AMBER Archive (2006)

Subject: Re: AMBER: Can't compile PMEMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Dec 14 2006 - 17:42:02 CST

Hi Michael,
All I can say is, "Oh, for goodness sake..., sorry". PMEMD is available as
part of the release in both amber 8 and amber 9; I thought that was pretty
clear from the amber.scripps.edu website. Look at the amber 8 and 9 manuals
under the section entitled "pmemd". Then go look at the README under
amber9/src/pmemd. Additional info scattered around the website. The
configure process remains separate so I get more control over optimizations
and can handle more parallel machines. Don't know exactly what you are
supporting, but there are really big jumps in performance since pmemd 3.1.
That stuff is 4 yrs old and still "out there" to support the amber 7
licensees. Pick up the new stuff; enjoy the speed! (I've been working hard
not only on speed but functionality - code includes generalized Born among
other things now).
Good luck; let us know if you have problems installing 9 - be prepared to
rebuild mpich (I would use mpich over lammpi myself but some folks like
lammpi). I would recommend intel fortran strongly for intel-based systems,
pathscale for opterons.
Best Regards - Bob

----- Original Message -----
From: "Michael John Hanby" <mhanby_at_uab.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, December 14, 2006 6:13 PM
Subject: RE: AMBER: Can't compile PMEMD

> Howdy Robert, you are correct, I'm using pmemd 3.1. I wasn't aware of a
> newer version, is pmemd maintained on a different site than this one
> now?
> http://amber.scripps.edu/pmemd-get.html
>
> I'm the sys admin in charge of compiling and installing Amber9 with
> PMEMD and wasn't given any restrictions on which version of PMEMD I
> compile, so if the newer version is available, I'd much rather install
> it.
>
> As for compilers go, I'm using the Intel compilers v9.1 (ifort, icc,
> icpc) and have compiled Amber9 and LAM MPI using these compilers, along
> with PMEMD (hopefully).
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Robert Duke
> Sent: Thursday, December 14, 2006 4:12 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Can't compile PMEMD
>
> 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
>>
> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu