Re: [gmx-users] gromacs-3.3 build on linux. make fails
David van der Spoel wrote: you do want to use mpicc which gives you all the libraries and include paths. but please check whether you have another gcc installed, or what the default gcc is (gcc -V). You can usually set a variable like MPICC=gcc3 if you have an executable gcc3 somewhere. ok. the make finally succeeded. I set cc=gcc4 instead of gcc(which failed). thank you all for the leads! Susan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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-3.3 build on linux. make fails
susan james wrote: here's a bit more(below) of the make build that failed. I've captured the last lines. I think it may indeed have something to do with gcc4. mpicc is in the path. I'm wondering if I should set this variable: CC=gcc4 instead of CC=mpicc any ideas on this? > you do want to use mpicc which gives you all the libraries and include paths. but please check whether you have another gcc installed, or what the default gcc is (gcc -V). You can usually set a variable like MPICC=gcc3 if you have an executable gcc3 somewhere. by the way, your log snippet did not have the info from compiling the src/gmxlib/nonbonded directory, where something went wrong, apparently -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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-3.3 build on linux. make fails
here's a bit more(below) of the make build that failed. I've captured the last lines. I think it may indeed have something to do with gcc4. mpicc is in the path. I'm wondering if I should set this variable: CC=gcc4 instead of CC=mpicc any ideas on this? == . . . if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/usr/local/gromacs-double/3.3/share/top\" -I/usr/local/fftw301/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT toputil.o -MD -MP -MF ".deps/toputil.Tpo" -c -o toputil.o toputil.c; \ then mv -f ".deps/toputil.Tpo" ".deps/toputil.Po"; else rm -f ".deps/toputil.Tpo"; exit 1; fi if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/usr/local/gromacs-double/3.3/share/top\" -I/usr/local/fftw301/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT topdirs.o -MD -MP -MF ".deps/topdirs.Tpo" -c -o topdirs.o topdirs.c; \ then mv -f ".deps/topdirs.Tpo" ".deps/topdirs.Po"; else rm -f ".deps/topdirs.Tpo"; exit 1; fi if mpicc -DHAVE_CONFIG_H -I. -I. -I../../src -I/usr/X11R6/include -I../../include -DGMXLIBDIR=\"/usr/local/gromacs-double/3.3/share/top\" -I/usr/local/fftw301/include -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT grompp.o -MD -MP -MF ".deps/grompp.Tpo" -c -o grompp.o grompp.c; \ then mv -f ".deps/grompp.Tpo" ".deps/grompp.Po"; else rm -f ".deps/grompp.Tpo"; exit 1; fi /bin/sh ../../libtool --mode=link --tag=CC mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -L/usr/local/fftw301/lib -o grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o ../mdlib/libmd_mpi_d.la ../gmxlib/libgmx_mpi_d.la -L/usr/X11R6/lib64 -lnsl -lfftw3 -lm -lSM -lICE -lX11 mkdir .libs mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -o .libs/grompp topio.o toppush.o topcat.o topshake.o convparm.o tomorse.o sorting.o splitter.o vsite_parm.o readir.o add_par.o topexcl.o toputil.o topdirs.o grompp.o -L/usr/local/fftw301/lib ../mdlib/.libs/libmd_mpi_d.so -L/usr/X11R6/lib64 -L/usr/local/fftw301-double/lib ../gmxlib/.libs/libgmx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = David van der Spoel wrote: susan james wrote: Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure --prefix=/usr/local/fftw301-double --enable-threads here's my gromacs configure string which succeeds: ./configure --enable-shared --without-motif-libraries --disable-float --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3 The gromacs configure succeeds: config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands * You are compiling a double precision version of Gromacs - program names will be suffixed with _d to avoid overwriting single precision files. You can override it with --program-suffix * Seems you are compiling with MPI support. You can install the MPI- enabled programs with suffixed names to have both MPI and non-MPI versions. This is useful e.g. on supercomputers where you usually cannot run MPI-linked programs on the login node. Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double). You only need MPI for mdrun, so if you already have non-MPI stuff installed you can issue make mdrun; make install-mdrun. the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Err
Re: [gmx-users] gromacs-3.3 build on linux. make fails
susan james wrote: Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure --prefix=/usr/local/fftw301-double --enable-threads here's my gromacs configure string which succeeds: ./configure --enable-shared --without-motif-libraries --disable-float --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3 The gromacs configure succeeds: config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands * You are compiling a double precision version of Gromacs - program names will be suffixed with _d to avoid overwriting single precision files. You can override it with --program-suffix * Seems you are compiling with MPI support. You can install the MPI- enabled programs with suffixed names to have both MPI and non-MPI versions. This is useful e.g. on supercomputers where you usually cannot run MPI-linked programs on the login node. Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double). You only need MPI for mdrun, so if you already have non-MPI stuff installed you can issue make mdrun; make install-mdrun. the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = for some reason it did not compile the assembly bits. it could be due to gcc4, or maybe because you did a single precision compilation first. in the latter case try make distclean before running configure. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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-3.3 build on linux. make fails
susan james wrote: Hello, I'm new to this list and hope I can get some help. Thanks for the good help request - lots of pertinent information can only improve your chances of getting help! the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = Unfortunately about another twenty lines of this will probably be instructive - you've actually cut off part of the command that failed. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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-3.3 build on linux. make fails
Hello, I'm new to this list and hope I can get some help. I'm seeking help with installing double precision gromacs-3.3 on Centos-4 linux. I'm using Lam-7.1.2 built with gcc4. I built fftw with this configure string which succeeded: ./configure --prefix=/usr/local/fftw301-double --enable-threads here's my gromacs configure string which succeeds: ./configure --enable-shared --without-motif-libraries --disable-float --prefix=/usr/local/gromacs-double/3.3 --enable-mpi --with-fft=fftw3 The gromacs configure succeeds: config.status: creating man/man1/Makefile config.status: creating src/config.h config.status: executing depfiles commands * You are compiling a double precision version of Gromacs - program names will be suffixed with _d to avoid overwriting single precision files. You can override it with --program-suffix * Seems you are compiling with MPI support. You can install the MPI- enabled programs with suffixed names to have both MPI and non-MPI versions. This is useful e.g. on supercomputers where you usually cannot run MPI-linked programs on the login node. Set a suffix with e.g. --program-suffix=_mpi (or _mpi_d for double). You only need MPI for mdrun, so if you already have non-MPI stuff installed you can issue make mdrun; make install-mdrun. the gromacs make fails. the complete log is too large to send. and, more precisely, here's where make bailed out. === mx_mpi_d.so -lnsl /usr/local/fftw301-double/lib/libfftw3.a -lm -lSM -lICE -lX11 -Wl,--rpath -Wl,/usr/local/gromacs-double/3.3/lib ../gmxlib/.libs/libgmx_mpi_d.so: undefined reference to `_nb_kerne010_x86_64_sse2' collect2: ld returned 1 exit status mpicc: No such file or directory make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/root/src/gromacs/gromacs-3.3-double/gromacs-3.3/src' make: *** [all-recursive] Error 1 = here's my env: LDFLAGS=-L/usr/local/fftw301/lib CPPFLAGS=-I/usr/local/fftw301/include LD_LIBRARY_PATH=/usr/local/fftw301-double/lib CC=/usr/bin/gcc4 PATH=/usr/local/fftw301-double/lib/:/usr/local/fftw301-double/include:/usr/local/lam/7.1.2-gcc4/bin:/usr/kerberos/sbin: /usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/usr/local/lam/7.1.2-gcc4/: /usr/local/lam/7.1.2-gcc4/bin/ CAN SOMEONE HELP? what am I missing? thank you. Susan ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
