Re: [AMBER] mpi4py building error during AmberTools 13 install

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 28 Aug 2013 10:56:41 -0400

On Tue, Aug 27, 2013 at 5:56 AM, sunyeping <sunyeping.aliyun.com> wrote:

> Dear everyone,
>
> I am try to install MPI version of AmberTools 13 into my Centos5.9 system.
> The config process seemed OK:
>
> ./config -mpi -gnu
> When I excute make command, I get the error message:
>
> building 'mpi4py.MPI' extensioncreating
> build/temp.linux-x86_64-2.7creating
> build/temp.linux-x86_64-2.7/src/opt/mpich2/bin/mpicc -fPIC
> -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes
> -I/usr/local/include/python2.7 -c src/MPI.c -o
> build/temp.linux-x86_64-2.7/src/MPI.o/opt/mpich2/bin/mpicc -shared
> build/temp.linux-x86_64-2.7/src/MPI.o -o
> build/lib.linux-x86_64-2.7/mpi4py/MPI.so/usr/bin/ld:
> /opt/mpich2/lib/libmpich.a(comm_create_keyval.o): relocation R_X86_64_32
> against `a local symbol' can not be used when making a shared object;
> recompile with -fPIC/opt/mpich2/lib/libmpich.a: could not read symbols: Bad
> valuecollect2: ld θΏ”ε›ž 1error: command '/opt/mpich2/bin/mpicc' failed with
> exit status 1
>
> According to these message, I searched google and tried to recompile
> mpi2ch by doing this
> cd mpich2-1.4.1p1
> ./config --enable-shared --prefix=/opt/mpich2
> make
> make install
>
> There seemed no problem during the mpich2 install


> However, when I try to install AmberTools 13, I get the same error message
> as above. Could you help me with this? Thanks in advance.
>

Configure mpich2 like this:

./configure CFLAGS="-fPIC" CXXFLAGS="-fPIC" FFLAGS="-fPIC" --enable-shared
--prefix=/opt/mpich2​​

Then try. On the other hand, you can use the configure_mpich script
bundled with AmberTools to build a compatible MPI.

Good luck,
Jason


>
>
> Yeping Sun
>
> Institute of Microbiology, Chinese Academy of Sciences
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> http://lists.ambermd.org/mailman/listinfo/amber
> 



-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 28 2013 - 08:00:02 PDT
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