Hello Jason and Paul
As paul advice I have instaled icc now.When I am compiling AmberTool in serial
with intel compiler
it is giving the following error:
Your AMBERHOME environment variable should be set to /home/sangita/amber11
Warning: the X11 libraries are not in the usual location !
To search for them try the command: locate libXt
On new Fedora OS's install the libXt-devel libXext-devel
libX11-devel libICE-devel libSM-devel packages.
On old Fedora OS's install the xorg-x11-devel package.
On RedHat OS's install the XFree86-devel package.
On Ubuntu OS's install the xorg-dev package.
For the moment Amber will be configured not to build XLEaP.
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/home/sangita/intel/Compiler/11.1/072/lib/intel64/ -lifport -lifcore
-lsvml
WARNING: Unable to compile mixed C/Fortran code.
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 NetCDF; (may be time-consuming)
NetCDF configure succeeded.
Configuring fftw-2.1.5; (may be time-consuming)
Altough my both icc and ifort version are same:
l_cproc_p_11.1.072_intel64.tgz
l_cprof_p_11.1.072_intel64.tgz
Both are in same path:
/intel/Compiler/11.1/072/bin/intel64/icc
/intel/Compiler/11.1/072/bin/intel64/ifort
Then agian I am getting problem please suggest me what to do next?
> Hello,
>
> It is possible in theory to compile Amber11 and AmberTools with ifort and
> gcc, but you have to figure out how to properly link gcc-created object
> files with ifort-created object files (I've never tried myself). It's
> easier with all GNU compilers or all intel compilers because that
> compatibility is well-documented. The mix-and-match is a little harder to
> set up, but I'm sure with a little google-magic you can get it figured out.
> Easiest thing to do would just be install icc OR use just the gnu compilers,
> following Paul's advice.
>
> Good luck!
> Jason
>
> On Fri, Sep 24, 2010 at 12:46 AM, Paul S. Nerenberg <psn.berkeley.edu>wrote:
>
>> Ah...I see now why you compiled AmberTools with the gnu compilers. In
>> that case, you've got two options:
>>
>> (1) If you have easy access to the intel compilers, you could install
>> icc. You would still need to re-build the MPICH2 installation,
>> because you need mpicc (and mpif90), but you could also download
>> OpenMPI and go from there (see below for more on that). Then you
>> would build AT and AMBER from scratch using the intel compilers.
>>
>> (2) You probably have the full set of gnu compilers (i.e., gcc, g++,
>> and gfortran) if you were able to compile the serial versions of AT
>> and AMBER. You could download OpenMPI and either build it with the
>> configure_openmpi script (since 1.4.2 is the latest version, you need
>> to edit the configure_openmpi script to look for that version number)
>> or just build it from scratch. Either way make sure that you put the
>> path for the OpenMPI installation after the path to the MPICH2
>> installation so that "which mpicc" and "which mpif90" are both
>> pointing to the OpenMPI installation and *not* MPICH2. Then build
>> parallel AMBER with the gnu compilers.
>>
>> I realize that these are somewhat barebones instructions for how to do
>> things, but I think it's the best I can do from afar. Hopefully it's
>> enough to get you started and/or you can find a (local) friend to help
>> you out...
>>
>> Best,
>>
>> Paul
>>
>>
>> On Sep 23, 2010, at 9:03 PM, Sangita Kachhap wrote:
>>
>> > 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
>> >
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> 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
>
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 24 2010 - 03:00:05 PDT
