AMBER Archive (2009)

Subject: Re: [AMBER] pmemd ifort problem

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Oct 23 2009 - 10:33:27 CDT

There can be problems with getting the mpi libraries and the libraries they
depend on right. Is this perhaps actually a mvapich installation
(infiniband), or is it really mpich/mpich2 running on shared memory and/or
ethernet?. At any rate, the README with pmemd discusses how to get around
this grief. There are a couple of basic approaches:
1) making sure that the correct mpi installation is in your path, do a
"mpif77 -link_info" and see what libraries the mpif77 command says you need
to link. Then replace the MPI_LIBS entry with this info; this only gets
sort of complicated if the information is in different directories (this
approach is discussed in the README).
2) I am leaning toward suggesting this approach more and more - simply hack
the pmemd config.h, replacing "F90 = ifort" with "F90 = mpif77" and "LOAD =
ifort" with "LOAD = mpif77". This is often an easy fix; in the past I have
not liked doing it because it puts you at the mercy of the mpif77 script
being right, and wierd and obscure things can happen; that said, we get a
lot of that going on with the config script facility as it is currently
written.
Regards - Bob Duke
----- Original Message -----
From: "Sel Ercan" <slmrcn_at_ymail.com>
To: <amber_at_ambermd.org>
Sent: Friday, October 23, 2009 10:57 AM
Subject: [AMBER] pmemd ifort problem

> Hi all.
> I have installed parallel installation of amber9 with success.But I have
> problem with PMEMD installation. Here is configuration options and error.
>>./configure linux_em64t ifort mpich2 pubfft bintraj
> and here is config.h:
> MATH_DEFINES =
> MATH_LIBS =
> IFORT_RPATH =
> /opt/intel/fce/9.0/lib:/opt/intel/fce/9.0/lib:/opt/intel/mkl/8.1.1/lib/em64t:/usr/local/mpich2/lib:/usr/local/vmd/lib:/usr/local/Accelrys/DSVisualizer20/lib
> MATH_DEFINES = -DMKL
> MATH_LIBS = -L/opt/intel/mkl/8.1.1/lib/em64t -lmkl_em64t -lpthread
> FFT_DEFINES = -DPUBFFT
> FFT_INCLUDE =
> FFT_LIBS =
> NETCDF_HOME = /usr/local/amber9/src/netcdf
> NETCDF_DEFINES = -DBINTRAJ
> NETCDF_MOD = netcdf.mod
> NETCDF_LIBS = $(NETCDF_HOME)/lib/libnetcdf.a
> MPI_HOME = /usr/local/mpich2
> MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
> MPI_INCLUDE = -I$(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 = /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)
>
> and this is error:
> ifort -c -auto -tpp7 -xW -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
> /usr/local/amber9/src/netcdf/lib/libnetcdf.a -L/opt/intel/mkl/8.1.1/lib/em64t
> -lmkl_em64t -lpthread -L/usr/local/mpich2/lib -lmpich -lrt -luuid -lpthread
> -limf -lsvml -Wl,-rpath=/opt/intel/fce/9.0/lib:/opt/intel/fce/9.0/lib:/opt/intel/mkl/8.1.1/lib/em64t:/usr/local/mpich2/lib:/usr/local/vmd/lib:/usr/local/Accelrys/DSVisualizer20/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 `/usr/local/amber9/src/pmemd/src'
> make: *** [install] Error 2
>
> best regards
>
>
>
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>
>

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