AMBER Archive (2004)

Subject: Re: AMBER: recompiling amber8

From: Xiao Jian Tan (xjtan_at_umich.edu)
Date: Tue Aug 03 2004 - 13:02:12 CDT

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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