AMBER Archive (2007)

Subject: Re: AMBER: PMEMD compilation problems !!

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Dec 06 2007 - 09:07:21 CST

Oh, and when sander does compile, and pmemd does not due to a missing
library (the case here), it is often worthwhile to just look at the library
lists in the sander.MPI config.h file for differences in what is specified
for the compiler and mpi, given that you do have sander.MPI building. The
sander build process actually does invoke 'mpif77 -link_info' or other
appropriate commands to extract the library lists - a good idea, but I just
have not taken pmemd config down that road (my primary focus in config is
not to make it dead easy but to make it likely that the best performance
options are chosen - it's all a matter of time and primary focus).
Regards - Bob
----- Original Message -----
From: "Sampath Koppole" <sampathkoppole_at_yahoo.com>
To: <amber_at_scripps.edu>
Sent: Thursday, December 06, 2007 9:42 AM
Subject: AMBER: PMEMD compilation problems !!

> Hello there,
> I am trying to install PMEMD but the installation
> fails with the follwing message:
>
> -------------------------------------------------------------------------------------------------
> camm25> make install
> cd src && make install
> make[1]: Entering directory
> `/netfs/people/camm/kopposa1/amber9/src/pmemd/src'
> cpp -traditional -P
> -I/usr/people/camm/kopposa1/mpich2-1.0.6/include
> -DPUBFFT -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS
> -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL
> -DFFTLOADBAL_2PROC gbl_constants.fpp gbl_constants.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/usr/prog/intel/mkl/100011/lib/em64t -lmkl_em64t
> -lpthread -L/usr/people/camm/kopposa1/mpich2-1.0.6/lib
> -lmpich -lrt -luuid -lpthread -limf -lsvml
> -Wl,-rpath=:/usr/people/camm/kopposa1/gcc/lib64:/usr/prog/msi/LicensePack/linux/lib:/usr/prog/msi/FELIX2004/Linux_2_Intel_32/lib:/usr/prog/msi/2000.3L/Linux_2_Intel_32/biosymso:/usr/prog/msi/CAT470/irix6m3/biosymso:/usr/prog/mdl/isis213/lib:/usr/prog/mdl/ih33/bin:/usr/prog/oracle/Linux/9.2.0/lib:/usr/prog/sge/60u3/lib/lx24-amd64:/usr/scnpr/intel/mkl/90/lib/32:/usr/scnpr/intel/mpi/30/lib:/usr/scnpr/intel/fc/91045/lib
> IPO link: can not find -luuid
> ifort: error: problem during multi-file optimization
> compilation (code 1)
> make[1]: *** [pmemd] Error 1
> make[1]: Leaving directory
> `/netfs/people/camm/kopposa1/amber9/src/pmemd/src'
> make: *** [install] Error 2
> -----------------------------------------------------------
>
> For your information, I have also attached the
> config.h file that was created with "./configure
> linux_em64t ifort mpich2"
>
> ---------------------------------------------------------------------
> MATH_DEFINES =
> MATH_LIBS =
> IFORT_RPATH =
> :/usr/people/camm/kopposa1/gcc/lib64:/usr/prog/msi/LicensePack/linux/lib:/usr/prog/msi/FELIX2004/Linux_2_Intel_32/lib:/usr/prog/msi/2000.3L/Linux_2_Intel_32/biosymso:/usr/prog/msi/CAT470/irix6m3/biosymso:/usr/prog/mdl/isis213/lib:/usr/prog/mdl/ih33/bin:/usr/prog/oracle/Linux/9.2.0/lib:/usr/prog/sge/60u3/lib/lx24-amd64:/usr/prog/intel/fce/101008/lib/:/usr/prog/intel/mkl/100011/lib/64:/usr/prog/intel/mkl/100011/lib/em64t
> MATH_DEFINES = -DMKL
> MATH_LIBS = -L/usr/prog/intel/mkl/100011/lib/em64t
> -lmkl_em64t -lpthread
> FFT_DEFINES = -DPUBFFT
> FFT_INCLUDE =
> FFT_LIBS =
> NETCDF_HOME =
> NETCDF_DEFINES =
> NETCDF_MOD =
> NETCDF_LIBS =
> MPI_HOME = /usr/people/camm/kopposa1/mpich2-1.0.6
> MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
> MPI_INCLUDE = -I$(MPI_HOME)/include
> MPI_LIBDIR = $(MPI_HOME)/lib
> MPI_LIBS = -L$(MPI_LIBDIR) -lmpich -lrt -luuid
> -lpthread
> DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS
> -DDIRFRC_NOVEC
> CPP = 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)
>
> ------------------------------------------------------------------
> FYI:
> 1) I have MPICH2 installation compiled with the same
> ifort compiler that I m using to compile pmemd
>
> 2) Same Ifort compiler was used to compile parallel
> Sander (Sander.MPI) which went quite smoothly without
> any problems.
>
> Thanks a lot for your help,
> Cheers,
> Sampath
>
>
>
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