AMBER Archive (2006)

Subject: AMBER: Amber8 parallel compilation problems on an OSCAR Cluster

From: Aaron J. Greenwood (agreenwo_at_uci.edu)
Date: Thu Feb 02 2006 - 16:18:59 CST

On our system the serial version of amber8 compiles without error but
the parallel version does not compile. I've looked but cannot find the
missing libraries. I get many messages of the form:

egb.o(.text+0x1eeb): In function `genborn_mp_egb_':
: undefined reference to `mpi_allreduce_'
sander.o(.text+0x28): In function `MAIN__':
: undefined reference to `mpi_init_'sander.o(.text+0xa17): more
undefined references to `mpi_bcast_' follow
: undefined reference to `mpi_comm_free_'
sander.o(.text+0x3bdf): In function `sander_':
: undefined reference to `mpi_bcast_'
runmd.o(.text+0x8a5): In function `runmd_':
: undefined reference to `mpi_allreduce_'
parallel.o(.text+0x52): In function `startup_':
: undefined reference to `mpi_bcast_'
: undefined reference to `mpi_allreduce_'
parallel.o(.text+0x1348): In function `fsum_':
: undefined reference to `mpi_sendrecv_'
ew_force.o(.text+0x34): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_force.o(.text+0x336): In function `ewald_force_':
: undefined reference to `mpi_barrier_'
ew_force.o(.text+0x16a2): In function `ewald_force_':
: undefined reference to `mpi_comm_rank_'
ew_fft.o(.text+0xd87): In function `xy_zx_transpose_.':
: undefined reference to `mpi_recv_'
debug.o(.text+0x74a): In function `debug_frc_':
: undefined reference to `mpi_barrier_'

The following variables were set:

AMBERHOME
MKL_HOME
LAM_HOME

Fortran Compiler ==> The Intel Fortran Compiler 9.0 for Linux
MKL ==> Math Kernel Library 8.0.1

I configured with both .configure -lam ifort and .configure -lam -static
ifort

Any suggestions would be appreciated.

Best regards,

Aaron

David A. Case wrote:
> On Thu, Feb 02, 2006, HL Eastwood wrote:
>
>> I have been trying to compile the parallel version of amber but nothing
>> I do seems to work. Here is how I configured it:
>>
>>
>> /opt/lam-7.1.1/lib/libmpi.a(malloc.o)(.text+0xa0): In function
>> `malloc_atfork':
>> : undefined reference to `pthread_getspecific'
>>
>
> LAM requires pthreads, but its "showme" option (which is supposed to list
> its dependencies) does not.
>
> Try this: edit your config.h file and add "-lpthread" to the end of the
> LOADLIB variable.
>
> Generically, when you have a "undefined reference", you need to figure out
> which library is missing, and add that to loadlib.
>
> (caveat: I haven't run LAM in a while, having moved over to its successor,
> openMPI. But this advice or something like it should be in the right
> direction.)
>
> ...good luck...dac
>
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