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

From: sunyeping <>
Date: Sun, 15 Sep 2013 01:18:23 +0800

Dear Mr. Swails,
Thank you for your reply last time for ambertool13 install. I have tried to confiure the mpich2 using:./configure CFLAGS="-fPIC" CXXFLAGS="-fPIC" FFLAGS="-fPIC" --enable-shared--prefix=/opt/mpich2​​
However, I receive error message:
configure: error: ****  Incompatible Fortran and C Object File Types!  ****F77 Object File Type produced by "ifort -fPIC " is : : ERROR: cannot open `' (No such file or directory). C  Object File Type produced by "gcc -fPIC   -O2" is : : ELF 64-bit LSB relocatable, AMD x86-64, version 1 (SYSV), not stripped.What does that mean and how to resolve the problem?

Institute of Microbiology, Chinese Academy of Sciences

------------------------------------------------------------------发件人:Jason Swails <>发送时间:2013年8月28日(星期三) 22:56收件人:AMBER Mailing List <>主 题:Re: [AMBER] mpi4py building error during AmberTools 13 installOn Tue, Aug 27, 2013 at 5:56 AM, sunyeping <> 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/> /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 返回 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 scriptbundled with AmberTools to build a compatible MPI.Good luck,Jason>>> Yeping Sun>> Institute of Microbiology, Chinese Academy of Sciences> _______________________________________________> AMBER mailing list>>>-- Jason M. SwailsBioMaPS,Rutgers UniversityPostdoctoral Researcher_______________________________________________AMBER mailing listAMBER.ambermd.org
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Received on Sat Sep 14 2013 - 10:30:02 PDT
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