[gmx-users] Gromacs-4.5.4 install error

[xuji]

Hi all gmx-users:

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

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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