AMBER Archive (2006)

Subject: Re: AMBER: Can't compile PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Dec 14 2006 - 16:12:12 CST

Michael -
I just looked quickly, but this looks like really old stuff, pmemd 3.0 or
thereabouts. The fortran compiler directives would have changed in the
interim from what was in the machine files, undoubtedly. Also, you are
using mpif77-script based stuff, which we never do. You need to get the
stuff building with the recommended scripts in uniprocessor mode, and then
move on to using mpi. For mpi, you still use our scripts, perhaps updated
if the compiler changed, and perhaps using a mpif77 -link_info command to
get the link libraries you need for your mpi implementation. It is critical
that the mpi you use be built with the same fortran compiler as was used to
build pmemd, so if your system shipped with lam mpi already installed, that
version typically won't work as it is typically built for linkage with
g77-built executables. I don't support any of the open source fortran
solutions (because they were still slow and buggy as of the last amber
release), and I require fortran 90. Anyway, your message below is a link
problem, not a compile problem, and I don't know where the -lmpga reference
is coming from (I have seen this used with mpich - I think it may be a math
lib but I am not sure - I don't reference it myself under pmemd 3 or 8, and
the only place I see it sucked in is for infiniband in pmemd 9.
Regards - Bob

----- Original Message -----
From: "Michael John Hanby" <mhanby_at_uab.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, December 14, 2006 4:47 PM
Subject: AMBER: Can't compile PMEMD

> 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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