Thanks for reply
which ifort gave following output:
/intel/Compiler/11.1/072/bin/intel64/ifort
which icc gave following output:
/usr/bin/which: no icc in
(/home/sangita/intel/Compiler/11.1/072/bin/intel64:/usr/kerberos/bin:/usr/local/bin:/usr/bin:/bin
:/usr/X11R6/bin:/home/sangita/bin:/home/sangita/mpich2-install/bin:/home/sangita/amber11/bin
:/home/sangita:/usr/local/bin/vmd:/home/sangita/intel/Compiler/11.1/072/bin/intel64/ifortvars_intel64.sh
:/usr/X11R6/lib/libXt.so.6)
That means icc is not insatalled in my system.
Can I install without icc because I have only ifort or I have to install icc
first then start compilation?
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
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Received on Thu Sep 23 2010 - 21:30:05 PDT
