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On 8/06/2011 7:06 PM, xuji wrote:
<blockquote cite="mid:201106081706428125758@home.ipe.ac.cn"
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<div><font color="#000080" face="Verdana" size="2">Hi all
gmx-users:</font></div>
</blockquote>
<br>
Please do not cross-post such questions to gmx-developers. This
question has nothing to do with development.<br>
<blockquote cite="mid:201106081706428125758@home.ipe.ac.cn"
type="cite">
<div><font color="#000080">I install gromacs-4.5.4, with</font></div>
<div> </div>
<div>
<div>tar xzf gromacs-4.5.4.tar.gz</div>
<div>cd gromacs-4.5.4</div>
</div>
<div>export MPICC=/usr/mpi/gcc/mvapich2-1.4.1/bin/mpicc </div>
<div>./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/
</div>
<div>
<div>make -j 8</div>
</div>
</blockquote>
<br>
--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.<br>
<br>
Mark<br>
<blockquote cite="mid:201106081706428125758@home.ipe.ac.cn"
type="cite">
<div><font color="#000080">but always got following errors:</font></div>
<div> </div>
<div>
<div>Making all in kernel</div>
<div>make[3]: Entering directory `/home/xuji/src/gromacs-4.5.4/src/kernel'</div>
<div>/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 </div>
<div>/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 </div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(simple_pmi.o): In function `PMI_Init':</div>
<div>(.text+0x1690): warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking</div>
<div>/usr/lib64/libc.a(malloc.o): In function `__malloc_check_init':</div>
<div>(.text+0x13d0): multiple definition of `__malloc_check_init'</div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x8c0): first defined here</div>
<div>/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)</div>
<div>/usr/lib64/libc.a(malloc.o): In function `free':</div>
<div>(.text+0x6da0): multiple definition of `free'</div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3260): first defined here</div>
<div>/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)</div>
<div>/usr/lib64/libc.a(malloc.o): In function `malloc':</div>
<div>(.text+0x55b0): multiple definition of `malloc'</div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3370): first defined here</div>
<div>/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)</div>
<div>/usr/lib64/libc.a(malloc.o): In function `realloc':</div>
<div>(.text+0x6f20): multiple definition of `realloc'</div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mvapich_malloc.o):(.text+0x3740): first defined here</div>
<div>/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)</div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function `set_real_munmap_ptr':</div>
<div>(.text+0x1e): undefined reference to `dlsym'</div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function `set_real_munmap_ptr':</div>
<div>(.text+0x26): undefined reference to `dlerror'</div>
<div>/usr/mpi/gcc/mvapich2-1.4.1/lib/libmpich.a(mem_hooks.o): In function `mvapich2_minit':</div>
<div>(.text+0x14c): undefined reference to `dlerror'</div>
<div>/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `load_driver':</div>
<div>(.text+0xc7): undefined reference to `dlopen'</div>
<div>/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `load_driver':</div>
<div>(.text+0x102): undefined reference to `dlerror'</div>
<div>/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `ibverbs_init':</div>
<div>(.text+0x11af): undefined reference to `dlopen'</div>
<div>/usr/lib64/libibverbs.a(src_libibverbs_la-init.o): In function `ibverbs_init':</div>
<div>(.text+0x11c0): undefined reference to `dlclose'</div>
<div>/usr/lib64/libibverbs.a(src_libibverbs_la-verbs.o): In function `ibv_create_comp_channel':</div>
<div>(.text+0xb76): undefined reference to `pthread_mutex_trylock'</div>
<div>collect2: ld returned 1 exit status</div>
<div>make[3]: *** [grompp] Error 1</div>
<div>make[3]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src/kernel'</div>
<div>make[2]: *** [all-recursive] Error 1</div>
<div>make[2]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src'</div>
<div>make[1]: *** [all] Error 2</div>
<div>make[1]: Leaving directory `/home/xuji/src/gromacs-4.5.4/src'</div>
<div>make: *** [all-recursive] Error 1</div>
</div>
<div> </div>
<div> </div>
<div><font color="#000080">Can someone show me what's wrong?</font></div>
<div><font color="#000080">Appreciate any help in advance!</font></div>
<div> </div>
<div> </div>
<div><font color="#c0c0c0" face="Verdana" size="2">2011-06-08 </font></div>
<font color="#000080" face="Verdana" size="2">
<hr style="width: 100px;" align="left" color="#b5c4df" size="1">
</font>
<div><font color="#c0c0c0" face="Verdana" size="2"><span>
<div>
<div>
<div> </div>
<div>Best </div>
<div> wishes£¡</div>
<div> </div>
<div>Ji Xu</div>
<div>The State Key Laboratory of Multiphase Complex System</div>
<div>Institute of Process Engineering</div>
<div>Chinese Academy of Sciences</div>
<div>Beijing 100190, China</div>
<div>Tel.: +86 10 8262 3713-804 </div>
</div>
</div>
</span></font></div>
<hr color="#b5c4df" size="1">
</blockquote>
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