AMBER Archive (2008)

Subject: Re: AMBER: problem to compile PMEMD?

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Jan 29 2008 - 20:11:57 CST

Oh, oops. The wrong compiler for mpi build is highly unlikely, given that
you have a working sander build. Sorry I forgot that detail... - Bob

----- Original Message -----
From: <fatima.chami_at_durham.ac.uk>
To: <amber_at_scripps.edu>
Sent: Tuesday, January 29, 2008 7:10 PM
Subject: Re: AMBER: problem to compile PMEMD?

> 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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>
>
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