Re: [gmx-users] TEE-REX installation error
Thanks for the answer, configuring with --enable-mpi solves the problem. Just to note it was not totally clear from the TEE-REX documentation that this had to be the case, however suppose i should have thought about it and realised replica exchange is usually ran on more than one processor! Tom --On Tuesday, June 10, 2008 02:14:40 +1000 Mark Abraham <[EMAIL PROTECTED]> wrote: TJ Piggot wrote: Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_parallel_3dfft.lo -MD -MP -MF .deps/gmx_parallel_3dfft.Tpo -c gmx_parallel_3dfft.c -o gmx_parallel_3dfft.o if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF ".deps/qm_gaussian.Tpo" -c -o qm_gaussian.lo qm_gaussian.c; \ then mv -f ".deps/qm_gaussian.Tpo" ".deps/qm_gaussian.Plo"; else rm -f ".deps/qm_gaussian.Tpo"; exit 1; fi if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF ".deps/gmx_fft_fftw3.Tpo" -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c; \ then mv -f ".deps/gmx_fft_fftw3.Tpo" ".deps/gmx_fft_fftw3.Plo"; else rm -f ".deps/gmx_fft_fftw3.Tpo"; exit 1; fi cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT teerex.lo -MD -MP -MF .deps/teerex.Tpo -c teerex.c -o teerex.o teerex.c: In function `init_TEEREX': teerex.c:167: warning: implicit declaration of function `MPI_Gather' teerex.c:167: error: `MPI_FLOAT' undeclared (first use in this function) teerex.c:167: error: (Each undeclared identifier is reported only once teerex.c:167: error: for each function it appears in.) teerex.c:167: error: `MPI_COMM_WORLD' undeclared (first use in this function) teerex.c:244: warning: implicit declaration of function `MPI_Barrier' These are occurring because teerex.c is expecting to be part of an MPI installation of GROMACS, and yours isn't. Thus either the installation documentation of TEE-REX, or your following of it, is suspect :-) I know nothing about TEE-REX, but your first move after checking their documentation again should be a "make distclean" and then to reconfigure GROMACS with the --enable-mpi flag. 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 -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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] TEE-REX installation error
TJ Piggot wrote: Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_parallel_3dfft.lo -MD -MP -MF .deps/gmx_parallel_3dfft.Tpo -c gmx_parallel_3dfft.c -o gmx_parallel_3dfft.o if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF ".deps/qm_gaussian.Tpo" -c -o qm_gaussian.lo qm_gaussian.c; \ then mv -f ".deps/qm_gaussian.Tpo" ".deps/qm_gaussian.Plo"; else rm -f ".deps/qm_gaussian.Tpo"; exit 1; fi if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF ".deps/gmx_fft_fftw3.Tpo" -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c; \ then mv -f ".deps/gmx_fft_fftw3.Tpo" ".deps/gmx_fft_fftw3.Plo"; else rm -f ".deps/gmx_fft_fftw3.Tpo"; exit 1; fi cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT teerex.lo -MD -MP -MF .deps/teerex.Tpo -c teerex.c -o teerex.o teerex.c: In function `init_TEEREX': teerex.c:167: warning: implicit declaration of function `MPI_Gather' teerex.c:167: error: `MPI_FLOAT' undeclared (first use in this function) teerex.c:167: error: (Each undeclared identifier is reported only once teerex.c:167: error: for each function it appears in.) teerex.c:167: error: `MPI_COMM_WORLD' undeclared (first use in this function) teerex.c:244: warning: implicit declaration of function `MPI_Barrier' These are occurring because teerex.c is expecting to be part of an MPI installation of GROMACS, and yours isn't. Thus either the installation documentation of TEE-REX, or your following of it, is suspect :-) I know nothing about TEE-REX, but your first move after checking their documentation again should be a "make distclean" and then to reconfigure GROMACS with the --enable-mpi flag. 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] TEE-REX installation error
Hi, I am trying to install the TEE-REX patch for gromacs 3.3.1 and am getting the following make error: cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_parallel_3dfft.lo -MD -MP -MF .deps/gmx_parallel_3dfft.Tpo -c gmx_parallel_3dfft.c -o gmx_parallel_3dfft.o if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF ".deps/qm_gaussian.Tpo" -c -o qm_gaussian.lo qm_gaussian.c; \ then mv -f ".deps/qm_gaussian.Tpo" ".deps/qm_gaussian.Plo"; else rm -f ".deps/qm_gaussian.Tpo"; exit 1; fi if /bin/sh ../../libtool --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF ".deps/gmx_fft_fftw3.Tpo" -c -o gmx_fft_fftw3.lo gmx_fft_fftw3.c; \ then mv -f ".deps/gmx_fft_fftw3.Tpo" ".deps/gmx_fft_fftw3.Plo"; else rm -f ".deps/gmx_fft_fftw3.Tpo"; exit 1; fi cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT teerex.lo -MD -MP -MF .deps/teerex.Tpo -c teerex.c -o teerex.o teerex.c: In function `init_TEEREX': teerex.c:167: warning: implicit declaration of function `MPI_Gather' teerex.c:167: error: `MPI_FLOAT' undeclared (first use in this function) teerex.c:167: error: (Each undeclared identifier is reported only once teerex.c:167: error: for each function it appears in.) teerex.c:167: error: `MPI_COMM_WORLD' undeclared (first use in this function) teerex.c:244: warning: implicit declaration of function `MPI_Barrier' make[3]: *** [teerex.lo] Error 1 make[3]: *** Waiting for unfinished jobs cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT qm_gaussian.lo -MD -MP -MF .deps/qm_gaussian.Tpo -c qm_gaussian.c -o qm_gaussian.o cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include -DGMXLIBDIR=\"/home/tp1821/Gromacs/teerex/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -funroll-all-loops -MT gmx_fft_fftw3.lo -MD -MP -MF .deps/gmx_fft_fftw3.Tpo -c gmx_fft_fftw3.c -o gmx_fft_fftw3.o make[3]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src/mdlib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/tp1821/Gromacs/gromacs-3.3.1-teerex/src' make: *** [all-recursive] Error 1 I am using the gcc 3.4.6 compiler on a CentOS 4 linux box and also gromacs 3.3.1 without the TEE-REX patch installs fine. Thanks for any advice you can give me to fix this problem. Tom Piggot -- TJ Piggot [EMAIL PROTECTED] University of Bristol, UK. ___ 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
