AMBER Archive (2008)

Subject: RE: AMBER: SANDER and PMEMD with openmpi. Failure 'make test.pmemd'

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat May 31 2008 - 15:57:48 CDT

Hi Francesco,

If you are using an AMD chip then you need to use different vectorization
options. The build I showed was for an Intel EM64T chip. I would suggest
changing the following:

Config.h

Line 27: F90_OPT_LO = -tpp7 -O0
To F90_OPT_LO = -O0

Line 28: F90_OPT_MED = -tpp7 -O2
To F90_OPT_MED = -O2

Line 29: F90_OPT_HI = -tpp7 -xP -ip -O3
To F90_OPT_HI = -axWPT -ip -O3

This set of options should work on all modern AMD and Intel x86_64 chips
using ifort > v10.0.1

All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Francesco Pietra
> Sent: Saturday, May 31, 2008 11:31 AM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: SANDER and PMEMD with openmpi. Failure 'make
> test.pmemd'
>
> Hi:
>
> With Amber10
>
> >cd $AMBERHOME/test/
> >make clean (which removed previous TEST_FAILURES.diff)
> >make test.PMEMD
> make: *** No rule to make target 'test.PMEMD'.stop
> I corrected PMEMD to pmemd, getting error about the cpu type
>
> What I did in detail:
> Renamed previous amber10 installation. Then, I begun from scratch as on
> previous compilation I applied bugfix.all to only amber10. Now also to
> amber_tools.
>
> >i-fort -V
> 10.1
>
> >icc -V
> 10.1
>
> >gcc -v
> 4.2.3 (Debian lenny 4.2.3-5)
>
> >uname -a
> 2.6.24-1-amd64 #1 SMP May 10 09:28:10 UTC 2008
>
> >cat /proc/cpuinfo
> ...
> cpu family: 15
> model: 33
> model name: Dual Core Opteron (tm) Processor 875 2000.006MHz cache 1024MB
>
> >echo $MKL_HOME
> /opt/intel/mkl/10.0.1.14/
>
> In my .bashrc:
> declare -x MPI_HOME='/usr/local'
> MPICH_HOME=/usr/local (this serves for DOCK6.2 nicely)
>
> >which mpirun
> /usr/local/bin/mpirun
>
> >mpif90 -show
> /opt/intel/fce/10.1.015/bin/ifort -I/usr/local/include -pthread
> -l/usr/local/lib -L/usr/local/lib -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -
> lopen-pal -ldl -Wl,--export-dynamic -lnsl -lutil
>
>
> --Installed amber_tools and recompiled after bugfix.all
>
> --untarred amber10 and applied its bugfix.all, compiled serial
> (.configure_amber ifort) all tests - including QMMM - PASSED)
>
> >cd src
> >make clean
> >./configure_amber -openmpi -nobintraj ifort
> >make parallel
>
> --all test.parallel.MM PASSED (-np 4)
>
> --test.parallel.QMM crashed at ./Run.1NLN.dspevd as expected for my system
> (see previous thread)
>
> >cd src/PMEMD
> >./configure linux_em64t ifort lam pubfft nobintraj
>
> ---Edited config.h as indicated below by Ross.
>
> >make
> (no errors reported)
>
> > make install
> installation of pmemd complete
>
> >export DO_PARALLEL='mpirun -np 2'
> >set | grep DO_PARALLEL
> (OK)
>
> >make test.parallel (OK, of course, it has already passed with -np 4)
>
> >make test.parallel.QMMM
> same crash as with -np 4
>
> >make clean
> (find . -name '*.dif' -o name 'profile_mpi' |\
> while read dif ;\
> do \
> rm -f $ dif ; \
> done ;\
> rm -f TEST_FAILURES.diff
>
> > make test. PMEMD
> make: *** No rule to make target 'test.PMEMD'. Stop
>
> Examining the Makefile, I corrected Ross' PMEMD with pmemd
>
> >make clean
> >make install 2>&1 | tee .....
> getting the error file:
>
> export TESTsander='../../exe/pmemd'; cd 4096wat && ./Run.pure_wat
>
> Fatal Error: This program was not built to run on the processor in your
> system.
> The allowed processors are: Intel(R) Pentium(R) 4 and compatible Intel
> processors with Streaming SIMD Extensions 3 (SSE3) instruction support.
>
>
> Fatal Error: This program was not built to run on the processor in your
> system.
> The allowed processors are: Intel(R) Pentium(R) 4 and compatible Intel
> processors with Streaming SIMD Extensions 3 (SSE3) instruction support.
>
> ./Run.pure_wat: Program error
> make: *** [test.pmemd] Error 1
> ______
> At this point I feel I need help. Even if I think about longer, little
> chance. It does not like dual-opteron or I missed an appropriate flag.
>
> Thanks for help
> francesco
>
>
> --- On Fri, 5/30/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
> > From: Ross Walker <ross_at_rosswalker.co.uk>
> > Subject: AMBER: SANDER and PMEMD with openmpi
> > To: amber_at_scripps.edu
> > Date: Friday, May 30, 2008, 3:18 PM
> > Hi All,
> >
> > It seems a number of people are interested in building both
> > sander and pmemd
> > using openmpi and so I thought I would post a description
> > of how I did this
> > on my machine so others can benefit:
> >
> > ----------
> > >ifort -V
> > Intel(R) Fortran Compiler for applications running on
> > Intel(R) 64, Version
> > 10.1 Build 20070913 Package ID: l_fc_p_10.1.008
> > >icc -V
> > Copyright (C) 1985-2007 Intel Corporation. All rights
> > reserved.
> >
> > >gcc -v
> > gcc version 3.4.6 20060404 (Red Hat 3.4.6-9)
> >
> > >cat /etc/redhat-release
> > Red Hat Enterprise Linux AS release 4 (Nahant Update 6)
> >
> > >uname -a
> > Linux ......... 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18
> > 05:00:00 EST 2008
> > x86_64 x86_64 x86_64 GNU/Linux
> >
> > >cat /proc/cpuinfo
> > ...
> > cpu family : 15
> > model : 6
> > model name : Intel(R) Pentium(R) D CPU
> > 3.20GHz
> > ...
> >
> > >echo $MKL_HOME
> > /opt/intel/mkl/10.0.1.014/
> >
> > >wget
> > http://www.open-mpi.org/software/ompi/v1.2/downloads/openmpi-
> 1.2.6.tar.gz
> > >tar xvzf openmpi-1.2.6.tar.gz
> > >cd openmpi-1.2.6
> > >export CC=gcc
> > >export CXX=g++
> > >export F77=ifort
> > >export FC=ifort
> >
> > >./configure
> > --prefix=/usr/local/mpi/openmpi-1.2.6_ifort10.1.008
> > >make
> > >make install
> >
> > >export
> > MPI_HOME=/usr/local/mpi/openmpi-1.2.6_ifort10.1.008
> > >export PATH=$MPI_HOME/bin:$PATH
> > >export LD_LIBRARY_PATH=$MPI_HOME/lib:$LD_LIBRARY_PATH
> >
> > >which mpirun
> > /usr/local/mpi/openmpi-1.2.6_ifort10.1.008/bin/mpirun
> >
> > >mpif90 -show
> > ifort -g -I/usr/local/mpi/mpich2-1.0.3_ifort9.1.039/include
> > -I/usr/local/mpi/mpich2-1.0.3_ifort9.1.039/include
> > -L/usr/local/mpi/mpich2-1.0.3_ifort9.1.039/lib -lmpichf90
> > -lmpichf90 -lmpich
> > -lpthread -lrt
> >
> > >cd ~/
> > >tar xvjf Amber10.tar.bz2
> > >export AMBERHOME=~/amber10/
> >
> > >cd $AMBERHOME/src/
> > >./configure_amber -openmpi -nobintraj ifort
> > >make parallel
> >
> > >cd $AMBERHOME/src/pmemd/
> > > ./configure linux_em64t ifort lam pubfft nobintraj
> >
> > edit config.h
> > Line 17:
> > Change MPI_LIBS = -L$(MPI_LIBDIR) -llamf77mpi -lmpi -llam
> > -ldl -lpthread
> > to MPI_LIBS = -L$(MPI_LIBDIR)
> >
> > Line 23:
> > Change F90 = ifort
> > to F90 = mpif90
> >
> > Line 35:
> > Change LOAD = ifort
> > to LOAD = mpif90
> >
> > >make
> > >make install
> >
> > >export DO_PARALLEL='mpirun -np 2'
> >
> > >cd $AMBERHOME/test/
> > >make test.parallel
> > >make test.parallel.QMMM
> >
> > (Check TEST_FAILURES.diff - all tests passed file did not
> > exist)
> >
> > >make clean
> > >make test.PMEMD
> >
> > (Check TEST_FAILURES.diff - all tests passed file did not
> > exist)
> >
> > --------
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on
> > request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of
> > delivery, may not
> > be read every day, and should not be used for urgent or
> > sensitive issues.
> >
> >
> >
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>
>
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