Dear Amber users,
I'm having a rather unsuccessfull attempt to compile amber11 on a IBM
cluster. The serial version seems to compile nicely, but my parallel
version crashes with a bunch of "undefined reference" messages when
trying to compile sander.MPI with mpif90. (see below).
Using my own compiled openmpi to compile sander.MPI seems to work
fine. However, in that case I'm limited to using only 1 node (8cores)
at most. Thus, I have to use the mpif90 version in /usr/bin (in which
I have problems with compiling)
Any tips on how to resolve?
All the best,
Lars Skjaerven
The following details of the compiler and error message is:
config.h was made with:
./configure -mpi gnu
./configure -mpi -static -nobintraj gnu
mpif90 has the following specs:
-bash-3.2$ mpif90 -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-libgcj-multifile
--enable-languages=c,c++,objc,obj-c++,java,fortran,ada
--enable-java-awt=gtk --disable-dssi --enable-plugin
--with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre
--with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20080704 (Red Hat 4.1.2-48)
ERROR MSG:
mpif90 -o sander.MPI constants.o state.o memory_module.o stack.o
nose_hoover.o nose_hoover_vars.o nose_hoover_init.o qmmm_module.o trace.o
lmod.o rand2.o ....... spatial_recip.o spatial_fft.o parms.o
softcore.o mbar.o molecule.o
qm_mm.o qm_ewald.o qm2_variable_solvent.o qmmm_qmtheorymodule.o \
.... [Lots of stuff] ....
error messages like:
_nose_hoover.f:(.text+0x1219): undefined reference to `mpi_allreduce_'
qmmm_module.o: In function `__qmmm_module__qmmm_mpi_setup':
_qmmm_module.f:(.text+0x742): undefined reference to `mpi_bcast_'
_qmmm_module.f:(.text+0x767): undefined reference to `mpi_bcast_'
_qmmm_module.f:(.text+0x78c): undefined reference to `mpi_bcast_'
.... [Lots of stuff] ....
... [terminates with this error] ....
/home/skjaerve/software/amber11/src/sander/_ncsu-utils.f:256:
undefined reference to `mpi_comm_rank_'
/home/skjaerve/software/amber11/src/sander/_ncsu-utils.f:259:
undefined reference to `mpi_comm_size_'
/home/skjaerve/software/amber11/src/sander/_ncsu-utils.f:269:
undefined reference to `mpi_recv_'
collect2: ld returned 1 exit status
mpif90: No such file or directory
make[1]: *** [sander.MPI] Error 1
make[1]: Leaving directory
`/home/skjaerve/software/amber11/src/sander'
make: *** [parallel] Error 2
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Received on Tue Sep 13 2011 - 06:30:03 PDT
