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
Received on Tue Jun 22 2010 - 10:00:05 PDT
