From mferre at bic.mni.mcgill.ca Mon Nov 5 17:22:18 2007 From: mferre at bic.mni.mcgill.ca (Michael Ferreira) Date: Mon, 05 Nov 2007 17:22:18 -0500 Subject: [MINC-development] bug in emma's miwriteimages Message-ID: <472F979A.3000204@bic.mni.mcgill.ca> Hi Minc-developers, There's a small, annoying bug in the compiled binary of emma's miwriteimages that people are running into a lot these days. This is an error message obtained when creating a file that has more than 160 slices: Error: Too many slices specified (max 160) I've checked the source code of miwriteimages.c which I found on the BIC network in Bert's web directory: /data/web/users/bert/emma-0.9.8.tar.gz The 160 comes from a #DEFINE at the start of miwriteimages.c: #define MAX_WRITEABLE 160 /* maximum number of images we can write */ /* in one go (this is the same as */ /* MAXREADABLE in mireadimages.c */ I changed this to 1024, compiled the binary on Irix and Linux and the error was avoided. Could anyone suggest a better way to deal with this issue? Would it be good idea to remove this limit completely? Thanks, mike From rhoge at nmr.mgh.harvard.edu Tue Nov 20 16:34:30 2007 From: rhoge at nmr.mgh.harvard.edu (Rick Hoge) Date: Tue, 20 Nov 2007 16:34:30 -0500 Subject: [MINC-development] Problem building MINC2 from pure static libs Message-ID: Hi - I tried building the minc-2.0.14 source, and had problems when trying to build all libs static. Basically I built SZIP, ZLIB, HDF5, and NetCDF all with --disable-static in the configure step If I configure MINC with --enable-minc2 and --disable-shared I get ... checking for library hdf5... no configure: error: cannot find required library hdf5 Even though libhdf5.a is in the required place. If I build HDF5 including shared libs, the problem goes away. Shouldn't the --disable-shared flag prevent any dependency on other shared libs? The full configure invocation I'm using is: ./configure --prefix=/Users/rhoge/src/MINC/install --with-build-path=/ Users/rhoge/src/MINC/install --enable-minc2 --enable-acr-nema -- disable-shared I'm building on a Mac Pro Intel Xeon running MacOSX 10.5 Thanks for any suggestions, Rick From a.janke at gmail.com Tue Nov 20 18:21:32 2007 From: a.janke at gmail.com (Andrew Janke) Date: Wed, 21 Nov 2007 10:21:32 +1100 Subject: [MINC-development] Problem building MINC2 from pure static libs In-Reply-To: References: Message-ID: Hi Rick, On Nov 21, 2007 8:34 AM, Rick Hoge wrote: > I tried building the minc-2.0.14 source, and had problems when trying > to build all libs static. > > Basically I built > > SZIP, ZLIB, HDF5, and NetCDF all with --disable-static in the > configure step Surely you mean --disable-shared ? > If I configure MINC with --enable-minc2 and --disable-shared I get > > checking for library hdf5... no > configure: error: cannot find required library hdf5 > > Even though libhdf5.a is in the required place. If I build HDF5 > including shared libs, the problem goes away. What does config.log say? I suspect that there is a linking problem with one of the dependencies of HDF rather than hdf itself. a From claude at bic.mni.mcgill.ca Tue Nov 20 18:33:41 2007 From: claude at bic.mni.mcgill.ca (Claude LEPAGE) Date: Tue, 20 Nov 2007 18:33:41 -0500 (EST) Subject: [MINC-development] Problem building MINC2 from pure static libs References: Message-ID: <200711202333.lAKNXflU70271807@yorick.bic.mni.mcgill.ca> I use: --enable-shared=no --enable-static=yes --enable-acr-nema --enable-minc2 From jharlap at bic.mni.mcgill.ca Tue Nov 20 19:01:44 2007 From: jharlap at bic.mni.mcgill.ca (Jonathan Harlap) Date: Tue, 20 Nov 2007 19:01:44 -0500 Subject: [MINC-development] Problem building MINC2 from pure static libs In-Reply-To: References: Message-ID: I'd agree with Andrew, and just point out that I've seen fun games with 64 vs 32 bit libs in Leopard... Perhaps check with `file` that the architecture of your objects and libraries match. Cheers, J On 20-Nov-07, at 6:21 PM, Andrew Janke wrote: > Hi Rick, > > On Nov 21, 2007 8:34 AM, Rick Hoge wrote: > >> I tried building the minc-2.0.14 source, and had problems when trying >> to build all libs static. >> >> Basically I built >> >> SZIP, ZLIB, HDF5, and NetCDF all with --disable-static in the >> configure step > > Surely you mean --disable-shared ? > >> If I configure MINC with --enable-minc2 and --disable-shared I get >> >> checking for library hdf5... no >> configure: error: cannot find required library hdf5 >> >> Even though libhdf5.a is in the required place. If I build HDF5 >> including shared libs, the problem goes away. > > What does config.log say? I suspect that there is a linking problem > with one of the dependencies of HDF rather than hdf itself. > > > a > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development From rhoge at nmr.mgh.harvard.edu Tue Nov 20 20:58:42 2007 From: rhoge at nmr.mgh.harvard.edu (Rick Hoge) Date: Tue, 20 Nov 2007 20:58:42 -0500 Subject: [MINC-development] Problem building MINC2 from pure static libs In-Reply-To: References: Message-ID: Hi - On 20-Nov-07, at 6:21 PM, Andrew Janke wrote: > Hi Rick, > > On Nov 21, 2007 8:34 AM, Rick Hoge wrote: > >> I tried building the minc-2.0.14 source, and had problems when trying >> to build all libs static. >> >> Basically I built >> >> SZIP, ZLIB, HDF5, and NetCDF all with --disable-static in the >> configure step > > Surely you mean --disable-shared ? Surely I do! (if only I could type...) thanks for picking that up. >> If I configure MINC with --enable-minc2 and --disable-shared I get >> >> checking for library hdf5... no >> configure: error: cannot find required library hdf5 >> >> Even though libhdf5.a is in the required place. If I build HDF5 >> including shared libs, the problem goes away. > > What does config.log say? I suspect that there is a linking problem > with one of the dependencies of HDF rather than hdf itself. Will have to check on that system tomorrow - Rick > > > > a > _______________________________________________ > MINC-development mailing list > MINC-development at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development > > From sean at rogue-research.com Fri Nov 23 13:14:03 2007 From: sean at rogue-research.com (Sean McBride) Date: Fri, 23 Nov 2007 13:14:03 -0500 Subject: [MINC-development] Problem building MINC2 from pure static libs In-Reply-To: References: Message-ID: <20071123181403.148575909@smtp1.sympatico.ca> Rick, Dunno if you got this working, but we are able to build MINC2 as static libs in 10.5. We even build them 4-way Universal. -- ____________________________________________________________ Sean McBride, B. Eng sean at rogue-research.com Rogue Research www.rogue-research.com Mac Software Developer Montr?al, Qu?bec, Canada From rhoge at nmr.mgh.harvard.edu Tue Nov 27 12:18:42 2007 From: rhoge at nmr.mgh.harvard.edu (Rick Hoge) Date: Tue, 27 Nov 2007 12:18:42 -0500 Subject: [MINC-development] Problem building MINC2 from pure static libs In-Reply-To: <20071123181403.148575909@smtp1.sympatico.ca> References: <20071123181403.148575909@smtp1.sympatico.ca> Message-ID: Thanks - I got the libs to build static as universal binaries (Intel/ PPC in 32 and 64 bit), so this part works. For some reason however the command-line executables that are generated always seem to be dynamically linked against some of the hdf libs. I mostly need the libs, so have not worked much more on it. Rick On 23-Nov-07, at 1:14 PM, Sean McBride wrote: > Rick, > > Dunno if you got this working, but we are able to build MINC2 as > static > libs in 10.5. We even build them 4-way Universal. > > -- > ____________________________________________________________ > Sean McBride, B. Eng sean at rogue-research.com > Rogue Research www.rogue-research.com > Mac Software Developer Montr?al, Qu?bec, Canada > >