[gmx-users] Gromacs-4.5.4 install error

[Mark Abraham]

On 8/06/2011 7:06 PM, xuji wrote:
> Hi all gmx-users:

Please do not cross-post such questions to gmx-developers. This question
has nothing to do with development.
> I install gromacs-4.5.4, with
> tar xzf gromacs-4.5.4.tar.gz
> cd gromacs-4.5.4
> export MPICC=/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc
> ./configure --prefix=/home/xuji/bin/gmx_4.5.4/parallel_float
> --enable-mpi --program-suffix=_mpi --without-x --with-fft=fftw3
> --enable-all-static --without-xml --with-pic
> CPPFLAGS=-I/home/xuji/bin/fftw3_f/include/
> LDFLAGS=-L/home/xuji/bin/fftw3_f/lib/
> make -j 8

--enable-all-static and --with-pic might be inconsistent with each other
or with your MVAPICH installation, and might be the reason for your
linker errors. Some older MPICH and MVAPICH versions are known to be
unsuitable for use with GROMACS, even if linking succeeds.

Mark
> but always got following errors:
> Making all in kernel
> make[3]: Entering directory `/home/xuji/src/gromacs-4.5.4/src/kernel'
> /bin/sh ../../libtool --tag=CC --mode=link
> /usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops
> -std=gnu99 -L/home/xuji/bin/fftw3_f/lib/ -all-static -o grompp
> grompp.o libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la
> ../gmxlib/libgmx_mpi.la -lnsl -lm
> /usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc -O3 -fomit-frame-pointer
> -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops
> -std=gnu99 -static -o grompp grompp.o -L/home/xuji/bin/fftw3_f/lib/
> ./.libs/libgmxpreprocess_mpi.a
> /home/xuji/src/gromacs-4.5.4/src/mdlib/.libs/libmd_mpi.a
> ../mdlib/.libs/libmd_mpi.a /home/xuji/bin/fftw3_f/lib/libfftw3f.a
> /home/xuji/src/gromacs-4.5.4/src/gmxlib/.libs/libgmx_mpi.a
> ../gmxlib/.libs/libgmx_mpi.a -lnsl -lm
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(simple_pmi.o): In function
> `PMI_Init':
> (.text+0x1690): warning: Using 'gethostbyname' in statically linked
> applications requires at runtime the shared libraries from the glibc
> version used for linking
> /usr/lib64/libc.a(malloc.o): In function `__malloc_check_init':
> (.text+0x13d0): multiple definition of `__malloc_check_init'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x8c0):
> first defined here
> /usr/bin/ld: Warning: size of symbol `__malloc_check_init' changed
> from 113 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 107 in
> /usr/lib64/libc.a(malloc.o)
> /usr/lib64/libc.a(malloc.o): In function `free':
> (.text+0x6da0): multiple definition of `free'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3260):
> first defined here
> /usr/bin/ld: Warning: size of symbol `free' changed from 247 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 375 in
> /usr/lib64/libc.a(malloc.o)
> /usr/lib64/libc.a(malloc.o): In function `malloc':
> (.text+0x55b0): multiple definition of `malloc'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3370):
> first defined here
> /usr/bin/ld: Warning: size of symbol `malloc' changed from 364 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 547 in
> /usr/lib64/libc.a(malloc.o)
> /usr/lib64/libc.a(malloc.o): In function `realloc':
> (.text+0x6f20): multiple definition of `realloc'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3740):
> first defined here
> /usr/bin/ld: Warning: size of symbol `realloc' changed from 508 in
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o) to 1123
> in /usr/lib64/libc.a(malloc.o)
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function
> `set_real_munmap_ptr':
> (.text+0x1e): undefined reference to `dlsym'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function
> `set_real_munmap_ptr':
> (.text+0x26): undefined reference to `dlerror'
> /usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function
> `mvapich2_minit':
> (.text+0x14c): undefined reference to `dlerror'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `load_driver':
> (.text+0xc7): undefined reference to `dlopen'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `load_driver':
> (.text+0x102): undefined reference to `dlerror'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `ibverbs_init':
> (.text+0x11af): undefined reference to `dlopen'
> /usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function
> `ibverbs_init':
> (.text+0x11c0): undefined reference to `dlclose'
> /usr/lib64/libibverbs.a(src_libibverbs_la-verbs.o): In function
> `ibv_create_comp_channel':
> (.text+0xb76): undefined reference to `pthread_mutex_trylock'
> collect2: ld returned 1 exit status
> make[3]: *** [grompp] Error 1
> make[3]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src'
> make: *** [all-recursive] Error 1
> Can someone show me what's wrong?
> Appreciate any help in advance!
> 2011-06-08
> ------------------------------------------------------------------------
> Best
> wishes！
> Ji Xu
> The State Key Laboratory of Multiphase Complex System
> Institute of Process Engineering
> Chinese Academy of Sciences
> Beijing 100190, China
> Tel.: +86 10 8262 3713-804
> ------------------------------------------------------------------------

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