AMBER Archive (2006)

Subject: AMBER: Can't compile PMEMD

From: Michael John Hanby (mhanby_at_uab.edu)
Date: Thu Dec 14 2006 - 15:47:15 CST

Howdy, I'm getting the following error when attempting to compile (make
install) src.pmemd (the last 20 or so lines of output are at the end of
this email):

 ld: cannot find -lmpga
 mpif77: No such file or directory
 make[1]: *** [pmemd] Error 1
 make[1]: Leaving directory `/share/apps/amber9/src.pmemd/pmemd'
 make: *** [install] Error 2

Here are the steps I'm following
# cd $AMBERHOME/src.pmemd
# export MPI_HOME=/share/apps/lam/7.1.2/intel
# export PATH=$MPI_HOME/bin:$PATH
# export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH
# export FC=mpif77
# export CC=mpicc
# ln -s Machines/Machine.lammpi_ifc MACHINE
# vi ./MACHINE

  setenv LAM_HOME /share/apps/lam/7.1.2/intel
  setenv CC "mpicc "
  setenv LOADCC "mpicc "
  setenv LOADLIB "-L$LAM_LIBDIR -llamf77mpi -lmpi -llam"

  ----> Change all occurrences of if7 to mpif77

# make install

And here's the last bit of output from the make command:
========================================================================
==
../Compile L2 -P runmin.f90
cat runmin.f90 | /usr/bin/cpp -traditional
-I/share/apps/lam/7.1.2/intel/include -P -DLinux -DREGNML -DMPI
-DNO_MPI_BUFFER_ALIASING -DSLOW_NONBLOC KING_MPI
-DSHORT=INTEGER(2) -DLOGICAL_BYTE=LOGICAL(1) > _runmin_.f90
mpif77 -c -auto -tpp6 -mp1 -ip -O3 _runmin_.f90
touch use_runmin.h
touch use_runmin_cit.h
../Compile L3 -P pmemd.f90
cat pmemd.f90 | /usr/bin/cpp -traditional
-I/share/apps/lam/7.1.2/intel/include -P -DLinux -DREGNML -DMPI
-DNO_MPI_BUFFER_ALIASING -DSLOW_NONBLOCK ING_MPI
-DSHORT=INTEGER(2) -DLOGICAL_BYTE=LOGICAL(1) > _pmemd_.f90
mpif77 -c -auto -tpp6 -mp1 -ip -O3 _pmemd_.f90
( SYSDIR=`../sysdir dir` ; echo sysdir is $SYSDIR ; \
                cd $SYSDIR ; make sys.a )
sysdir is /share/apps/amber9/src.pmemd/Machines/intel
make[2]: Entering directory
`/share/apps/amber9/src.pmemd/Machines/intel'
../../Compile CPPONLY -DDPREC -o sys.f90 sys_proto.f90
Making source: machine is LINUX_INTEL
cat sys_proto.f90 | /usr/bin/cpp -traditional
-I/share/apps/lam/7.1.2/intel/include -P -DDPREC -DLinux -DREGNML
-DMPI -DNO_MPI_BUFFER_ALIASING - DSLOW_NONBLOCKING_MPI
-DSHORT=INTEGER(2) -DLOGICAL_BYTE=LOGICAL(1) >> sys.f90
Made source for machine: LINUX_INTEL
../../Compile L1 -DDPREC -P sys.f90
cat sys.f90 | /usr/bin/cpp -traditional
-I/share/apps/lam/7.1.2/intel/include -P -DDPREC -DLinux -DREGNML
-DMPI -DNO_MPI_BUFFER_ALIASING -DSLOW_ NONBLOCKING_MPI
-DSHORT=INTEGER(2) -DLOGICAL_BYTE=LOGICAL(1) > _sys_.f90
mpif77 -c -auto -tpp6 -mp1 -O2 _sys_.f90
../../Compile CC erfcfun.c
 mpicc -c -DLinux -DREGNML -DMPI -DNO_MPI_BUFFER_ALIASING
-DSLOW_NONBLOCKING_MPI -DSHORT=INTEGER(2) -DLOGICAL_BYTE=LOGICAL(1)
erfcfun.c
ar r sys.a sys.o erfcfun.o
ar: creating sys.a
../../Compile RANLIB sys.a
ranlib sys.a
rm sys.o erfcfun.o
make[2]: Leaving directory `/share/apps/amber9/src.pmemd/Machines/intel'
SYSLIB=`../sysdir lib` ; ../Compile LOAD -o pmemd \
                gbl_datatypes.o file_io_dat.o parallel_dat.o
mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o gbl_dat.o
ew_dat.o ew_direct_c it_dat.o ew_direct_dat.o ew_dipole_dat.o
ew_direct_cit.o ew_recip_cit.o ew_fft_cit.o ew_force_cit.o ew_fft.o
ew_bspline.o ew_box.o force_cit.o runmd_c it.o runmd_cit7.o
shake_cit.o runmin_cit.o axis_optimize_cit.o ew_lib.o pmemd_lib.o
runfiles.o file_io.o parallel.o ew_direct.o ew_recip.o ew_force.o
ew_dipole.o ew_recip_dipole.o ew_recip_reg.o shake.o pmemd_clib.o
pmemd.o random.o runmin.o force.o runmd.o degcnt.o nmr_calls.o nmr_lib.o
get_cmdline .o master_setup.o alltasks_setup.o ew_setup.o
nextprmtop_section.o help.o $SYSLIB;
mpif77 -static -o pmemd gbl_datatypes.o file_io_dat.o parallel_dat.o
mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o inpcrd_dat.o gbl_dat.o
ew_dat.o ew_ direct_cit_dat.o ew_direct_dat.o ew_dipole_dat.o
ew_direct_cit.o ew_recip_cit.o ew_fft_cit.o ew_force_cit.o ew_fft.o
ew_bspline.o ew_box.o force_cit.o runmd_cit.o runmd_cit7.o
shake_cit.o runmin_cit.o axis_optimize_cit.o ew_lib.o pmemd_lib.o
runfiles.o file_io.o parallel.o ew_direct.o ew_recip.o ew_ force.o
ew_dipole.o ew_recip_dipole.o ew_recip_reg.o shake.o pmemd_clib.o
pmemd.o random.o runmin.o force.o runmd.o degcnt.o nmr_calls.o nmr_lib.o
get _cmdline.o master_setup.o alltasks_setup.o ew_setup.o
nextprmtop_section.o help.o
/share/apps/amber9/src.pmemd/Machines/intel/sys.a -L/share/apps/lam/
7.1.2/intel/lib -llamf77mpi -lmpi -llam
ld: cannot find -lmpga
mpif77: No such file or directory
make[1]: *** [pmemd] Error 1
make[1]: Leaving directory `/share/apps/amber9/src.pmemd/pmemd'
make: *** [install] Error 2
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