Re: [AMBER] parallel compiling failure of Amber 11

From: Yubo Fan <yubofan.mail.chem.tamu.edu>
Date: Tue, 22 Jun 2010 12:49:25 -0500

Jason,

The configure works now as you pointed out. But there is still an
error about a program named _memory_module.f. The error message is
attached. Please take a look. Thanks a lot.

Best,
Yubo


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
Chemistry Department
Texas A & M University
Tel: (979) 845-5237
Email: yubofan.mail.chem.tamu.edu


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Received on Tue Jun 22 2010 - 11:00:03 PDT
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