AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Sat May 31 2008 - 13:31:04 CDT

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 |
>
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>
>
>
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