I'd clean the mpich compilation (make clean) and try again (or better
yet, remove your mpich directory and untar it again before compilation).
Your mpich libraries are most likely compiled with a different compiler
than sander. Also make sure you're really pointing to the right location
where your compiled mpich libraries are (Carsten said this fixed his
compilation problems).
-Viktor
Xiao Jian Tan wrote:
> Dear all,
>
> I have the same problem as Carsten when I tried to complile amber8 on a
> linux cluster. We use Redhat7.3.
>
> I followed the instruction on the web page
> http://amber.scripps.edu/cluster_info/index.html,
>
> -------------------------
> # first patch all the bugfixs.
>
> # using Intel C Compiler (icc8.0)
> source /opt/intel_cc_80/bin/iccvars.sh
> source /opt/intel_fc_80/bin/ifortvars.sh
>
> # compile MPICH libraries with Intel compilers
> export CC=icc
> export FC=ifort
> ./configure --prefix=/usr/local/mpich-1.2.5.2_icc -cc=$CC -fc=$FC
> make install
>
> # setenv for amber8 and MPICH
> export AMBERHOME="/usr/local/amber8_mpich"
> export MPICH_HOME="/usr/local/mpich-1.2.5.2_icc"
>
> # 3a. Compile a serial (without MPI) version of all programs:
> cd $AMBERHOME/src
> ./configure ifort
> make serial
> # without problems !!
>
> #3b. Compile a parallel version of sander (and sander.LES)
> cd $AMBERHOME/src
> make clean
> ./configure -mpich ifort
> make parallel
>
> Then it complained
> ...
> `mpi_reduce_'> debug.o(.text+0xc7fe): undefined reference to
> `mpi_reduce_'>>ew_dipole_recip.o(.text+0x74e): undefined reference to
> `mpi_barrier_' debug.o(.text+0xcafe): undefined reference to
> `mpi_barrier_'> debug.o(.text+0xccd3): undefined reference to
> `mpi_reduce_'>>ew_dipole_recip.o(.text+0xa64): undefined reference to
> `mpi_barrier_' debug.o(.text+0xcd71): undefined reference to
> `mpi_reduce_'> > debug.o(.text+0xd04f): undefined reference to
> `mpi_barrier_'> > debug.o(.text+0xd226): undefined reference to
> `mpi_reduce_'> > debug.o(.text+0xd2bb): undefined reference to
> `mpi_reduce_'> > http://amber.scripps.edu/cluster_info/index.html # Intel
> C Compiler (icc8.0), Fortran compiler (ifort8.0)# Intel C Compiler
> (icc8.0), Fortran compiler (ifort8.0)> > source
> /opt/intel_cc_80/bin/iccvars.sh source /opt/intel_fc_80/bin/ifortvars.sh
> 2. Compile and install MPI libraries (mpich-1.2.5.2) To compile MPICH
> libraries with Intel compilers, configure for example like this: export
> CC=icc export FC=ifort ./configure --prefix=/usr/local/mpich-1.2.5.2_icc
> -cc=$CC -fc=$FC make install source /opt/intel_cc_80/bin/iccvars.sh source
> /opt/intel_fc_80/bin/ifortvars.sh 2. Compile and install MPI libraries
> (mpich-1.2.5.2) To compile MPICH libraries with Intel compilers, configure
> for example like this: export CC=icc export FC=ifort ./configure
> --prefix=/usr/local/mpich-1.2.5.2_icc -cc=$CC -fc=$FC make install
> debug.o(.text+0xd673): undefined reference to `mpi_barrier_'
> debug.o(.text+0xd84a): undefined reference to `mpi_reduce_'
> debug.o(.text+0xd8dd): undefined reference to `mpi_reduce_'
> ew_dipole_recip.o: In function `do_pmesh_dipole_kspace_':
> ew_dipole_recip.o(.text+0x6b0): undefined reference to `mpi_barrier_'
> ew_dipole_recip.o(.text+0x836): undefined reference to `mpi_barrier_'
> ew_dipole_recip.o(.text+0xb93): undefined reference to `mpi_barrier_'
> mexit.o: In function `mexit_': mexit.o(.text+0x28): undefined reference to
> `mpi_abort_' mexit.o(.text+0x4e): undefined reference to `mpi_finalize_'
> new_time.o: In function `timer_barrier_': new_time.o(.text+0x230):
> undefined reference to `mpi_barrier_' new_time.o: In function
> `profile_time_': new_time.o(.text+0x7cb): undefined reference to
> `mpi_send_' new_time.o(.text+0xc4d): undefined reference to `mpi_recv_'
> make[1]: *** [sander] Error 1 make[1]: Leaving directory
> `/users/xjtan/amber8/src/sander' make: *** [parallel] Error 2
>
> ---------------------------------
>
> How can I solve this problem? Any suggestion would be highly appreciated!
>
>
> Best regards,
>
> Xiaojian Tan
>
>
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--
===================================================================
Viktor Hornak
Center for Structural Biology Phone: (631)632-1439
SUNY at Stony Brook Fax: (631)632-1555
Stony Brook, NY 11794-5115 E-mail: viktor.hornak.sunysb.edu
===================================================================
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Received on Tue Aug 03 2004 - 21:53:00 PDT
