RE: [gmx-users] GROMACS on Bluegene
Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on Bluegene Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official distribution. Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h contains the contents of file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which obviously won't work. Further, GROMACS configure won't work out-of-the-box on this platform (see also http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and discussions on this list months back). Since I can see in the source code that Mathias Puetz at IBM has done (at least some of) the development work here, then I suggest that IBM may like to provide some official build instructions. I have my own black magic that makes configure work on my machine, and I'm prepared to make that available off-list to interested parties, but I don't know how portable it will be between Bluegene installations. A better solution should be available if one of the GROMACS developers can approach the IBM people for us, please. 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
I am interested in this as well, since I am planning to compile version 4.0.2 in Blue Gene within a few days (once I get hold of my account!). -- Suman Chakrabarty. On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby [EMAIL PROTECTED] wrote: Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on Bluegene Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official distribution. Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h contains the contents of file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which obviously won't work. Further, GROMACS configure won't work out-of-the-box on this platform (see also http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and discussions on this list months back). Since I can see in the source code that Mathias Puetz at IBM has done (at least some of) the development work here, then I suggest that IBM may like to provide some official build instructions. I have my own black magic that makes configure work on my machine, and I'm prepared to make that available off-list to interested parties, but I don't know how portable it will be between Bluegene installations. A better solution should be available if one of the GROMACS developers can approach the IBM people for us, please. 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
Mathias has updated the wiki: http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene On Wed, Nov 12, 2008 at 11:57 AM, Suman Chakrabarty [EMAIL PROTECTED] wrote: I am interested in this as well, since I am planning to compile version 4.0.2 in Blue Gene within a few days (once I get hold of my account!). -- Suman Chakrabarty. On Wed, Nov 12, 2008 at 8:21 PM, Mike Hanby [EMAIL PROTECTED] wrote: Has there been any further discussion about fixing the issues discussed below regarding Blue Gene? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mark Abraham Sent: Thursday, October 16, 2008 10:43 PM To: Gromacs Users Subject: [gmx-users] GROMACS on Bluegene Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official distribution. Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h contains the contents of file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which obviously won't work. Further, GROMACS configure won't work out-of-the-box on this platform (see also http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and discussions on this list months back). Since I can see in the source code that Mathias Puetz at IBM has done (at least some of) the development work here, then I suggest that IBM may like to provide some official build instructions. I have my own black magic that makes configure work on my machine, and I'm prepared to make that available off-list to interested parties, but I don't know how portable it will be between Bluegene installations. A better solution should be available if one of the GROMACS developers can approach the IBM people for us, please. 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov ___ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
Roland Schulz wrote: Mathias has updated the wiki: http://wiki.gromacs.org/index.php/GROMACS_on_BlueGene That's great, there's a lot of useful info here. There are still outstanding issues with the kernels - see the discussion here and my various bugzillas http://www.gromacs.org/pipermail/gmx-developers/2008-November/002873.html 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] GROMACS on Bluegene
Mike Hanby wrote: I keep failing the ../configure when I have -lmass or -lmassv in LIBS for the frontend gromacs configure: - checking for C compiler default output file name... configure: error: C compiler cannot create executables - XLMASS=/opt/ibmcmp/xlmass/bg/4.4 ESSL=/opt/ibmmath MPI=/bgl/BlueLight/ppcfloor/bglsys BG_INCLUDE=-I$ESSL/include -I$MPI/include -I$XLMASS/include -I$VAC/include -I$XLF/include MPILIBS=-L$MPI/lib -lmpich.rts -lmsglayer.rts -ldevices.rts -lrts.rts -ldevices.rts -lrts.rts ESSLLIBS=-L$ESSL/lib -lesslbg BG_LIBS=-L$VAC/lib $ESSLLIBS -lxlopt -lnss_files -lnss_dns -lresolv -lc -lnss_files -lnss_dns -lresolv $MPILIBS ../configure --prefix=$PREFIX \ --enable-fortran \ --enable-ppc-sqrt \ --disable-ppc-altivec \ --enable-fortran \ --with-fft=fftw3 \ --without-x \ CC=xlc_r -q64 CFLAGS=-O3 -qarch=auto -qtune=auto \ CXX=xlC_r -q64 CXXFLAGS=-O3 -qarch=auto -qtune=auto \ CPPFLAGS=-I$FFTW/include $OTHERINCLUDES \ F77=xlf_r -q64 FFLAGS=-O3 -qnoprefetch -qarch=auto -qtune=auto \ LDFLAGS=-L$FFTW/lib \ LIBS=$XLMASS/lib -lmass -L$FFTW/lib If I remove $XLMASS/lib -lmass LIBS variable, the configure continues on. The /opt/ibmcmp/xlmass/bg/4.4 directory has the following libraries /opt/ibmcmp/xlmass/bg/4.4/bglib: libmass.a libmassv.a /opt/ibmcmp/xlmass/bg/4.4/lib: libmass.a libmassvp4.a libmassvp5.a /opt/ibmcmp/xlmass/bg/4.4/lib64: libmass_64.a libmassvp4_64.a libmassvp5_64.a Any suggestions? MASS and MASSV are some optimized math libraries with and without vectorization - anything in a bg subdirectory is only suitable for execution on the back end. Even if you have a MASS/MASSV for the front end, unless you're planning on running mdrun on it, you won't want it for 99% of GROMACS usage. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS on Bluegene
Hi, I can see GROMACS 4.0 has inner loops apparently optimized for BlueGene, however the distribution is incomplete. At least the files interaction.h nb_kernel_w3_bluegene.h nb_kernel_w3w3_bluegene.h nb_kernel_w4_bluegene.h nb_kernel_w4w4_bluegene.h nb_kernel_gen_bluegene.h are missing from src/gmxlib/nonbonded/nb_kernel_bluegene in the official distribution. Further, src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_bluegene.h contains the contents of file src/gmxlib/nonbonded/nb_kernel_x86_64_sse/nb_kernel_x86_64_sse.h which obviously won't work. Further, GROMACS configure won't work out-of-the-box on this platform (see also http://www.gromacs.org/pipermail/gmx-users/2008-October/037179.html and discussions on this list months back). Since I can see in the source code that Mathias Puetz at IBM has done (at least some of) the development work here, then I suggest that IBM may like to provide some official build instructions. I have my own black magic that makes configure work on my machine, and I'm prepared to make that available off-list to interested parties, but I don't know how portable it will be between Bluegene installations. A better solution should be available if one of the GROMACS developers can approach the IBM people for us, please. 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
