AMBER Archive (2008)

Subject: AMBER: AMBER10 compiling SANDER parallel problem

From: Hazard, E. Starr (hazards_at_musc.edu)
Date: Tue Nov 18 2008 - 14:48:31 CST

Folks,

I have AMBER 10 and Amber tools 1.2. I downloaded PATCH files on Nov 17.

I have successfully compiled the serial version. I have undertaken to try the parallel compilation.
I have lam-7.1.4 installed but parallel compiling fails

I execute these lines to point to my MKL
export MKL_HOME=/opt/intel/mkl/10.0.011
source /opt/intel/mkl/10.0.011/tools/environment/mklvarsem64t.sh

./configure_amber -lam g95
make parallel

The final lines include:
Fortran 90 feature at (^) unsupported
_constants.f:215:
   end module constants
       ^
Invalid form for END statement at (^)
_constants.f:102:
   double precision, parameter :: TEN_TO_MINUS2 = 1.0d-2
   ^
End of source file before end of block started at (^)
/share/apps/lam-7.1.4/bin/mpif77: No such file or directory
make[1]: *** [constants.o] Error 1
make[1]: Leaving directory `/home/hazards/COMPILE/amber10/src/sander'
make: *** [parallel] Error 2

The mpif77 does exist where the error above says it does not.

$ ls /share/apps/lam-7.1.4/bin/
hboot hcp lamboot lamclean lamexec lamhalt lamnodes lamshrink lamwipe mpicc mpiexec mpimsg mpitask tkill wipe
hcc hf77 lamcheckpoint lamd lamgrow laminfo lamrestart lamtrace mpic++ mpiCC mpif77 mpirun recon tping

When I build with the lamsource option

make clean
./configure_amber -lamsource g95
./configure_lam
make parallel
../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
        ../lib/nxtsec.o ../lib/sys.a mt19937.o ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-colvar.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o ../netcdf/lib/libnetcdf.a -L/opt/intel/mkl/10.0.011/lib/em64t -lvml -lmkl_lapack -lmkl -lguide -lpthread
ld: cannot find -lvml

The MKL library directory has these files including several vml source entries:

ls /opt/intel/mkl/10.0.011/lib/em64t
libguide.a libmkl_blacs_openmpi_lp64.a libmkl_gnu_thread.a libmkl_lapack.so libmkl_solver_ilp64_sequential.a
libguide.so libmkl_cdft.a libmkl_gnu_thread.so libmkl_mc.so libmkl_solver_lp64.a
libiomp5.a libmkl_cdft_core.a libmkl_intel_ilp64.a libmkl_p4n.so libmkl_solver_lp64_sequential.a
libiomp5.so libmkl_core.a libmkl_intel_ilp64.so libmkl_scalapack.a libmkl_vml_def.so
libmkl_blacs_ilp64.a libmkl_core.so libmkl_intel_lp64.a libmkl_scalapack_ilp64.a libmkl_vml_mc2.so
libmkl_blacs_intelmpi20_ilp64.a libmkl_def.so libmkl_intel_lp64.so libmkl_scalapack_lp64.a libmkl_vml_mc.so
libmkl_blacs_intelmpi20_lp64.a libmkl_em64t.a libmkl_intel_sp2dp.a libmkl_sequential.a libmkl_vml_p4n.so
libmkl_blacs_intelmpi_ilp64.a libmkl_gf_ilp64.a libmkl_intel_sp2dp.so libmkl_sequential.so
libmkl_blacs_intelmpi_lp64.a libmkl_gf_ilp64.so libmkl_intel_thread.a libmkl.so
libmkl_blacs_lp64.a libmkl_gf_lp64.a libmkl_intel_thread.so libmkl_solver.a
libmkl_blacs_openmpi_ilp64.a libmkl_gf_lp64.so libmkl_lapack.a libmkl_solver_ilp64.a

So, I am not sure why this is happening. What should I try next?

Starr

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