AMBER Archive (2008)

Subject: Re: AMBER: problem to compile PMEMD?

From: fatima.chami_at_durham.ac.uk
Date: Tue Jan 29 2008 - 18:10:48 CST

Sander.MPI runs smoothly but for some reasons PMEMD DOESNT EVEN COMPILE
CORRECTLY !
I dont know why it did not compile at least the uniprocessor pmemd.
I didnt edit the config.h file which looks like:
===================================================================
 ./configure linux64_opteron ifort mpich
Intel ifort compiler found; version information:
Version 9.0
Use Intel MKL? (better performance) (answer yes or no):

./configure: line 356: [: too many arguments
./configure: line 367: [: =: unary operator expected
./configure: line 376: [: =: unary operator expected
File config_data/fft.pubfft being used...
File config_data/linux64_opteron.ifort being used...
File config_data/interconnect.mpich being used...
configure assumes mpich files are in /usr/local/Cluster-
Apps/mpich/mx/intel/64/1.2.6..0.94/.
PMEMD Configurate successfully completed.
====================================================================
more config.h :
---------------------------------------------------------------------------
MATH_DEFINES =
MATH_LIBS =
IFORT_RPATH = /usr/local/lib:/usr/X11R6/lib:/usr/local/Cluster-
Apps/sge/lib/lx26-amd64:/usr/local/Cluster-Apps/intel/cce/9.1
.046/lib:/usr/local/Cluster-Apps/intel/fce/9.0//lib:/usr/local/Cluster-
Apps/intel/idbe/9.0//lib:/usr/local/Cluster-Apps/mx/m
x-1.1.1/lib64:/usr/local/Cluster-Apps/mpich/mx/intel/64/1.2.6..0.94//lib/shared
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_HOME = /usr/local/Cluster-Apps/mpich/mx/intel/64/1.2.6..0.94/
MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib
MPI_LIBS = -L$(MPI_LIBDIR) -lmpich
DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_NOVEC
CPP = /lib/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = ifort
MODULE_SUFFIX = mod
F90FLAGS = -c -auto
F90_OPT_DBG = -g -traceback
F90_OPT_LO = -tpp7 -O0
F90_OPT_MED = -tpp7 -O2
F90_OPT_HI = -tpp7 -xW -ip -O3
F90_OPT_DFLT = $(F90_OPT_HI)

CC = gcc
CFLAGS =

LOAD = ifort
LOADFLAGS =
LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
hamilton [x86_64.linux] 173% vim config.h
MATH_DEFINES =
MATH_LIBS =
IFORT_RPATH = /usr/local/lib:/usr/X11R6/lib:/usr/local/Cluster-
Apps/sge/lib/lx26-amd64:/usr/local/Cluster-
Apps/intel/cce/9.1.046/lib:/usr/local/Cluster-
Apps/intel/fce/9.0//lib:/usr/local/Cluster-
Apps/intel/idbe/9.0//lib:/usr/local/Cluster-Apps/mx/mx-
1.1.1/lib64:/usr/local/Cluster-Apps/mpich/mx/intel/64/1.2.6..0.94//lib/shared
FFT_DEFINES = -DPUBFFT
FFT_INCLUDE =
FFT_LIBS =
NETCDF_HOME =
NETCDF_DEFINES =
NETCDF_MOD =
NETCDF_LIBS =
MPI_HOME = /usr/local/Cluster-Apps/mpich/mx/intel/64/1.2.6..0.94/
MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
MPI_INCLUDE = -I$(MPI_HOME)/include
MPI_LIBDIR = $(MPI_HOME)/lib
MPI_LIBS = -L$(MPI_LIBDIR) -lmpich
DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_NOVEC
CPP = /lib/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = ifort
MODULE_SUFFIX = mod
F90FLAGS = -c -auto
F90_OPT_DBG = -g -traceback
F90_OPT_LO = -tpp7 -O0
F90_OPT_MED = -tpp7 -O2
F90_OPT_HI = -tpp7 -xW -ip -O3
------------------------------------------------------------------------------
Quoting Robert Duke <rduke_at_email.unc.edu>:

>
> Not sure what you have done here. You configure for uniprocessor, and then
> are getting errors over mpi stuff not being defined. Did you hand-edit the
> config.h for pmemd to include -DMPI (not a good idea...)? Something else
> nonstandard? Did you read the README under amber9/src/pmemd? If you send
> your config.h with info about your machine, I'll look at it, but you are
> really not providing much info here, and to do the parallel build, it really
>
> helps to have somebody at your facility that knows how to build/test mpi.
> Now, if you got parallel sander running okay, it should be relatively easy
> to get pmemd running too...
> Regards - Bob Duke
>
> ----- Original Message -----
> From: <fatima.chami_at_durham.ac.uk>
> To: <amber_at_scripps.edu>
> Sent: Tuesday, January 29, 2008 5:45 PM
> Subject: AMBER: problem to compile PMEMD?
>
>
> > Dear Amber's users,
> >
> > I configured PMEMD but failed to install it !!
> > I tried both nopar and mpich and got the same error
> >
> > any help !
> > thanks
> > fatima
> >
> > -------------------------------------------------------------
> >
> > ./configure linux64_opteron ifort nopar
> > Intel ifort compiler found; version information:
> > Version 9.0
> > Use Intel MKL? (better performance) (answer yes or no):
> > no
> > File config_data/fft.pubfft being used...
> > File config_data/linux64_opteron.ifort being used...
> > File config_data/interconnect.nopar being used...
> > PMEMD Configurate successfully completed.
> > hamilton [x86_64.linux] 78% make install
> > .....
> > pmemd.f90:(.text+0x58): undefined reference to `mpi_init_'
> > pmemd.f90:(.text+0x6e): undefined reference to `mpi_comm_rank_'
> > pmemd.f90:(.text+0x84): undefined reference to `mpi_comm_size_'
> > pmemd.f90:(.text+0x9a): undefined reference to `mpi_comm_group_'
> > pmemd.f90:(.text+0x6ca): undefined reference to `mpi_bcast_'
> > nmr_calls.o: In function `nmr_calls_mod_mp_bcast_nmr_dat_':
> > nmr_calls.f90:(.text+0x37f): undefined reference to `mpi_bcast_'
> > nmr_calls.f90:(.text+0x3a6): undefined reference to `mpi_bcast_'
> > nmr_calls.f90:(.text+0x5f8): undefined reference to `mpi_bcast_'
> > nmr_calls.f90:(.text+0x621): undefined reference to `mpi_bcast_'
> > ene_frc_splines.o:ene_frc_splines.f90:(.text+0x1e0): more undefined
> > references
> > to `mpi_bcast_' follow
> > make[1]: *** [pmemd] Error 1
> > make[1]: Leaving directory
> > `/data/hamilton/dch1fc/amber/amber9/src/pmemd/src'
> > make: *** [install] Error 2
> > -----------------------------------------------------------------------
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>
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