From paxton at kitp.ucsb.edu Sun Jun 8 23:21:08 2008 From: paxton at kitp.ucsb.edu (Bill Paxton) Date: Sun, 8 Jun 2008 20:21:08 -0700 Subject: [Tioga-users] tioga install problem on mac -- zlib reported missing References: Message-ID: Hi Vincent, Does this sound familiar? What's the solution? Thanks, Bill Begin forwarded message: > From: starrfield > Date: June 8, 2008 7:53:33 PM PDT > To: Bill Paxton > Subject: Re: pgplot on the mac > > Hi Bill > Guess what... > > /Users/starrfie/dnova/dtioga/tioga-1.8->sudo ./QUICK_INSTALL > Password: > checking for zlib.h... yes > checking for compress() in -lz... no > Error: you should have zlib (including development files) installed to > build and run Tioga. You can get it there: > > http://www.zlib.net/ > > If that doesn't solve your problem, please report it on the Tioga > tracker: > > http://rubyforge.org/tracker/?group_id=701 > > I went looking and it said I should have zlib installed. I did > try to install it through macports and it claims to have > installed it but doing a whereis or a which shows nothing. > cheers > Sumner > > > -- > ______________________________________________________________ > Sumner Starrfield Phone: (480) 965 -7569 > Regents Professor of Astrophysics Fax: (480) 965 -8102 > School of Earth and Space Exploration Msg: (480) 965 -5081 > Arizona State University > PO Box 871404 sumner.starrfield at asu.edu > Tempe, AZ 85287-1404 http://starrfield.asu.edu > ______________________________________________________________ > -------------- next part -------------- An HTML attachment was scrubbed... URL: From fourmond at gmail.com Mon Jun 9 15:38:39 2008 From: fourmond at gmail.com (Vincent Fourmond) Date: Mon, 09 Jun 2008 21:38:39 +0200 Subject: [Tioga-users] tioga install problem on mac -- zlib reported missing In-Reply-To: References:

Message-ID: <484D86BF.6080906@gmail.com> Hello, Bill Paxton wrote: > Does this sound familiar? What's the solution? The problem has already occurred, but if the solution has been tested, I didn't hear about it. Please see the thread starting there: http://rubyforge.org/pipermail/tioga-users/2008-April/000173.html I'm of course available for any other kind of information ;-)... Cheers, Vincent -- Au royaume des aveugles, il y a des borgnes ? ne pas d?passer. -- Soeur Marie-Th?r?se des Batignoles (Ma?ster) Vincent, listening to Harbor Song (Suzanne Vega) From fourmond at gmail.com Mon Jun 9 15:41:26 2008 From: fourmond at gmail.com (Vincent Fourmond) Date: Mon, 09 Jun 2008 21:41:26 +0200 Subject: [Tioga-users] tioga install problem on mac -- zlib reported missing In-Reply-To: <484D86BF.6080906@gmail.com> References:

<484D86BF.6080906@gmail.com> Message-ID: <484D8766.6000700@gmail.com> Hello, again ;-)... Vincent Fourmond wrote: >> Does this sound familiar? What's the solution? > The problem has already occurred, but if the solution has been tested, > I didn't hear about it. Please see the thread starting there: > > http://rubyforge.org/pipermail/tioga-users/2008-April/000173.html And this one too, first: http://rubyforge.org/pipermail/tioga-users/2008-April/000171.html Vincent -- The moon was high now, in a sky as black as a cup of coffee that wasn't very black at all. -- Terry Pratchet, Men at arms Vincent, listening to Luka (Suzanne Vega) From boris.schmid at gmail.com Fri Jun 13 06:30:45 2008 From: boris.schmid at gmail.com (Boris Schmid) Date: Fri, 13 Jun 2008 12:30:45 +0200 Subject: [Tioga-users] ruby-1.9.0-1 and tioga 1.8 installation problems (both gem and source) Message-ID: Have been browsing the mailing list and faq, and trying some of the solutions on there, but I can't seem to install Tioga on CentOS release 5, 2.6.18-8.1.14.el5, Ruby 1.9.0-1. Did a fresh install of rubygems 1.1.1 and ruby 1.9.0-1, and then tried to call gem install tioga. This resulted in: _____________ checking for zlib.h... yes checking for compress() in -lz... yes creating Makefile make gcc -I. -I/home/boris/.local/include/ruby-1.9.0/x86_64-linux -I/home/boris/.local/include/ruby-1.9.0 -I. -DHAVE_ZLIB_H -fPIC -g -O2 -o flate.o -c flate.c In file included from flate.c:5: ../symbols.c:23:20: error: intern.h: No such file or directory make: *** [flate.o] Error 1 ======== intern.h seemed to be just where it had to be (/linuxhome/boris2/programs/include/ruby-1.9.0/ruby/intern.h). Couldn't find any information on how to get it working, so I moved to trying to install the tar.gz. QUICK_INSTALL already gives an error I can't resolve. ________________________ checking for zlib.h... yes checking for compress() in -lz... yes checking for ieee754.h... yes checking for isnan() ... yes Skipping MacOS-specific files Writing Makefile gcc -shared -o Dvector.so Dvector/dvector.o -Wl,-R -Wl,/home/boris/.local/lib -L/home/boris/.local/lib -lpthread -lrt -ldl -lcrypt -lm -lz /usr/bin/ld: Dvector/dvector.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC Dvector/dvector.o: could not read symbols: Bad value collect2: ld returned 1 exit status make: *** [Dvector.so] Error 1 ================== The recompile with -fPIC has been mentioned before on the mailing list, but I'm not sure which program I should recompile (the linker ld?). I did add -fPIC to a few of the cflag variants in rbconfig ________________________ boris:falcon:~/.local/lib/ruby/1.9.0/x86_64-linux:grep 'flag' rbconfig.rb CONFIG["CFLAGS"] = "-g -O2 $(cflags)" CONFIG["CPPFLAGS"] = " $(DEFS) $(cppflags)" CONFIG["cppflags"] = "-fPIC" CONFIG["cflags"] = " -fPIC" CONFIG["optflags"] = "" CONFIG["debugflags"] = "" =================== ____________ boris:falcon:~/.local/src/tioga-1.8:env | grep ruby RUBYLIB=/home/boris/.local/lib/ruby ========== With these changes, QUICK_INSTALL still gives exactly the same error output. I had expected "gcc-shared -o Dvector.so etc" to include an fpic somewhere, but it isn't, even though the makefile in split does contain references to fPIC. _____________ boris:falcon:~/.local/src/tioga-1.8/split:grep fPIC Makefile CFLAGS=-g -O2 -fPIC -O2 -g -Wall -Werror-implicit-function-declaration $(ARCH_FLAG) CPPFLAGS= -fPIC CXXFLAGS=-g -fPIC -O2 ============== Any suggestions what to try next? Thanks, boris. -------------- next part -------------- An HTML attachment was scrubbed... URL: From fourmond at gmail.com Fri Jun 13 08:59:07 2008 From: fourmond at gmail.com (Vincent Fourmond) Date: Fri, 13 Jun 2008 14:59:07 +0200 Subject: [Tioga-users] ruby-1.9.0-1 and tioga 1.8 installation problems (both gem and source) In-Reply-To: References: Message-ID: <2e474d6f0806130559u5555029fkbff47cc34488a1af@mail.gmail.com> Hello, On Fri, Jun 13, 2008 at 12:30 PM, Boris Schmid wrote: > Did a fresh install of rubygems 1.1.1 and ruby 1.9.0-1, and then tried to > call gem install tioga. This resulted in: > _____________ > checking for zlib.h... yes > checking for compress() in -lz... yes > creating Makefile > > make > gcc -I. -I/home/boris/.local/include/ruby-1.9.0/x86_64-linux > -I/home/boris/.local/include/ruby-1.9.0 -I. -DHAVE_ZLIB_H -fPIC -g -O2 > -o flate.o -c flate.c > In file included from flate.c:5: > ../symbols.c:23:20: error: intern.h: No such file or directory > make: *** [flate.o] Error 1 > ======== > > intern.h seemed to be just where it had to be > (/linuxhome/boris2/programs/include/ruby-1.9.0/ruby/intern.h). Couldn't find > any information on how to get it working, so I moved to trying to install > the tar.gz. I tried compiling with ruby 1.9 some time ago, but I never tried with the gem, so I'm a little confused here. I'll try to reproduce the problem home, but I'm not sure I will have time in a reasonably close future. > QUICK_INSTALL already gives an error I can't resolve. > ________________________ > checking for zlib.h... yes > checking for compress() in -lz... yes > checking for ieee754.h... yes > checking for isnan() ... yes > Skipping MacOS-specific files > Writing Makefile > gcc -shared -o Dvector.so Dvector/dvector.o -Wl,-R > -Wl,/home/boris/.local/lib -L/home/boris/.local/lib -lpthread -lrt -ldl > -lcrypt -lm -lz > /usr/bin/ld: Dvector/dvector.o: relocation R_X86_64_32 against `a local > symbol' can not be used when making a shared object; recompile with -fPIC > Dvector/dvector.o: could not read symbols: Bad value > collect2: ld returned 1 exit status > make: *** [Dvector.so] Error 1 > ================== > > The recompile with -fPIC has been mentioned before on the mailing list, but > I'm not sure which program I should recompile (the linker ld?). I did add > -fPIC to a few of the cflag variants in rbconfig I might be wrong, but this is typical of a broken rbconfig.rb in ruby's installation... Unless I'm very wrong, try adding -fPIC to CCDLFLAGS or CFLAGS, and run make clean in the split/ subdirectory before doing ./QUICK_INSTALL again. > With these changes, QUICK_INSTALL still gives exactly the same error output. > I had expected "gcc-shared -o Dvector.so etc" to include an fpic > somewhere, but it isn't, even though the makefile in split does contain > references to fPIC. This is because the -fPIC is necessary for producing the .o file, but not for the .so file. Running make clean should fix that. Happy hacking, Vincenrt From boris.schmid at gmail.com Sun Jun 15 10:52:11 2008 From: boris.schmid at gmail.com (Boris Schmid) Date: Sun, 15 Jun 2008 16:52:11 +0200 Subject: [Tioga-users] how can I let tioga ruby files pick up command line parameters? Message-ID: Hi all. Spend a nice day to get my first graphs from Tioga (and they're looking fine). The question I have is this: is it possible to feed command line parameters to the .rb file you call with tioga? I tried adding an ARGV argument to the ruby file, and run this: >tioga 'mygraph.rb results-20-0.05' but that doesn't work (I guess because tioga imports mygraph.rb using the ruby command 'require', which doesn't take arguments). A second way in which I'd hoped to pass a variable to tioga was by seeing if I could make use of the >tioga mygraph -m 'somenamehere' syntax, but that was stopped dead in its tracks when I found out that calling by graph name doesn't seem to work (any more?.. it's still an example in the tutorial). ---------------- loading /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/samples/sample.rb 0 Blue 1 Red boris:mutant3:~/.local/src/tioga-1.8/samples:tioga sample.rb -m 1 loading /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/samples/sample.rb 1 /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/samples/figures_out/Red.pdf boris:mutant3:~/.local/src/tioga-1.8/samples:tioga sample.rb -m Red loading /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/samples/sample.rb =============== The only solution I know of now is to have a ruby script that creates a custom mygraph.rb file with the correct input file, and call tioga from that ruby script, but I had hoped for something more elegant. Have I missed an obvious solution? P.S. 6 more months to go till my phd is ending ;). Boris.Schmid at gmail.com Theoretical Biology, Utrecht University Netherlands A child of five could understand this. Fetch me a child of five. ------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From paxton at kitp.ucsb.edu Sun Jun 15 11:48:29 2008 From: paxton at kitp.ucsb.edu (Bill Paxton) Date: Sun, 15 Jun 2008 08:48:29 -0700 Subject: [Tioga-users] how can I let tioga ruby files pick up command line parameters? In-Reply-To: References: Message-ID: <72F2D81F-2672-40CE-8E96-B21F16096F16@kitp.ucsb.edu> Hi Boris, On Jun 15, 2008, at 7:52 AM, Boris Schmid wrote: > Hi all. > > Spend a nice day to get my first graphs from Tioga (and they're > looking fine). Great! > The question I have is this: is it possible to feed command line > parameters to the .rb file you call with tioga? I tried adding an > ARGV argument to the ruby file, and run this: > >tioga 'mygraph.rb results-20-0.05' > but that doesn't work (I guess because tioga imports mygraph.rb > using the ruby command 'require', which doesn't take arguments). Interesting idea -- if you'd like to check the source, the 'tioga' command runs the program tioga_ui_cmds.rb, and it of course grabs the ARGV info and saves it in a variable called $tioga_args. It could make that available somehow -- any suggestions? > A second way in which I'd hoped to pass a variable to tioga was by > seeing if I could make use of the > >tioga mygraph -m 'somenamehere' > syntax, but that was stopped dead in its tracks when I found out > that calling by graph name doesn't seem to work (any more?.. it's > still an example in the tutorial). Hmm. It still works on my machine as you can see from the following: /Users/billpaxton/tioga/samples: tioga sample -l loading /Users/billpaxton/tioga/samples/sample.rb 0 Blue 1 Red /Users/billpaxton/tioga/samples: tioga sample -m Red loading /Users/billpaxton/tioga/samples/sample.rb Red_figure.pdf > ---------------- > loading /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/ > samples/sample.rb > 0 Blue > 1 Red > boris:mutant3:~/.local/src/tioga-1.8/samples:tioga sample.rb -m 1 > loading /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/ > samples/sample.rb > 1 /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/samples/ > figures_out/Red.pdf > boris:mutant3:~/.local/src/tioga-1.8/samples:tioga sample.rb -m Red > loading /hosts/linuxhome/falcon/boris2/programs/src/tioga-1.8/ > samples/sample.rb > =============== Are you finding that the command using a number works but the command with a name doesn't? > P.S. 6 more months to go till my phd is ending ;). > Congrats! --Bill From fourmond at gmail.com Sun Jun 15 13:46:16 2008 From: fourmond at gmail.com (Vincent Fourmond) Date: Sun, 15 Jun 2008 19:46:16 +0200 Subject: [Tioga-users] how can I let tioga ruby files pick up command line parameters? In-Reply-To: <72F2D81F-2672-40CE-8E96-B21F16096F16@kitp.ucsb.edu> References: <72F2D81F-2672-40CE-8E96-B21F16096F16@kitp.ucsb.edu> Message-ID: <48555568.1080909@gmail.com> Hello ! Bill Paxton wrote: >> The question I have is this: is it possible to feed command line >> parameters to the .rb file you call with tioga? I tried adding an ARGV >> argument to the ruby file, and run this: >> >tioga 'mygraph.rb results-20-0.05' >> but that doesn't work (I guess because tioga imports mygraph.rb using >> the ruby command 'require', which doesn't take arguments). > > Interesting idea -- if you'd like to check the source, the 'tioga' > command runs the program tioga_ui_cmds.rb, and it of course > grabs the ARGV info and saves it in a variable called $tioga_args. It > could make that available somehow -- any suggestions? If it is indeed saved in $tioga_args, you just need to use that variable exactly as you would use ARGV. BTW, I'm surprised ARGV does not work directly (but I didn't have a look at the code). Bill, when you say 'saved', does that mean you use .dup at some point, or just a plain = ? If that is the latter, ARGV and $tioga_args are probably killed by the command-line parsing. >> P.S. 6 more months to go till my phd is ending ;). Good luck for the last bits ! Vincent, who has gone through that more than a year ago, though he only officially got proof of that last week ! -- find(1): A `%' at the end of the format argument causes undefined behaviour since there is no following character. In some locales, it may hide your door keys, while in others it may remove the final page from the novel you are reading. Vincent, listening to Sit Down By The Fire (The Pogues) From paxton at kitp.ucsb.edu Sun Jun 15 13:53:46 2008 From: paxton at kitp.ucsb.edu (Bill Paxton) Date: Sun, 15 Jun 2008 10:53:46 -0700 Subject: [Tioga-users] how can I let tioga ruby files pick up command line parameters? In-Reply-To: <48555568.1080909@gmail.com> References: <72F2D81F-2672-40CE-8E96-B21F16096F16@kitp.ucsb.edu> <48555568.1080909@gmail.com> Message-ID: <73DD40E3-4D11-4640-9EAA-CAF76827A21B@kitp.ucsb.edu> On Jun 15, 2008, at 10:46 AM, Vincent Fourmond wrote: > Bill, when you say 'saved', does that mean you use .dup at some > point, > or just a plain = ? If that is the latter, ARGV and $tioga_args are > probably killed by the command-line parsing. Hi Vincent, The $tioga_args variable is a copy of the ARGV array. ; - ) --Bill -------------- next part -------------- An HTML attachment was scrubbed... URL: From paxton at kitp.ucsb.edu Sun Jun 15 14:06:52 2008 From: paxton at kitp.ucsb.edu (Bill Paxton) Date: Sun, 15 Jun 2008 11:06:52 -0700 Subject: [Tioga-users] how can I let tioga ruby files pick up command line parameters? In-Reply-To: References: Message-ID: On Jun 15, 2008, at 7:52 AM, Boris Schmid wrote: > The question I have is this: is it possible to feed command line > parameters to the .rb file you call with tioga? Hi, I noticed that the code currently checks for unrecognized parameter names and writes out the help info if it finds one. So we'll need to remove that "feature" before you can use your own parameters. --Bill -------------- next part -------------- An HTML attachment was scrubbed... URL: From fourmond at gmail.com Sun Jun 15 14:19:29 2008 From: fourmond at gmail.com (Vincent Fourmond) Date: Sun, 15 Jun 2008 20:19:29 +0200 Subject: [Tioga-users] how can I let tioga ruby files pick up command line parameters? In-Reply-To: <73DD40E3-4D11-4640-9EAA-CAF76827A21B@kitp.ucsb.edu> References: <72F2D81F-2672-40CE-8E96-B21F16096F16@kitp.ucsb.edu> <48555568.1080909@gmail.com> <73DD40E3-4D11-4640-9EAA-CAF76827A21B@kitp.ucsb.edu> Message-ID: <48555D31.8050402@gmail.com> Hello ! Bill Paxton wrote: > On Jun 15, 2008, at 10:46 AM, Vincent Fourmond wrote: >> Bill, when you say 'saved', does that mean you use .dup at some point, >> >> or just a plain = ? If that is the latter, ARGV and $tioga_args are >> >> probably killed by the command-line parsing. >> > The $tioga_args variable is a copy of the ARGV array. ; - ) Indeed ;-)... BTW, when I add p ARGV p $tioga_args to example -38 in samples/plots/plots.rb, I get the following: ~ tioga plots.rb -38 ... ["plots.rb", "-38"] ["plots.rb", "-38"] ~ tioga plots.rb -38 lksdf ... ["plots.rb", "-38", "lksdf"] ["plots.rb", "-38", "lksdf"] So, both ARGV and $tioga_args work ! Enjoy... Vincent -- If there was anything that depressed him more than his own cynism, it was that quite often, it still wasn't as cynical as real life. -- Terry Pratchet, Guards, guards ! Vincent, listening to Rainbow Man (Pogues)