[mpich-discuss] mpif.h

Gustavo Correa gus at ldeo.columbia.edu
Sun Sep 14 20:58:02 CDT 2014


On Sep 14, 2014, at 9:16 PM, Kenneth Raffenetti wrote:

> Based on the comments in the Makefile, it looks like you need to set USE_MPI and USE_MPIF90 to "on" and set FORT to "gfortran".
> 
> Ken
> 

Agreed.

Also, besides Ken's suggestion, note also these comments in the makefile:

#  This makefile is designed to work only with GNU Make version 3.80 or :::
#  higher. It can be used in any architecture provided that there is a  :::
#  machine/compiler rules file in the  "Compilers"  subdirectory.  You  :::
#  may need to modify the rules file to specify the  correct path  for  :::
#  the NetCDF and ARPACK libraries. The ARPACK library is only used in  :::
#  the Generalized Stability Theory analysis and Laczos algorithm.      :::

You may need to look for a Linux/gfortran directory/file (or similar).
There may be additional items that you may need to edit there.
I would guess one would be the path to your mpif90, 
maybe the INCLUDE macro mentioned in your original email, 
and if you're using input/output files in NetCDF format, the location of your NetCDF library.
 
Anyway, these are mostly guesses, not knowing anything about this model (which seems
to be moslty based on ROMS.)

I hope it helps,
Gus Correa

> On 09/14/2014 02:35 PM, fereshteh komijani wrote:
>> thanks for your reply
>> in attach there is COAWST make file,
>> i become so appreciate if you help me
>> cheers
>> fereshte
>> 
>> On Sun, Sep 14, 2014 at 1:40 AM, Gustavo Correa <gus at ldeo.columbia.edu
>> <mailto:gus at ldeo.columbia.edu>> wrote:
>> 
>>    Hi Fereshteh
>> 
>>    <guess>
>>    The model probably comes with a Makefile,
>>    or a configuration script, where you can  choose
>>    the compiler (which presumably you chose as F77 or FC=mpif90, which
>>    is a good choice,
>>    not gfortran, which is not so good a choice).
>>    It may also have a INCLUDE variable where you can add the
>>    location of your mpif.h file.
>>    Something like this:
>> 
>>    INCLUDE= [whatever is already there]
>>    -I/home/fkomijani/program_install/mpich-3.0.4/include
>> 
>> 
>>    Normally mpif90 is able to locate the mpif.h include file and all
>>    needed mpi libraries as well,
>>    which is a big advantage over the barebones compiler (gfortran), as
>>    Ken and Junchao said.
>>    However, I've seen makefiles and build scripts that go a long way to
>>    strip off or override that capability,
>>    by redefining the compiler to be the one underlying the mpif90
>>    wrapper (i.e go back to
>>    gfortran in your case), which is not a very good idea but happens.
>> 
>>    It is hard to tell exactly what is going on not knowing the
>>    Makefile, configure script,
>>    or the model code.
>>    Unfortunately the COAWST model is not readily available to download
>>    and check, requires the developer permission.
>>    If you post the Makefile or configure script things may become a
>>    little clearer.
>> 
>>    </guess>
>> 
>>    My two cents,
>>    Gus Correa
>> 
>>    On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote:
>> 
>>    >                  After compiling my model (coawst) it gives me following
>>    >         error :
>>    >
>>    >                  mod_parallel.f90:17: Error: Can't open included file
>>    >         'mpif.h'
>>    >
>>    >                  coaws's developer tell me :
>>    >
>>    >                  *check your environment and see if the location of
>>    >         mpif.h is in your
>>    >                  INCLUDE list*.
>>    >
>>    >                  But I don't know what is its mean? Where and how I can
>>    >         do that? Does
>>    >                  environment mean .bashrc?
>> 
>>    On Sep 13, 2014, at 10:23 AM, fereshteh komijani wrote:
>> 
>>     > thanks so much for your attention
>>     > i will check in again
>>     > cheers
>>     > fereshte
>>     >
>>     > On Sat, Sep 13, 2014 at 6:30 PM, Junchao Zhang
>>    <jczhang at mcs.anl.gov <mailto:jczhang at mcs.anl.gov>> wrote:
>>     > As you can see, hello.f90 contains
>>     >   include 'mpif.h'
>>     > and mpif90 found it and correctly compiled the code.
>>     >
>>     > So, mpich installation is correct. You need to double check your
>>    code and compilation commands.
>>     >
>>     > --Junchao Zhang
>>     >
>>     > On Sat, Sep 13, 2014 at 8:41 AM, fereshteh komijani
>>    <fereshtehkomijani at gmail.com <mailto:fereshtehkomijani at gmail.com>>
>>    wrote:
>>     > i have created hello.F90 and after compiling, it gives
>>     >
>>     > fkomijani at fk1:~/program_install/COAWST$ mpif90 -v -o hello hello.F90
>>     > mpif90 for MPICH version 3.0.4
>>     > Driving: gfortran -v -o hello hello.F90
>>    -I/home/fkomijani/program_install/mpich-3.0.4/include
>>    -I/home/fkomijani/program_install/mpich-3.0.4/include
>>    -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich
>>    -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc
>>     > Using built-in specs.
>>     > COLLECT_GCC=gfortran
>>     > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper
>>     > Target: i686-linux-gnu
>>     > Configured with: ../src/configure -v
>>    --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5'
>>    --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs
>>    --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
>>    --program-suffix=-4.6 --enable-shared --enable-linker-build-id
>>    --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
>>    --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6
>>    --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu
>>    --enable-libstdcxx-debug --enable-libstdcxx-time=yes
>>    --enable-gnu-unique-object --enable-plugin --enable-objc-gc
>>    --enable-targets=all --disable-werror --with-arch-32=i686
>>    --with-tune=generic --enable-checking=release --build=i686-linux-gnu
>>    --host=i686-linux-gnu --target=i686-linux-gnu
>>     > Thread model: posix
>>     > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
>>     > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include'
>>    '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc'
>>    '-mtune=generic' '-march=i686'
>>     >  /usr/lib/gcc/i686-linux-gnu/4.6/f951 hello.F90
>>    -cpp=/tmp/ccgJjtSb.f90 -quiet -v -I
>>    /home/fkomijani/program_install/mpich-3.0.4/include -I
>>    /home/fkomijani/program_install/mpich-3.0.4/include -imultilib .
>>    -imultiarch i386-linux-gnu hello.F90 -quiet -dumpbase hello.F90
>>    -mtune=generic -march=i686 -auxbase hello -version
>>    -fintrinsic-modules-path /usr/lib/gcc/i686-linux-gnu/4.6/finclude -o
>>    /tmp/ccV5Pu7p.s
>>     > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3
>>    (i686-linux-gnu)
>>     >     compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR
>>    version 3.1.0-p3, MPC version 0.9
>>     > GGC heuristics: --param ggc-min-expand=100 --param
>>    ggc-min-heapsize=131072
>>     > ignoring nonexistent directory "/usr/local/include/i386-linux-gnu"
>>     > ignoring nonexistent directory
>>    "/usr/lib/gcc/i686-linux-gnu/4.6/../../../../i686-linux-gnu/include"
>>     > ignoring duplicate directory
>>    "/home/fkomijani/program_install/mpich-3.0.4/include"
>>     > #include "..." search starts here:
>>     > #include <...> search starts here:
>>     >  /home/fkomijani/program_install/mpich-3.0.4/include
>>     >  /usr/lib/gcc/i686-linux-gnu/4.6/finclude
>>     >  /usr/lib/gcc/i686-linux-gnu/4.6/include
>>     >  /usr/local/include
>>     >  /usr/lib/gcc/i686-linux-gnu/4.6/include-fixed
>>     >  /usr/include/i386-linux-gnu
>>     >  /usr/include
>>     > End of search list.
>>     > GNU Fortran (Ubuntu/Linaro 4.6.3-1ubuntu5) version 4.6.3
>>    (i686-linux-gnu)
>>     >     compiled by GNU C version 4.6.3, GMP version 5.0.2, MPFR
>>    version 3.1.0-p3, MPC version 0.9
>>     > GGC heuristics: --param ggc-min-expand=100 --param
>>    ggc-min-heapsize=131072
>>     > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include'
>>    '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc'
>>    '-mtune=generic' '-march=i686'
>>     >  as --32 -o /tmp/ccPO4WoE.o /tmp/ccV5Pu7p.s
>>     > Reading specs from /usr/lib/gcc/i686-linux-gnu/4.6/libgfortran.spec
>>     > rename spec lib to liborig
>>     > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include'
>>    '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc'
>>    '-mtune=generic' '-march=i686'
>>     >
>>    COMPILER_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/
>>     >
>>    LIBRARY_PATH=/usr/lib/gcc/i686-linux-gnu/4.6/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib/:/lib/i386-linux-gnu/:/lib/../lib/:/usr/lib/i386-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/i686-linux-gnu/4.6/../../../:/lib/:/usr/lib/
>>     > COLLECT_GCC_OPTIONS='-v' '-o' 'hello' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include' '-I'
>>    '/home/fkomijani/program_install/mpich-3.0.4/include'
>>    '-L/home/fkomijani/program_install/mpich-3.0.4/lib' '-shared-libgcc'
>>    '-mtune=generic' '-march=i686'
>>     >  /usr/lib/gcc/i686-linux-gnu/4.6/collect2 --sysroot=/ --build-id
>>    --no-add-needed --as-needed --eh-frame-hdr -m elf_i386
>>    --hash-style=gnu -dynamic-linker /lib/ld-linux.so.2 -z relro -o
>>    hello /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crt1.o
>>    /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crti.o
>>    /usr/lib/gcc/i686-linux-gnu/4.6/crtbegin.o
>>    -L/home/fkomijani/program_install/mpich-3.0.4/lib
>>    -L/usr/lib/gcc/i686-linux-gnu/4.6
>>    -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu
>>    -L/usr/lib/gcc/i686-linux-gnu/4.6/../../../../lib
>>    -L/lib/i386-linux-gnu -L/lib/../lib -L/usr/lib/i386-linux-gnu
>>    -L/usr/lib/../lib -L/usr/lib/gcc/i686-linux-gnu/4.6/../../..
>>    /tmp/ccPO4WoE.o -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread
>>    -lgfortran -lm -lgcc_s -lgcc -lquadmath -lm -lgcc_s -lgcc -lc
>>    -lgcc_s -lgcc /usr/lib/gcc/i686-linux-gnu/4.6/crtend.o
>>    /usr/lib/gcc/i686-linux-gnu/4.6/../../../i386-linux-gnu/crtn.o
>>     >
>>     >
>>     > On Sat, Sep 13, 2014 at 5:28 PM, Junchao Zhang
>>    <jczhang at mcs.anl.gov <mailto:jczhang at mcs.anl.gov>> wrote:
>>     > "gfortran: error: hello.F90: No such file or directory"
>>     > You need to create hello.F90 as I said in the previous email.
>>     >
>>     > "mpif90 -v -o hello hello.F90 ./coawst.bash"
>>     > Also, do not add ./coawst.bash
>>     >
>>     >
>>     >
>>     > --Junchao Zhang
>>     >
>>     > On Sat, Sep 13, 2014 at 7:15 AM, fereshteh komijani
>>    <fereshtehkomijani at gmail.com <mailto:fereshtehkomijani at gmail.com>>
>>    wrote:
>>     >
>>     > fkomijani at fk1:~/program_install/COAWST$  mpif90 -v -o hello
>>    hello.F90 ./coawst.bash
>>     > mpif90 for MPICH version 3.0.4
>>     > Driving: gfortran -v -o hello hello.F90 ./coawst.bash
>>    -I/home/fkomijani/program_install/mpich-3.0.4/include
>>    -I/home/fkomijani/program_install/mpich-3.0.4/include
>>    -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich
>>    -lopa -lmpl -lrt -lpthread -l gfortran -l m -shared-libgcc
>>     > gfortran: error: hello.F90: No such file or directory
>>     > Using built-in specs.
>>     > COLLECT_GCC=gfortran
>>     > COLLECT_LTO_WRAPPER=/usr/lib/gcc/i686-linux-gnu/4.6/lto-wrapper
>>     > Target: i686-linux-gnu
>>     > Configured with: ../src/configure -v
>>    --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5'
>>    --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs
>>    --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr
>>    --program-suffix=-4.6 --enable-shared --enable-linker-build-id
>>    --with-system-zlib --libexecdir=/usr/lib --without-included-gettext
>>    --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6
>>    --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu
>>    --enable-libstdcxx-debug --enable-libstdcxx-time=yes
>>    --enable-gnu-unique-object --enable-plugin --enable-objc-gc
>>    --enable-targets=all --disable-werror --with-arch-32=i686
>>    --with-tune=generic --enable-checking=release --build=i686-linux-gnu
>>    --host=i686-linux-gnu --target=i686-linux-gnu
>>     > Thread model: posix
>>     > gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
>>     >
>>     >
>>     > On Sat, Sep 13, 2014 at 4:33 PM, Junchao Zhang
>>    <jczhang at mcs.anl.gov <mailto:jczhang at mcs.anl.gov>> wrote:
>>     > That is strange.
>>     > Could you compile the following program with "mpif90 -v -o hello
>>    hello.F90" and paste the output?
>>     >
>>     > ! hello.F90
>>     > program main
>>     >     implicit none
>>     >     include 'mpif.h'
>>     >     integer :: ierr
>>     >
>>     >     call MPI_Init(ierr)
>>     >     call MPI_Finalize(ierr)
>>     > end program
>>     >
>>     >
>>     > --Junchao Zhang
>>     >
>>     > On Sat, Sep 13, 2014 at 6:24 AM, fereshteh komijani
>>    <fereshtehkomijani at gmail.com <mailto:fereshtehkomijani at gmail.com>>
>>    wrote:
>>     > sorry that is my fault, it is mpif.h
>>     >
>>     > it seems that COAWST model is searching it, in -I/user/include
>>    directory not in
>>     > /home/fkomijani/program_install/mpich-3.0.4/include.
>>     > so how can i set mentined directory in system environment?
>>     >
>>     > On Sat, Sep 13, 2014 at 3:45 PM, Junchao Zhang
>>    <jczhang at mcs.anl.gov <mailto:jczhang at mcs.anl.gov>> wrote:
>>     > The file name should be mpif.h, but not mpih.f.
>>     >
>>     > On Sep 13, 2014 1:45 AM, "fereshteh komijani"
>>    <fereshtehkomijani at gmail.com <mailto:fereshtehkomijani at gmail.com>>
>>    wrote:
>>     > yes, /home/fkomijani/program_install/mpich-3.0.4/include contains
>>    mpih.f
>>     >
>>     > On Sat, Sep 13, 2014 at 11:07 AM, Kenneth Raffenetti
>>    <raffenet at mcs.anl.gov <mailto:raffenet at mcs.anl.gov>> wrote:
>>     > If you 'ls /home/fkomijani/program_install/mpich-3.0.4/include'
>>    does it contain an mpif.h file? If not, your MPICH installation
>>    might be bad.
>>     >
>>     > On 09/13/2014 03:24 PM, fereshteh komijani wrote:
>>     > gfortran -I/home/fkomijani/program_install/mpich-3.0.4/include
>>     > -I/home/fkomijani/program_install/mpich-3.0.4/include
>>     > -L/home/fkomijani/program_install/mpich-3.0.4/lib -lmpichf90 -lmpich
>>     > -lopa -lmpl -lrt -lpthread
>>     >
>>     >
>>     > On Sat, Sep 13, 2014 at 10:52 AM, Kenneth Raffenetti
>>     > <raffenet at mcs.anl.gov <mailto:raffenet at mcs.anl.gov>
>>    <mailto:raffenet at mcs.anl.gov <mailto:raffenet at mcs.anl.gov>>> wrote:
>>     >
>>     >     What is the output from 'mpif90 -show'?
>>     >
>>     >     On 09/13/2014 03:19 PM, fereshteh komijani wrote:
>>     >
>>     >         dear Kenneth Raffenetti
>>     >         i am using mpif90 compiler.
>>     >         if it is, why i have got that error?
>>     >
>>     >         On Sat, Sep 13, 2014 at 10:47 AM, Kenneth Raffenetti
>>     >         <raffenet at mcs.anl.gov <mailto:raffenet at mcs.anl.gov>
>>    <mailto:raffenet at mcs.anl.gov <mailto:raffenet at mcs.anl.gov>>
>>     >         <mailto:raffenet at mcs.anl.gov
>>    <mailto:raffenet at mcs.anl.gov> <mailto:raffenet at mcs.anl.gov
>>    <mailto:raffenet at mcs.anl.gov>>>> wrote:
>>     >
>>     >              Are you using the mpif77 or mpif90 compiler wrappers to
>>     >         build your
>>     >              program? They will automatically add the location of
>>    mpif.h
>>     >         to your
>>     >              include path.
>>     >
>>     >              On 09/13/2014 02:56 PM, fereshteh komijani wrote:
>>     >
>>     >                  Dear friends
>>     >
>>     >                  recently I have installed mpich 3.0.4 in my system
>>     >         (Ubuntu).
>>     >
>>     >                  After compiling my model (coawst) it gives me
>>    following
>>     >         error :
>>     >
>>     >                  mod_parallel.f90:17: Error: Can't open included file
>>     >         'mpif.h'
>>     >
>>     >                  coaws's developer tell me :
>>     >
>>     >                  *check your environment and see if the location of
>>     >         mpif.h is in your
>>     >                  INCLUDE list*.
>>     >
>>     >                  But I don't know what is its mean? Where and how
>>    I can
>>     >         do that? Does
>>     >                  environment mean .bashrc?
>>     >
>>     >                  many thanks for any reply
>>     >
>>     >                  fereshteh
>>     >
>>     >
>>     >
>>     >                  --
>>     >                  ***Angel***
>>     >                  *__*
>>     >
>>     >
>>     >                  ___________________________________________________
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