AMBER Archive (2004)

Subject: Re: AMBER: recompiling amber8

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Tue Aug 03 2004 - 15:31:00 CDT

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_at_sunysb.edu
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