Hi all,
I'm compiling AMBER 11 on a new system (using the Intel compilers) and
running into some trouble at more or less the last step of "make
parallel" -- compiling pmemd.MPI. The serial versions of sander and
pmemd both compile without a problem on this system, and the parallel
version of sander also compiles correctly (*and* passes the parallel
test cases). Here is the error that I get when compiling pmemd.MPI:
mpif90 -fast -o pmemd.MPI gbl_constants.o ...bunch of object files...
charmm_gold.o ../../netcdf/lib/libnetcdf.a -L/global/software/
centos-5.x86_64/modules/intel/Compiler/11.1/072/mkl/lib/em64t -Wl,--
start-group /global/software/centos-5.x86_64/modules/intel/Compiler/
11.1/072/mkl/lib/em64t/libmkl_intel_lp64.a /global/software/
centos-5.x86_64/modules/intel/Compiler/11.1/072/mkl/lib/em64t/
libmkl_sequential.a /global/software/centos-5.x86_64/modules/intel/
Compiler/11.1/072/mkl/lib/em64t/libmkl_core.a -Wl,--end-group -lpthread
ipo: remark #11000: performing multi-file optimizations
ipo: remark #11005: generating object file /tmp/ipo_ifortx3AcWQ.o
ld: cannot find -lmpi_f90
make[2]: *** [pmemd.MPI] Error 1
make[2]: Leaving directory `/global/home/users/psn/amber11/src/pmemd/
src'
make[1]: *** [parallel] Error 2
make[1]: Leaving directory `/global/home/users/psn/amber11/src/pmemd'
make: *** [parallel] Error 2
Here is the output of "mpif90 -show":
[psn.ln000 bin]$ mpif90 -show
ifort -I/global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/
include -I/global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/
lib -L/global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/lib
-lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-
dynamic -lnsl -lutil
And finally, here are relevant details of the system configuration:
* OS: CentOS 5.5
* Compilers: Intel v11.1.072
* Math library: Intel MKL (also v11.1.072)
* OpenMPI 1.4.2
* AMBER was configured using ./configure -mpi -noX11 intel
Any suggestions? This seems similar to an error that I saw in the
archive for compiling pmemd in AMBER 9, but the resolution to the
problem was never posted (as far as I can tell)...and it's been my
experience that pmemd in AMBER11 is so much more straightforward to
configure that I'm actually quite surprised I ran into any trouble.
Best,
Paul
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 10 2010 - 16:30:03 PDT
