AMBER Archive (2006)

Subject: Re: AMBER: Parallel error in Amber 8

From: Wei Zhang (zweig_at_scripps.edu)
Date: Mon Feb 06 2006 - 17:06:07 CST

Hello,

The system says it can't find ifort, maybe you should run the script
ifortvars.sh(if you are using bash or sh) or iforvars.csh(if your
are using csh) under you intel fortran compiler's bin directory, which
usually is /opt/intel/fc/x.0/bin,

Good Luck!

Sincerely,

Wei Zhang

On Mon, 2006-02-06 at 17:47 -0500, snoze pa wrote:
> Hi Amber community.
> I am getting following error message when compiling amber with LAM.
> Following is the error message.
>
> make[2]: Leaving directory `/amber8/src/lmod'
> ifort -FR -o sander trace.o lmod.o decomp.o icosasurf.o egb.o
> findmask.o pb_force.o sander.o cshf.o noecalc.o noeread.o caldis.o
> calrate.o dinten.o drates.o indexn.o kmat.o pearsn.o plane.o remarc.o
> nmrcal.o nmrred.o restal.o getnat.o nmrnrg.o modwt.o disnrg.o angnrg.o
> tornrg.o nmrprt.o nmrgrp.o nmrcms.o nmrcmf.o impnum.o nmrsht.o
> at2res.o chklin.o opnmrg.o printe.o runmin.o ndvprt.o force.o rdparm.o
> mdread.o locmem.o runmd.o getcor.o r6ave.o r6drv.o aveint.o degcnt.o
> corf.o threeb.o tripl.o nmrrad.o decnvh.o fastwt.o echoin.o parallel.o
> jnrg.o shake.o ene.o mdwrit.o minrit.o set.o setmm.o dynlib.o mdfil.o
> nmlsrc.o ew_force.o ew_setup.o ew_box.o ew_bspline.o ew_fft.o
> ew_direct.o ew_recip.o pcshift.o align.o rstack.o istack.o rfree.o
> rgroup.o random.o lsqfit.o amopen.o debug.o ew_recip_reg.o
> ew_handle_dips.o ew_dipole_recip.o mexit.o new_time.o extra_pts.o
> thermo_int.o matinv.o assert.o mmtsb.o mmtsb_client.o erfcfun.o
> veclib.o mdm.o pb_init.o constantph.o prn_dipoles.o \
> ../lmod/lmod.a -L/lam/lib -llammpio -llamf77mpi -lmpi -llam -
> laio -laio -lutil -ldl -L/usr/local/inte/mkl/8.0.1//lib/32 -lvml -
> lmkl_lapack64 -lmkl -lguide -lpthread \
> ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a
> make[1]: ifort: Command not found
> make[1]: *** [sander] Error 127
> make[1]: Leaving directory `/amber8/src/sander'
> make: *** [parallel] Error 2
>
> I am also sending my config.h file. Anybody can help me to check this
> file. Here is the file
>
> #==============================================================================
> # AMBER Makefile configuration for compiler/architecture: ifort
> # Generated via command: ./configure -lam ifort
> #
> # Configuration script written mainly by Joe Krahn, Scott Brozell, and
> # Dave Case, with contributions from lots of people.
> #==============================================================================
>
> #------------------------------------------------------------------------------
> # Main AMBER source root directory
> #------------------------------------------------------------------------------
> AMBER_SRC=/amber8/src
>
> #------------------------------------------------------------------------------
> # AMBERBUILDFLAGS provides a hook into the build process for
> installers;
> # for example, to build debug versions of the amber programs
> # make -e AMBERBUILDFLAGS="-DDEBUG -g"
> #------------------------------------------------------------------------------
> AMBERBUILDFLAGS=
>
> #------------------------------------------------------------------------------
> # LOCALFLAGS is intended for program specific modifications to the
> # Fortran build process and may be modified by the program's local
> makefile
> #------------------------------------------------------------------------------
> LOCALFLAGS=
>
> #------------------------------------------------------------------------------
> # Availability and method of delivery of math and optional libraries
> #------------------------------------------------------------------------------
> USE_BLASLIB=$(VENDOR_SUPPLIED)
> USE_LAPACKLIB=$(VENDOR_SUPPLIED)
> USE_LMODLIB=$(LMOD_UNAVAILABLE)
>
> #------------------------------------------------------------------------------
> # C compiler
> #------------------------------------------------------------------------------
> CC= gcc
> CPLUSPLUS=g++
> ALTCC=gcc
> CFLAGS=-O2 $(AMBERBUILDFLAGS)
> ALTCFLAGS= $(AMBERBUILDFLAGS)
> CPPFLAGS= $(AMBERBUILDFLAGS)
>
> #------------------------------------------------------------------------------
> # Fortran preprocessing and compiler.
> # FPPFLAGS holds the main Fortran options, such as whether MPI is
> used.
> #------------------------------------------------------------------------------
> FPPFLAGS= -I/lam/include -P -I$(AMBER_SRC)/include -DMPI -DMKL
> $(AMBERBUILDFLAGS)
> FPP= cpp -traditional $(FPPFLAGS)
> FC= /usr/local/intel/fc/9.0/bin/ifort
> FFLAGS= -w95 -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> FOPTFLAGS= -w95 -mp1 -ip -O3 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> FPP_PREFIX= _
> FREEFORMAT_FLAG= -FR
>
> #------------------------------------------------------------------------------
> # Loader:
> #------------------------------------------------------------------------------
> LOAD= ifort $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> LOADCC= gcc $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> LOADLIB= -L/lam/lib -llammpio -llamf77mpi -lmpi -llam -laio -laio -
> lutil -ldl -L/usr/local/inte/mkl/8.0.1//lib/32 -lvml -lmkl_lapack64 -
> lmkl -lguide -lpthread
> LOADPTRAJ= ifort -nofor_main $(LOCALFLAGS) $(AMBERBUILDFLAGS)
> XHOME= /usr/X11R6
>
> #------------------------------------------------------------------------------
> # Other stuff:
> #------------------------------------------------------------------------------
> .SUFFIXES: .f90
> SYSDIR=lib
> AR=ar rv
> M4=m4
> RANLIB=ranlib
> SFX=
> MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
>
> # default rules for Fortran and C compilation:
>
> .f.o: $<
> $(FPP) $< > $(FPP_PREFIX)$<
> $(FC) -c $(FFLAGS) -o $@ $(FPP_PREFIX)$<
>
> .f90.o: $<
> $(FPP) $< > $(FPP_PREFIX)$<
> $(FC) -c $(FFLAGS) -o $@ $(FPP_PREFIX)$<
>
> .c.o:
> $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $<
>
> ------------------------
> any help, thanks in advance 

-- 
Wei Zhang <zweig_at_scripps.edu>
The Scripps Research Institute

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