Re: AMBER: PMEMD compilation error

From: Robert Duke <>
Date: Mon, 8 May 2006 16:18:05 -0400

Joseph -
The nmropt=1/ntr=1 problem has not been fixed because there are generally
workarounds, and because it has not really been "in my face". Tell me
exactly what you are trying to do (better yet, just send me a copy of your
mdin file), and I'll attempt to tell you how to get it to run. Note that
with nmropt and restraints selected, pmemd will probably still be faster
than sander, but not by as large a margin, and high end scaling won't be as
impressive. This is true due to additional information exchange required by
these options. But you are trying a simple mpich2 setup, so that probably
does not matter much. Okay, point 2. If your mpich2 is not more-or-less
standard, different libraries may be required (basically if you selected
different configure options in building mpich2, it can cause trouble; also,
different mpich2 versions may not require the same libraries - a pain). Go
to your mpich2 bin directory (presumably /opt/mpich2_icc/bin) and enter
"./mpif77 -link_info". Look at the list of libraries given. If this list
is different han the stuff listed after "MPI_LIBS =" in your config.h file,
modify this line accordingly. If this does not work, then something is
broken about the libraries available on your system vs. the libraries that
mpich2 expects to find (this does not seem likely).
Regards - Bob Duke

----- Original Message -----
From: "Joseph Fernandez" <>
To: <>
Sent: Monday, May 08, 2006 3:37 PM
Subject: AMBER: PMEMD compilation error

>I have not been able to successfully use PMEMD in
> amber8 with the options ntr=1 and nmropt=1 (when
> ntr=0, the simulation runs fine). So I am attempting
> to compile PMEMD from AMBER9 and hoping that this
> issue has been resolved. I have successfully compiled
> AMBER 9 in parallel, but I get an error when I attempt
> to compile pmemd (see below). The configure option
> thatI use is the following:
> ./configure linux_p4 ifort mpich2
> I would be grateful for any assistance on this matter.
> JF
> erfcfun.fpp erfcfun.f90
> ifort -c -auto -tpp7 -xN -ip -O3 erfcfun.f90
> ifort -o pmemd gbl_constants.o gbl_datatypes.o
> state_info.o file_io_dat.o parallel_dat.o
> mdin_ctrl_dat.o mdin_ewald_dat.o prmtop_dat.o
> inpcrd_dat.o dynamics_dat.o img.o parallel.o
> pme_direct.o pme_recip.o pme_fft.o fft1d.o bspline.o
> pme_force.o pbc.o nb_pairlist.o cit.o dynamics.o
> bonds.o angles.o dihedrals.o runmd.o loadbal.o shake.o
> runmin.o constraints.o axis_optimize.o gb_ene.o
> veclib.o gb_force.o timers.o pmemd_lib.o runfiles.o
> file_io.o bintraj.o pmemd_clib.o pmemd.o random.o
> degcnt.o erfcfun.o nmr_calls.o nmr_lib.o get_cmdline.o
> master_setup.o alltasks_setup.o pme_setup.o
> ene_frc_splines.o nextprmtop_section.o
> -L/opt/mpich2_icc/lib -lmpich -lrt -luuid -lpthread
> -limf -lsvml -Wl,-rpath=/opt/intel/lib
> ld: cannot find -luuid
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory `/opt/amber9/src/pmemd/src'
> make: *** [install] Error 2
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Received on Tue May 09 2006 - 17:06:51 PDT
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