Re: [gmx-users] Shared library version binary on CYGWIN
Makoto Yoneya wrote: Dear Mark and GMX users: Mark wrote: Where did cyggmx-4.dll come from? What build tools are you using? No GROMACS distribution version of src/gmxlib/Makefile.in has such a make target - I checked 3.3.1, 3.3.3 and 4.0.5. What conditions induced its creation? Could you try a tiny patch, http://staff.aist.go.jp/makoto-yoneya/MDonWINPC/gromacs-3.3.3-cygwin-shared. patch , at the gromacs-3.3.3 dir and then, ./configure --without-x --with-fft=fftpack --enable-shared and make. OK that worked for 3.3.3 - I got a 1.8MB cyggmx-4.dll installed along with a working 600K mdrun. The catch is that this extra "-no-undefined" is an argument to libtool, rather than the underlying linker. You can use "./configure CFLAGS=blah LDFLAGS=blahblah" to pass things to the compiler and linker, but I don't know of technique to pass things to libtool without the editing you suggest. I'll see if I can figure something out, check it on 4.0.5 and wikify the outcome. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Shared library version binary on CYGWIN
Dear Mark and GMX users: Mark wrote: > Where did cyggmx-4.dll come from? What build tools are you using? > No GROMACS distribution version of src/gmxlib/Makefile.in has such a > make target - I checked 3.3.1, 3.3.3 and 4.0.5. What conditions induced > its creation? Could you try a tiny patch, http://staff.aist.go.jp/makoto-yoneya/MDonWINPC/gromacs-3.3.3-cygwin-shared. patch , at the gromacs-3.3.3 dir and then, ./configure --without-x --with-fft=fftpack --enable-shared and make. Regards. Makoto Yoneya, Dr. AIST, Japan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Shared library version binary on CYGWIN
Makoto Yoneya wrote: Dear Lehtola and GMX users: Thanks a lot for your comments on re-autoconf. I'd tried a few but finally found that was not necessary. I'd obtained shared gromacs-3.3.3 binary on CYGWIN just add -no-undefined option (needed to obtain DLL on CYGWIN) for linkage of cyggmx-4.dll with libtool in src/gmxlib/Makefile.in and then compiled with ./configure --without-x --with-fft=fftpack --enable-shared (--disable-float). The above also works for the shared binary build with MinGW32. Where did cyggmx-4.dll come from? What build tools are you using? No GROMACS distribution version of src/gmxlib/Makefile.in has such a make target - I checked 3.3.1, 3.3.3 and 4.0.5. What conditions induced its creation? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Shared library version binary on CYGWIN
Dear Lehtola and GMX users: Thanks a lot for your comments on re-autoconf. I'd tried a few but finally found that was not necessary. I'd obtained shared gromacs-3.3.3 binary on CYGWIN just add -no-undefined option (needed to obtain DLL on CYGWIN) for linkage of cyggmx-4.dll with libtool in src/gmxlib/Makefile.in and then compiled with ./configure --without-x --with-fft=fftpack --enable-shared (--disable-float). The above also works for the shared binary build with MinGW32. Kind Regards. Makoto Yoneya, Dr. AIST, Japan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Shared library version binary on CYGWIN
On Wed, 2009-05-27 at 15:05 +0900, Makoto Yoneya wrote: > I found the libtool within gromacs source (both 3.3.3 and 4.0.4) is not as > new as that of e.g. fftw-3.2.1 (which use the libtool-2.2.6). > I'm wondering if the libtool version was updated to the newer one, > then the DLLs could be generated properly, because fftw-3.2.1 can > build DLL on cygwin if it configured with --enable-shared. > I'd tried that with gromacs a little but no success as I have no detailed > knowledge on GNU autotools. You can of course try $ autoreconf -f which regenerates the build scripts and updates libtool and compiling with $ configure --enable-shared --disable-static after that. -- -- Jussi Lehtola, FM, Tohtorikoulutettava Fysiikan laitos, Helsingin Yliopisto jussi.leht...@helsinki.fi, p. 191 50632 -- Mr. Jussi Lehtola, M. Sc., Doctoral Student Department of Physics, University of Helsinki, Finland jussi.leht...@helsinki.fi -- ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Shared library version binary on CYGWIN
Dear Mark and GROMACS users: Mark wrote. > You can't build DLLs since the cygwin build tools are unix-style, and > the GROMACS build strategy is unix-specific. --enable-shared also > probably won't work for unix-style shared libraries, because the dynamic > linker is probably the Windows ld.exe, which can't deal with unix-style > shared libraries. Thanks a lot for the comment. > It would be possible to make GROMACS write proper DLLs using the cygwin > dlltool functionality, but nobody has ever cared enough to do it. I'd > struggle to imagine a useful Windows environment where providing 100MB > of statically-linked executables was a serious problem. I found the libtool within gromacs source (both 3.3.3 and 4.0.4) is not as new as that of e.g. fftw-3.2.1 (which use the libtool-2.2.6). I'm wondering if the libtool version was updated to the newer one, then the DLLs could be generated properly, because fftw-3.2.1 can build DLL on cygwin if it configured with --enable-shared. I'd tried that with gromacs a little but no success as I have no detailed knowledge on GNU autotools. > For a course, > you won't even need the whole executable set. mdrun, grompp, editconf, > pdb2gmx, genion, g_energy, trjconv and maybe one or two more analysis > tools to suit the course should do it. You're right. That may be a practical solution in the current situation. Kind Regards. Makoto Yoneya, Dr. AIST, Japan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Shared library version binary on CYGWIN
Makoto Yoneya wrote: Dear GROMACS users: I'd like to get small sized shared library version GROMACS binary on windows-PC with CYGWIN (to use in some course). Even configured with "--enable-shared", the compiled binary set looks not the shared library version (no DLLs and the total binary set size was over 100MB). You can't build DLLs since the cygwin build tools are unix-style, and the GROMACS build strategy is unix-specific. --enable-shared also probably won't work for unix-style shared libraries, because the dynamic linker is probably the Windows ld.exe, which can't deal with unix-style shared libraries. It would be possible to make GROMACS write proper DLLs using the cygwin dlltool functionality, but nobody has ever cared enough to do it. I'd struggle to imagine a useful Windows environment where providing 100MB of statically-linked executables was a serious problem. For a course, you won't even need the whole executable set. mdrun, grompp, editconf, pdb2gmx, genion, g_energy, trjconv and maybe one or two more analysis tools to suit the course should do it. Mark Actually the compiled GROMACS binary correctly runs. The problem was just the GROMACS was not shared library version I'd expected. I'd tried both gromacs-3.3.3 and gromacs-4.0.4 but the situations were same (with ./configure --enable-shared --without-x and appropriate CPPFLAGS and LDFLAGS). So, my question was just how to get the shared library version on CYGWIN with DLLs (like cyggmx-4.dll, cygmd-4.dll etc.). Could someone kindly give me info? Thank you for advance. Makoto Yoneya, Dr. AIST, Japan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Shared library version binary on CYGWIN
Dear GROMACS users: I'd like to get small sized shared library version GROMACS binary on windows-PC with CYGWIN (to use in some course). Even configured with "--enable-shared", the compiled binary set looks not the shared library version (no DLLs and the total binary set size was over 100MB). Actually the compiled GROMACS binary correctly runs. The problem was just the GROMACS was not shared library version I'd expected. I'd tried both gromacs-3.3.3 and gromacs-4.0.4 but the situations were same (with ./configure --enable-shared --without-x and appropriate CPPFLAGS and LDFLAGS). So, my question was just how to get the shared library version on CYGWIN with DLLs (like cyggmx-4.dll, cygmd-4.dll etc.). Could someone kindly give me info? Thank you for advance. Makoto Yoneya, Dr. AIST, Japan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
