler. > > 1) download the source (and examples) from > http://www.research.ibm.com/dx/download/ > > 2) The configuration code uses the value of SHELL rather than > /bin/sh, so if you have a non-sh compatible shell (like tcsh) > you are best off starting 'sh' then doing > SHELL=/bin/sh > export SHELL > > 3) If you want to use SGI's C++ compiler over GNU, you also need > to set the CXX environment variable to "CC", as in > CXX=CC > export CXX > > 4) Configure by running "./configure" > > 5) The default 'make' on SGIs isn't very good. Use "smake" or > GNU make ("gmake" or "gnumake") instead. This can best be > done by adding > > #!/usr/sbin/smake > > to the top of the newly created Makefile. The normal make will > restart with the #! indicated make if given. > > This is needed for compiling dx because otherwise every time > you run "make" it will try to recompile some of the files. This > is annoying because it will try to recompile even when using > "make install" after the system has been built. > > 6) The file "src/exec/libdx/memory.c" didn't compile because of > the code: > === > #ifdef SYSTYPE_SVR4 > if (inv->inv_class==INV_MEMORY && inv->inv_type==INV_MAIN) { > physmem = (uint)((double)inv->inv_state / 1024. / 1024.); > break; > } > #else > if (inv->class==INV_MEMORY && inv->type==INV_MAIN) { > physmem = (uint)((double)inv->inv_state / 1024. / 1024.); > break; > } > #endif /* SVR4 */ > === > > It is supposed to use the first block but instead uses the second. > Easiest fix is to replace #ifdef with #ifndef . > > 7) Once the "#!" was added, "make" it. > > 8) Become root and "make install". There is a problem with the > code -- some of it assumes data files are in "/usr/lpp/dx" instead > of "/usr/local/dx" and it will complain about missing files during > startup. The only fix I know so far is to make a symbolic link, > as in > > cd /usr > ln -s local lpp > > 9) Some of the help files are sym linked to themselves. > > val> pwd > /usr/local/dx/help > val> ls -l GarHelpDir BMHelpDir > lrwxr-xr-x 1 root sys 28 May 27 10:48 BMHelpDir -> > /usr/local/dx/help/MBHelpDir > lrwxr-xr-x 1 root sys 29 May 27 10:48 GarHelpDir -> > /usr/local/dx/help/GarHelpDir > > There is no fix for this, but it hasn't been a problem (yet?). > > 10) To use the sample files, set the environment variable DXDATA > to point to your dxsamples-4.0/data directory. > > 11) Start the program by running "/usr/local/dx/bin_sgi/startupui". > > There may be other ways to start it, but I'm not sure what they > are. Also, looking at the memory usage with "gmemusage", at least > some of the time DX wants up to 400 MB of memory. If you run > "dxui" directly, it seems to keep that memory need, but starting > >from the startupui makes that need be only transient. I don't > understand the behaviour, but it may be because dxui isn't meant > to be started directly. > > Then take a look at some of the Chemistry extensions developed > by Richard Gililan and others at the Theory Center, under > > http://www.tc.cornell.edu/DX/ > > > Andrew Dalke > dalke@bioreason.com > -= 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 > > > > I have been able to get the code to compile under Redhat Linux 5.2 on a Pentium II. I used the lesstif, Mesa, and hdf5 rpms from the redhat contrib ftp site. The only problem I ran into was that the configure step was unable to find the lesstif libraries that were installed. I manually changed the include/dxconfig.h so that the line #define USING_LESSTIF 0 is changed to #define USING_LESSTIF 1 I also did a sym link from /usr/lib/libMesaGL.a to /usr/lib/libGL.a I am now trying to put dx through it's paces. I have never used it before having previously used AVS for visualization. Steve Castillo Klipsch School of Electrical and Computer Engineering New Mexico State University scastill@nmsu.edu From chemistry-request@server.ccl.net Sat May 29 08:49:18 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA08822 for ; Sat, 29 May 1999 08:49:18 -0400 Received: from tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.244.22]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id IAA21849; Sat, 29 May 1999 08:45:28 -0400 Sender: richard@tc.cornell.edu Message-ID: <374FE167.B5A45D30@tc.cornell.edu> Date: Sat, 29 May 1999 08:45:27 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.2 IP22) X-Accept-Language: en MIME-Version: 1.0 To: Andrew Dalke CC: chemistry@server.ccl.net Subject: Re: CCL:DX goes open source References: <374D76F3.AE9E2952@tc.cornell.edu> <374D9DFB.636E7699@bioreason.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You all are way ahead of me in bringing up the Open version of DX. I have not tested any of my old chem modules with this version, however they should work. For any interested, the modules could be made more efficient by compiling as loadables (an option not available to me when I started writing them a few years ago). This should simply be a matter of changing the makefile but I've never found the time. Supposedly, the latest build of DX has built-in stereo ... a feature I have wanted for years. Also, the SuperviseWindow/SuperviseState modules supposedly allow lower-level access to mouse events within the Image window so that users could, for example, emulate InsightII-style interactivity etc. As always, Chris and I are happy to answer questions about DX usage as time permits. Cornell's web site should still contain many nice DX resources that we have built over the years with the help of countless CS490/CS790 students. Richard > > Then take a look at some of the Chemistry extensions developed > by Richard Gililan and others at the Theory Center, under > > http://www.tc.cornell.edu/DX/ > > Andrew Dalke > dalke@bioreason.com