Hi Sangita,
The error you got when you tried building in parallel suggests that
your system has the intel compilers. Moreover, the output of your
"mpif90 -show" command clearly shows that the intel compilers are the
ones linked to your mpich2 installation, *not* the gnu compilers. You
need to be consistent about which compilers you are using, so I would
suggest doing a "make clean" everywhere, and then configuring/building
everything from the beginning using the intel compilers. (In addition
these compilers usually generate faster code than the gnu compilers,
so that's another reason to use them.)
Just to be sure we know what you've got, can you also type "which icc"
and "which ifort" (and maybe "icc -v" and "ifort -v" just to be very
thorough)?
Paul
On Sep 23, 2010, at 10:11 AM, Sangita Kachhap wrote:
>
> Thanks for reply
>
> Then should I configure AmberTool-1.4 with intel compiler? Since I
> have configured
> it with gnu compiler.
>
>> Sangita,
>>
>> You need to type "./configure_openmpi intel" -- or whatever compiler
>> you are using (looks like intel though). The OpenMPI configuration
>> script is much like the AMBER configure script...
>>
>> Best,
>>
>> Paul
>>
>>
>> On Sep 23, 2010, at 9:50 AM, Sangita Kachhap wrote:
>>
>>>
>>> Thanks to quick reply
>>> sorry for incomplete mail
>>>
>>> Error which I have got was :
>>>
>>> [sangita.localhost src]$ make parallel > amber-6.log &
>>> [1] 8628
>>> [sangita.localhost src]$ ifort: command line warning #10006:
>>> ignoring unknown
>>> option '-ffree-form'
>>> : error #5149: Illegal character in statement label field [m]
>>>
>>> : error #5149: Illegal character in statement label field [o]
>>>
>>> : error #5149: Illegal character in statement label field [d]
>>>
>>> : error #5149: Illegal character in statement label field [u]
>>>
>>> : error #5149: Illegal character in statement label field [l]
>>>
>>> : error #5118: First statement in file must not be continued
>>>
>>> _constants.f(223): error #5149: Illegal character in statement label
>>> field [i]
>>> integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
>>> palindromic
>>> prime
>>> ^
>>> _constants.f(223): error #5149: Illegal character in statement label
>>> field [n]
>>> integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
>>> palindromic
>>> prime
>>> -^
>>> _constants.f(223): error #5149: Illegal character in statement label
>>> field [t]
>>> integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
>>> palindromic
>>> prime
>>> --^
>>> _constants.f(223): error #5149: Illegal character in statement label
>>> field [e]
>>> integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
>>> palindromic
>>> prime
>>> ---^
>>> _constants.f(223): error #5149: Illegal character in statement label
>>> field [g]
>>> integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
>>> palindromic
>>> prime
>>> ----^
>>> _constants.f(224): error #5149: Illegal character in statement label
>>> field [i]
>>> integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
>>> ^
>>> _constants.f(224): error #5149: Illegal character in statement label
>>> field [n]
>>> integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
>>> -^
>>> _constants.f(224): error #5149: Illegal character in statement label
>>> field [t]
>>> integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
>>> --^
>>> _constants.f(224): error #5149: Illegal character in statement label
>>> field [e]
>>> integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
>>> ---^
>>> _constants.f(224): error #5149: Illegal character in statement label
>>> field [g]
>>> integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
>>> ----^
>>> _constants.f(226): error #5149: Illegal character in statement label
>>> field [e]
>>> end module constants
>>> ^
>>> _constants.f(226): error #5149: Illegal character in statement label
>>> field [n]
>>> end module constants
>>> -^
>>> _constants.f(226): error #5149: Illegal character in statement label
>>> field [d]
>>> end module constants
>>> --^
>>> _constants.f(226): error #5149: Illegal character in statement label
>>> field [m]
>>> end module constants
>>> ----^
>>> _constants.f(223): error #5082: Syntax error, found ',' when
>>> expecting one of: (
>>> % : . = =>
>>> integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
>>> palindromic
>>> prime
>>> -------^
>>> _constants.f(223): error #5082: Syntax error, found '=' when
>>> expecting one of: (
>>> * ) :: , <END-OF-STATEMENT> ; + . - % (/ [ : ] /) . ** / // ...
>>> integer, parameter :: RETIRED_INPUT_OPTION = -10301 ! first 5 digit
>>> palindromic
>>> prime
>>> -------------------------------------------^
>>> _constants.f(227): error #5082: Syntax error, found END-OF-FILE when
>>> expecting
>>> one of: <END-OF-STATEMENT> ; <LABEL> BLOCK BLOCKDATA PROGRAM MODULE
>>> TYPE COMPLEX
>>> BYTE ...
>>>
>>> ^
>>> compilation aborted for _constants.f (code 1)
>>> make[1]: *** [constants.o] Error 1
>>> make: *** [parallel] Error 2
>>>
>>>
>>> mpif90 -show gave following output:
>>>
>>> ifort -I/home/sangita/mpich2-install/include
>>> -I/home/sangita/mpich2-install/include -L/home/sangita/mpich2-
>>> install/lib
>>> -L/home/sangita/mpich2-install/lib -lmpichf90 -lmpichf90 -lmpich -
>>> lopa -lpthread
>>> -lrt
>>>
>>>
>>> When I ran configure_openmpi it telles that compiler is not
>>> supported
>>>
>>> [sangita.localhost src]$ ./configure_openmpi
>>> Setting AMBERHOME to /home/sangita/amber11/AmberTools
>>>
>>> Architecture/compiler is not supported
>>>
>>> Usage: ./configure_openmpi [flags] compiler
>>>
>>> where compiler is one of:
>>>
>>> gnu (=gcc/gfortran), intel (=icc/ifort), pgi (=pgcc/pgf90),
>>> solaris (=cc/f90)
>>>
>>> Option flags:
>>> -static Create statically linked executables (not
>>> recommended for
>>> MacOSX)
>>>
>>> Note: See http://www.open-mpi.org/software/ompi/v1.4/ for
>>> information
>>> on how to obtain openmpi.
>>>
>>>
>>>
>>>> On Thu, Sep 23, 2010, Sangita Kachhap wrote:
>>>>>
>>>>> I have installed amber11 in serial using gnu compiler for
>>>>> AmberTool1.4. But when compiling it in parallel using same and
>>>>> mpicc of
>>>>> Mpich2 which I have installed in my home directory it is giving
>>>>> follwing
>>>>> error:
>>>>>
>>>>> compilation aborted for _constants.f (code 1)
>>>>> make[1]: *** [constants.o] Error 1
>>>>
>>>> We need more information about the error messages: there must have
>>>> been
>>>> something before the snippet you quote above.
>>>>
>>>> I think the constants.f is the first file that is compiled in a
>>>> parallel
>>>> install, so there is probably something wrong with the compiler.
>>>> Note that
>>>> constants.f is a fortran file, so the key quantity is mpif90, not
>>>> mpicc.
>>>> What does "mpif90 -show" report?
>>>>
>>>> The easiest and recommended path for parallel installations is to
>>>> run the
>>>> "configure_openmpi" script in $AMBERHOME/AmberTools/src, and to use
>>>> that
>>>> installation (which will automatically be in your PATH if your PATH
>>>> includes
>>>> $AMBERHOME/bin). We know that this is configured correctly, and
>>>> works for
>>>> all the compilers we support.
>>>>
>>>> The case where this won't work is if you have a specialized
>>>> interconnect (say,
>>>> infiniband) which is not supported by generic openmpi. Even then,
>>>> I would
>>>> recommend using "configure_openmpi" first, so that you will have a
>>>> baseline
>>>> and some experience, before trying to link to an external MPI
>>>> library.
>>>>
>>>> ....hope this helps....dac
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>
>>>
>>> Sangita Kachhap
>>> JRF
>>> BIC,IMTECH
>>> CHANDIGARH
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> Sangita Kachhap
> JRF
> BIC,IMTECH
> CHANDIGARH
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Sep 23 2010 - 11:00:03 PDT
