Hello,
I didn't mean to reinstall the entire system. I meant to remove the amber11
directory and untar it again. Did you remember to source the ifortvars and
iccvars? At the moment, icc is not working, which could be due to libraries
that can't be found.
All the best,
Jason
On Tue, Jun 22, 2010 at 9:05 PM, Yubo Fan <yubofan.mail.chem.tamu.edu>wrote:
> Jason,
>
> Sorry to bother you again. I reinstall the system and installed Intel
> Compilers at /opt/intel. But when I compile openmpi with Intel
> Compilers, it failed with the following message. Any advice?
>
> [root.localhost openmpi-1.4.2]# ./configure
> --prefix=/opt/openmpi-1.4.2 F90=ifort F77=ifort CC=icc CXX=icpc
> checking for a BSD-compatible install... /usr/bin/install -c
> checking whether build environment is sane... yes
> checking for a thread-safe mkdir -p... /bin/mkdir -p
> checking for gawk... gawk
> checking whether make sets $(MAKE)... yes
> checking how to create a ustar tar archive... gnutar
>
>
> ============================================================================
> == Configuring Open MPI
>
> ============================================================================
>
> *** Checking versions
> checking Open MPI version... 1.4.2
> checking Open MPI release date... May 04, 2010
> checking Open MPI Subversion repository version... r23093
> checking Open Run-Time Environment version... 1.4.2
> checking Open Run-Time Environment release date... May 04, 2010
> checking Open Run-Time Environment Subversion repository version...
> r23093
> checking Open Portable Access Layer version... 1.4.2
> checking Open Portable Access Layer release date... May 04, 2010
> checking Open Portable Access Layer Subversion repository version...
> r23093
>
> *** Initialization, setup
> configure: builddir: /opt/openmpi-1.4.2
> configure: srcdir: /opt/openmpi-1.4.2
> checking build system type... x86_64-unknown-linux-gnu
> checking host system type... x86_64-unknown-linux-gnu
> installing to directory "/opt/openmpi-1.4.2"
>
> *** Configuration options
> checking whether to run code coverage... no
> checking whether to compile with branch probabilities... no
> checking whether to debug memory usage... no
> checking whether to profile memory usage... no
> checking if want developer-level compiler pickyness... no
> checking if want developer-level debugging code... no
> checking if want sparse process groups... no
> checking if want Fortran 77 bindings... yes
> checking if want Fortran 90 bindings... yes
> checking desired Fortran 90 bindings "size"... small
> checking whether to enable PMPI... yes
> checking if want C++ bindings... yes
> checking if want MPI::SEEK_SET support... yes
> checking if want to enable weak symbol support... yes
> checking if want run-time MPI parameter checking... runtime
> checking if want to install OMPI header files... no
> checking if want pretty-print stacktrace... yes
> checking if peruse support is required... no
> checking max supported array dimension in F90 MPI bindings... 4
> checking if pty support should be enabled... yes
> checking if user wants dlopen support... yes
> checking if heterogeneous support should be enabled... no
> checking if want trace file debugging... no
> checking if want full RTE support... yes
> checking if want fault tolerance... Disabled fault tolerance
> checking if want IPv6 support... yes (if underlying system supports
> it)
> checking if want orterun "--prefix" behavior to be enabled by
> default... no
> checking for package/brand string... Open MPI
> root.localhost.localdomain Distribution
> checking for ident string... 1.4.2
> checking whether to add padding to the openib control header... no
> checking whether to use an alternative checksum algo for messages...
> no
>
>
> ============================================================================
> == Compiler and preprocessor tests
>
> ============================================================================
>
> *** C compiler and preprocessor
> checking for style of include used by make... GNU
> checking for gcc... icc
> checking for C compiler default output file name...
> configure: error: in `/opt/openmpi-1.4.2':
> configure: error: C compiler cannot create executables
> See `config.log' for more details.
> [root.localhost openmpi-1.4.2]#
>
>
>
>
> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>
>
> On Tue, 22 Jun 2010 12:58:16 -0400
> Jason Swails <jason.swails.gmail.com> wrote:
> > Do not put commas after the compilers.
> >
> > ./configure --prefix=/opt/openmpi-1.4.1 F90=ifort F77=ifort CC=icc
> >CXX=icpc
> >
> > On Tue, Jun 22, 2010 at 12:13 PM, Yubo Fan
> ><yubofan.mail.chem.tamu.edu>wrote:
> >
> >> Jason,
> >>
> >> I did what you suggested but still get errors. Is there anything
> >>wrong
> >> about my settings for Intel compiler? Or the source code downloaded
> >>from
> >> www.open-mpi.org.
> >>
> >>
> >> environment setting in ~/.bash_profile
> >>
> >>
> ***********************************************************************************************************************
> >> # .bash_profile
> >>
> >> # Get the aliases and functions
> >> if [ -f ~/.bashrc ]; then
> >> . ~/.bashrc
> >> fi
> >>
> >> # User specific environment and startup programs
> >> source /opt/intel/Compiler/11.1/072/bin/intel64/iccvars_intel64.sh
> >> source /opt/intel/Compiler/11.1/072/bin/intel64/ifortvars_intel64.sh
> >> source
> >>/opt/intel/Compiler/11.1/072/mkl/tools/environment/mklvarsem64t.sh
> >>
> >> export AMBERHOME="/opt/amber11"
> >>
> >> export MKL_HOME="/opt/intel/Compiler/11.1/072/mkl"
> >>
> >> unset USERNAME
> >>
> >>
> ***********************************************************************************************************************
> >>
> >>
> ***********************************************************************************************************************
> >> [root.localhost openmpi-1.4.2]# ./configure
> >>--prefix=/opt/openmpi-1.4.2
> >> F90=ifort, F77=ifort, CC=icc, CXX=icpc
> >> checking for a BSD-compatible install... /usr/bin/install -c
> >> checking whether build environment is sane... yes
> >> checking for a thread-safe mkdir -p... /bin/mkdir -p
> >> checking for gawk... gawk
> >> checking whether make sets $(MAKE)... yes
> >> checking how to create a ustar tar archive... gnutar
> >>
> >>
> >>
> ============================================================================
> >> == Configuring Open MPI
> >>
> >>
> ============================================================================
> >>
> >> *** Checking versions
> >> checking Open MPI version... 1.4.2
> >> checking Open MPI release date... May 04, 2010
> >> checking Open MPI Subversion repository version... r23093
> >> checking Open Run-Time Environment version... 1.4.2
> >> checking Open Run-Time Environment release date... May 04, 2010
> >> checking Open Run-Time Environment Subversion repository version...
> >>r23093
> >> checking Open Portable Access Layer version... 1.4.2
> >> checking Open Portable Access Layer release date... May 04, 2010
> >> checking Open Portable Access Layer Subversion repository version...
> >>r23093
> >>
> >> *** Initialization, setup
> >> configure: builddir: /opt/openmpi-1.4.2
> >> configure: srcdir: /opt/openmpi-1.4.2
> >> checking build system type... x86_64-unknown-linux-gnu
> >> checking host system type... x86_64-unknown-linux-gnu
> >> installing to directory "/opt/openmpi-1.4.2"
> >>
> >> *** Configuration options
> >> checking whether to run code coverage... no
> >> checking whether to compile with branch probabilities... no
> >> checking whether to debug memory usage... no
> >> checking whether to profile memory usage... no
> >> checking if want developer-level compiler pickyness... no
> >> checking if want developer-level debugging code... no
> >> checking if want sparse process groups... no
> >> checking if want Fortran 77 bindings... yes
> >> checking if want Fortran 90 bindings... yes
> >> checking desired Fortran 90 bindings "size"... small
> >> checking whether to enable PMPI... yes
> >> checking if want C++ bindings... yes
> >> checking if want MPI::SEEK_SET support... yes
> >> checking if want to enable weak symbol support... yes
> >> checking if want run-time MPI parameter checking... runtime
> >> checking if want to install OMPI header files... no
> >> checking if want pretty-print stacktrace... yes
> >> checking if peruse support is required... no
> >> checking max supported array dimension in F90 MPI bindings... 4
> >> checking if pty support should be enabled... yes
> >> checking if user wants dlopen support... yes
> >> checking if heterogeneous support should be enabled... no
> >> checking if want trace file debugging... no
> >> checking if want full RTE support... yes
> >> checking if want fault tolerance... Disabled fault tolerance
> >> checking if want IPv6 support... yes (if underlying system supports
> >>it)
> >> checking if want orterun "--prefix" behavior to be enabled by
> >>default... no
> >> checking for package/brand string... Open MPI
> >>root.localhost.localdomainDistribution
> >> checking for ident string... 1.4.2
> >> checking whether to add padding to the openib control header... no
> >> checking whether to use an alternative checksum algo for messages...
> >>no
> >>
> >>
> >>
> ============================================================================
> >> == Compiler and preprocessor tests
> >>
> >>
> ============================================================================
> >>
> >> *** C compiler and preprocessor
> >> checking for style of include used by make... GNU
> >> checking for gcc... icc,
> >> checking for C compiler default output file name...
> >> configure: error: in `/opt/openmpi-1.4.2':
> >> configure: error: C compiler cannot create executables
> >> See `config.log' for more details.
> >>
> >>
> ***********************************************************************************************************************
> >>
> >> More helps. Thanks a lot.
> >>
> >> Best,
> >> Yubo
> >>
> >>
> >> On Tue, 22 Jun 2010 11:12:26 -0400
> >>
> >> Jason Swails <jason.swails.gmail.com> wrote:
> >>
> >>> Hello,
> >>>
> >>> Your problem is that you're installing openMPI with the gnu
> >>>compilers, but
> >>> you're telling configure to use the intel compilers for some reason.
> >>>Run
> >>> configure like this instead:
> >>>
> >>> ./configure -mpi gnu
> >>>
> >>> Then make parallel. You have to use the compilers used to build the
> >>>MPI
> >>> you're using to compile Amber in parallel. If you want an MPI to
> >>>build
> >>> with
> >>> the intel compilers, you will have to compile from source, setting
> >>> F90=ifort, F77=ifort, CC=icc, and CXX=icpc.
> >>>
> >>> All the best,
> >>> Jason
> >>>
> >>> On Tue, Jun 22, 2010 at 10:56 AM, Yubo Fan
> >>><yubofan.mail.chem.tamu.edu
> >>> >wrote:
> >>>
> >>> Jason,
> >>>>
> >>>> I reinstalled openmpi and it is in /usr/lib/openmpi/1.4-gcc/. I ran
> >>>> ./configure -mpi intel in /opt/amber11/AmberTools/src and the error
> >>>> message
> >>>> came out as:
> >>>> Configuring Parallel NetCDF; (may be time-consuming)
> >>>>
> >>>> Error: parallel NetCDF configure returned 77
> >>>> Parallel NetCDF configure failed! Check the pnetcdf/config.log
> >>>>file.
> >>>> Continuing but parallel NetCDF will be skipped.
> >>>>
> >>>> Configuring NetCDF; (may be time-consuming)
> >>>>
> >>>> NetCDF configure succeeded.
> >>>>
> >>>> Configuring fftw-2.1.5; (may be time-consuming)
> >>>>
> >>>> Error: fftw configure returned 1
> >>>> fftw configure failed! Check the fftw2_config.log file.
> >>>>
> >>>> The two log files are attached.
> >>>>
> >>>> I used "yum install openmpi*" to install openmpi. Do I have install
> >>>> openmpi
> >>>> individually?
> >>>>
> >>>> Thanks,
> >>>> Yubo
> >>>>
> >>>>
> >>>> mpif90 -show
> >>>>
> >>>>>
> >>>>> gfortran -I/usr/lib/openmpi/1.4-gcc/include -m32 -pthread
> >>>> -I/usr/lib/openmpi/1.4-gcc/lib -L/usr/lib/openmpi/1.4-gcc/lib
> >>>>-lmpi_f90
> >>>> -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-dynamic
> >>>>-lnsl
> >>>> -lutil
> >>>> -lm -ldl
> >>>>
> >>>> mpicc -show
> >>>>
> >>>>>
> >>>>> gcc -I/usr/lib/openmpi/1.4-gcc/include -m32 -pthread
> >>>> -L/usr/lib/openmpi/1.4-gcc/lib -lmpi -lopen-rte -lopen-pal -ldl
> >>>> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> >>>>
> >>>> On Mon, 21 Jun 2010 16:29:43 -0400
> >>>> Jason Swails <jason.swails.gmail.com> wrote:
> >>>>
> >>>> Hello,
> >>>>>
> >>>>> See my comments below.
> >>>>>
> >>>>> On Mon, Jun 21, 2010 at 4:25 PM, Yubo Fan
> >>>>><yubofan.mail.chem.tamu.edu
> >>>>> >wrote:
> >>>>>
> >>>>> Dr. Case,
> >>>>>
> >>>>>>
> >>>>>> I got a problem to compile parallel version of Amber on my local
> >>>>>> machine. The commands and error message are shown below:
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> =================================================================================
> >>>>>> [root.localhost src]# ./configure -mpi intel
> >>>>>> Your AMBERHOME environment variable should be set to /opt/amber11
> >>>>>>
> >>>>>> Using Intel MKL libraries in
> >>>>>> /opt/intel/Compiler/11.1/072/mkl/lib/em64t
> >>>>>> MKL Version 10 or 11 assumed.
> >>>>>>
> >>>>>> Testing the icc compiler:
> >>>>>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> >>>>>> OK
> >>>>>>
> >>>>>> Testing the ifort compiler:
> >>>>>> ifort -O0 -o testp testp.f
> >>>>>> OK
> >>>>>>
> >>>>>> Testing mixed C/Fortran compilation:
> >>>>>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> >>>>>> testp.c
> >>>>>> ifort -O0 -c -o testp.f.o testp.f
> >>>>>> icc -o testp testp.c.o testp.f.o
> >>>>>> -L/opt/intel/Compiler/11.1/072/lib/intel64/ -lifport -lifcore -lsvml
> >>>>>> /opt/intel/Compiler/11.1/072/lib/intel64/libimf.so: warning:
> >>>>>>warning:
> >>>>>> feupdateenv is not implemented and will always fail
> >>>>>> OK
> >>>>>>
> >>>>>> Testing pointer size:
> >>>>>> icc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
> >>>>>> test_pointer_size test_pointer_size.c
> >>>>>> Detected 64 bit operating system.
> >>>>>>
> >>>>>> Testing flex:
> >>>>>> OK
> >>>>>>
> >>>>>> Configuring Parallel NetCDF; (may be time-consuming)
> >>>>>>
> >>>>>> Error: parallel NetCDF configure returned 77
> >>>>>> Parallel NetCDF configure failed! Check the pnetcdf/config.log
> >>>>>> file.
> >>>>>>
> >>>>>>
> >>>>>> What does pnetcdf/config.log say?
> >>>>>
> >>>>>
> >>>>> Continuing but parallel NetCDF will be skipped.
> >>>>>
> >>>>>>
> >>>>>> Configuring NetCDF; (may be time-consuming)
> >>>>>>
> >>>>>> NetCDF configure succeeded.
> >>>>>>
> >>>>>> Configuring fftw-2.1.5; (may be time-consuming)
> >>>>>>
> >>>>>> Error: fftw configure returned 1
> >>>>>> fftw configure failed! Check the fftw2_config.log file.
> >>>>>>
> >>>>>>
> >>>>>> What does this file say?
> >>>>>
> >>>>> It may be that you don't have a working MPI, or you're using a
> >>>>>mis-match
> >>>>> of
> >>>>> MPIs. This is especially true for personal systems, since users may
> >>>>>not
> >>>>> have properly built their MPIs. What does "mpif90 -show" and "mpicc
> >>>>> -show"
> >>>>> return on your system?
> >>>>>
> >>>>> Good luck!
> >>>>> Jason
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>>
> >>>>>>
> =================================================================================
> >>>>>>
> >>>>>> Any advice?
> >>>>>>
> >>>>>> Regards,
> >>>>>> Yubo
> >>>>>>
> >>>>>> On Mon, 14 Jun 2010 12:34:13 -0400
> >>>>>> case <case.biomaps.rutgers.edu> wrote:
> >>>>>> > On Mon, Jun 14, 2010, Yubo Fan wrote:
> >>>>>> >>
> >>>>>> >> When I ran 'make parallel' at $AMBERHOME/src, the error message
> >>>>>> >> appears as:
> >>>>>> >> Error: config.h is not of type parallel!
> >>>>>> >> Rerun ./configure and specify an MPI implementation.
> >>>>>> >> make: *** [configured_parallel] Error 2
> >>>>>> >>
> >>>>>> >> The making of AmberTools and 'make serial' passed already. I ran
> >>>>>> >> './configure -openmp intel' to create a config.h file at
> >>>>>> >
> >>>>>> > This is wrong, although perhaps an understandable error.
> >>>>>> >
> >>>>>> > 1. AmberTools can be made in parallel in two ways: using openmp
> >>>>>>or
> >>>>>> >MPI.
> >>>>>> >
> >>>>>> > 2. However, Amber itself can only be made in parallel using MPI.
> >>>>>> > So, from
> >>>>>> > the point of view of Amber, using the "-openmp" option is not
> >>>>>>enough
> >>>>>> >to give
> >>>>>> > a "parallel" config.h. You need to run the configure script using
> >>>>>> >the "-mpi"
> >>>>>> > option, not the "openmp" one.
> >>>>>> >
> >>>>>> > ....dac
> >>>>>>
> >>>>>> >
> >>>>>> >
> >>>>>> > _______________________________________________
> >>>>>> > AMBER mailing list
> >>>>>> > AMBER.ambermd.org
> >>>>>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>> Yubo Fan
> >>>>>> Chemistry Department
> >>>>>> Texas A & M University
> >>>>>> Tel: (979) 845-5237
> >>>>>> Email: yubofan.mail.chem.tamu.edu
> >>>>>>
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>
> >>>>> --
> >>>>> Jason M. Swails
> >>>>> Quantum Theory Project,
> >>>>> University of Florida
> >>>>> Ph.D. Graduate Student
> >>>>> 352-392-4032
> >>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>>
> >>>> Yubo Fan
> >>>> Chemistry Department
> >>>> Texas A & M University
> >>>> Tel: (979) 845-5237
> >>>> Email: yubofan.mail.chem.tamu.edu
> >>>>
> >>>>
> >>>
> >>>
> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Graduate Student
> >>> 352-392-4032
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >> Yubo Fan
> >> Chemistry Department
> >> Texas A & M University
> >> Tel: (979) 845-5237
> >> Email: yubofan.mail.chem.tamu.edu
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> Yubo Fan
> Computational Chemistry and Drug Design Lab
> Bioengineering and Bioinformatics Program
> The Methodist Hospital Research Institute (TMHRI)
> 6565 Fannin St B5-022
> Houston, TX 77030
> Email: yfan.tmhs.org
> Phone: (713) 441-8681
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 22 2010 - 18:30:05 PDT
