[gmx-users] error while install GMX4.5.5
Dear GMX users: While I am installing gmx4.5.5, an error occured after "make" command : cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/grompp grompp.o -L/home/hzj1000/software/fftw/lib ./.libs/libgmxpreprocess.so /home/hzj1000/gromacs-4.5.5/src/mdlib/.libs/libmd.so ../mdlib/.libs/libmd.so /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so ../gmxlib/.libs/libgmx.so -ldl -lnsl -lm -Wl,--rpath -Wl,/home/hzj1000/software/GMX/gromacs4.5.5/lib /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' Zhongjin He-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
[gmx-users] error while install GMX4.5.5
Thanks Mark for your reply. First I want to know do I have to update GMX? for example, when GMX4.5.5 come out, and I use GMX4.5.5 instead of GMX4.5.4. I think GMX4.0.7 is even more stable. Second is the error while install GMX4.5.5. I use configure instead of CMake. I have successfully installed GMX4.5.4 and GMX4.0.7 with these command . I use GNU C compiler, and hareware is a 8 core Dell sever. Command line used is : tar xzvf gromacs-4.5.5.tar.gz ./configure --prefix=/home/hzj1000/software/GMX/4.5.5 --with-gsl --with-fft=fftw3 make and an error cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/grompp grompp.o -L/home/hzj1000/software/fftw/lib ./.libs/libgmxpreprocess.so /home/hzj1000/gromacs-4.5.5/src/mdlib/.libs/libmd.so ../mdlib/.libs/libmd.so /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so ../gmxlib/.libs/libgmx.so -ldl -lnsl -lm -Wl,--rpath -Wl,/home/hzj1000/software/GMX/4.5.5/lib /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' make: *** [all-recursive] Error 1 The output of configure: checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking how to create a ustar tar archive... gnutar checking for cc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking dependency style of cc... gcc3 checking how to run the C preprocessor... cc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking whether ln -s works... yes checking whether cc accepts -O3... yes checking whether cc accepts -msse2... yes checking whether cc accepts -funroll-all-loops... yes checking whether cc accepts -std=gnu99... yes checking whether cc accepts -fexcess-precision=fast... no checking whether cc accepts -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99... yes checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for unistd.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking sched.h usability... yes checking sched.h presence... yes checking for sched.h... yes checking for sysconf... yes checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... no checking whether pthreads work with -Kthread... no checking whether pthreads work with -kthread... no checking for the pthreads library -llthread... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... cc checking if atomic operations are supported... yes checking if pthread_setaffinity_np is available... yes checking whether byte ordering is bigendian... no checking that size_t can hold pointers... yes checking for SIGUSR1... yes checking for pipes... yes checking floating-point format... IEEE754 (little-endian byte and word order) checking whether ln -s works... yes checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /bin/sed checking for ld used by cc ... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking dependency style of g
[gmx-users] error while install GMX4.5.5
The system is Rocks 4.3 (Mars Hill), and [hzj1000@ZhouGroup ~]$ rpm -aq |grep glibc glibc-kernheaders-2.4-9.1.100.EL glibc-2.3.4-2.36 glibc-headers-2.3.4-2.36 glibc-common-2.3.4-2.36 glibc-devel-2.3.4-2.36 [hzj1000@ZhouGroup ~]$ gcc -v Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-java-awt=gtk --host=i386-redhat-linux Thread model: posix gcc version 3.4.6 20060404 (Red Hat 3.4.6-8)-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error while install GMX4.5.5
On 21/09/2011 7:27 PM, zhongjin wrote: Dear GMX users: While I am installing gmx4.5.5, an error occured after "make" command : cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/grompp grompp.o -L/home/hzj1000/software/fftw/lib ./.libs/libgmxpreprocess.so /home/hzj1000/gromacs-4.5.5/src/mdlib/.libs/libmd.so ../mdlib/.libs/libmd.so /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so ../gmxlib/.libs/libgmx.so -ldl -lnsl -lm -Wl,--rpath -Wl,/home/hzj1000/software/GMX/gromacs4.5.5/lib /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference to `pthread_setaffinity_np' collect2: ld returned 1 exit status make[3]: *** [grompp] Error 1 make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' make[1]: *** [all] Error 2 make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' This shouldn't happen. What compiler and hardware? configure or CMake? What command lines? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error while install GMX4.5.5
On Wed, Sep 21, 2011 at 9:01 PM, Mark Abraham wrote: > On 21/09/2011 7:27 PM, zhongjin wrote: > > Dear GMX users: > While I am installing gmx4.5.5, an error occured after "make" command : > cc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 > -funroll-all-loops -std=gnu99 -pthread -I./include -o .libs/grompp grompp.o > -L/home/hzj1000/software/fftw/lib ./.libs/libgmxpreprocess.so > /home/hzj1000/gromacs-4.5.5/src/mdlib/.libs/libmd.so ../mdlib/.libs/libmd.so > /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so > ../gmxlib/.libs/libgmx.so -ldl -lnsl -lm -Wl,--rpath > -Wl,/home/hzj1000/software/GMX/gromacs4.5.5/lib > /home/hzj1000/gromacs-4.5.5/src/gmxlib/.libs/libgmx.so: undefined reference > to `pthread_setaffinity_np' > collect2: ld returned 1 exit status > make[3]: *** [grompp] Error 1 > make[3]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src/kernel' > make[2]: *** [all-recursive] Error 1 > make[2]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' > make[1]: *** [all] Error 2 > make[1]: Leaving directory `/home/hzj1000/gromacs-4.5.5/src' > > > > This shouldn't happen. What compiler and hardware? configure or CMake? What > command lines? > Please also add: Which Unix? Is it Linux? Distribution? What libc version? Roland > Mark > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] error while install GMX4.5.5
On Thu, Sep 22, 2011 at 8:11 PM, zhongjin wrote: > The system is Rocks 4.3 (Mars Hill), and > [hzj1000@ZhouGroup ~]$ rpm -aq |grep glibc > glibc-kernheaders-2.4-9.1.100.EL > glibc-2.3.4-2.36 > glibc-headers-2.3.4-2.36 > glibc-common-2.3.4-2.36 > glibc-devel-2.3.4-2.36 > > [hzj1000@ZhouGroup ~]$ gcc -v > Reading specs from /usr/lib/gcc/i386-redhat-linux/3.4.6/specs > Configured with: ../configure --prefix=/usr --mandir=/usr/share/man > --infodir=/usr/share/info --enable-shared --enable-threads=posix > --disable-checking --with-system-zlib --enable-__cxa_atexit > --disable-libunwind-exceptions --enable-java-awt=gtk > --host=i386-redhat-linux > Thread model: posix > gcc version 3.4.6 20060404 (Red Hat 3.4.6-8) > > My gcc version is 4.6.1 probably it's nothing to do with your problem. just probably you may wanna to undate your gcc. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Best Regards, lina -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
