[mpich-discuss] mpich compilation issue
Gus Correa
gus at ldeo.columbia.edu
Tue Sep 13 12:00:40 CDT 2011
Hi Akshar
Before you invest a lot of time trying to compile your program,
test if your mpich-1 at least works in your machine/cluster
with a very simple program.
You can compile examples/cpi.c with mpicc,
and run it with mpirun on as many processors
you would use for your real program or more.
Something like this:
mpicc cpi.c
mpirun -n 8 ./a.out
If you get P4 errors, it is very likely that you're not going
to be able to run your application with mpich-1 either.
Those errors have been reported on this list and in other lists
several times, by people that were trying to continue to use mpich-1,
just like you.
As everybody has been saying all along,
it may be easier to port your program to MPICH2 instead.
Actually the MPI calls should be backward compatible,
you probably don't need to change anything in the code itself.
At most you will have to adjust the launching mechanism,
i.e. mpirun and friends, to the MPICH2 environment, I suppose.
I hope this helps,
Gus Correa
akshar bhosale wrote:
> thanks for reply.
>
> Goal is to generate mpif90 using mpich-1.2.7p1 using gfortran which will
> generate executable from our fortran code.
>
> source files to be compiled are .f and .f90 files.
>
> f2c flag is given because mp[if90 was not getting generated. no other
> reason. we want mpif90.
>
> Now we have tried giving only FC=gfortran and no other flag of option
> except prefix, but still it is not generating mpif90 nor mpif77.
>
> mpif90 generated by using [export F90=fortran;F90FLAGS="-ff2c".]
> options if tries to compile our code, it throws error
>
>
> <path to mpif90>/mpif90 -f90=gfortran -Wl -o ../output_code.x set.o
> inp.o otp.o bvsol.o user_kg.o mpi_util.o mpi_communication.o
> mpi_memalloc.o driver.o rxn.o advdi_1d_finitediff_mf.o aq_lib.o \
> -L/ioapi/Linux2_x86_64gfort -lioapi -L/np_cs/netcdf/INSTALL/lib
> -lnetcdf -L/usr/lib64/
> -lgomp /np_cs/lapack/lapack-3.2.1/lapack_LINUX.a
> /np_cs/lapack/lapack-3.2.1/blas_LINUX.a
> /build/lib/libmpich.a(farg.o): In function `mpir_iargc__':
> farg.f:(.text+0x6): undefined reference to `f__xargc'
> /build/lib/libmpich.a(farg.o): In function `mpir_getarg__':
> farg.f:(.text+0x38): undefined reference to `getarg_'
> collect2: ld returned 1 exit status
> make: *** [../output_code.x] Error 1
>
> -akshar
>
>
>
>
>
> On Tue, Sep 13, 2011 at 8:52 PM, Gus Correa <gus at ldeo.columbia.edu
> <mailto:gus at ldeo.columbia.edu>> wrote:
>
> Hi Pavan and Akshar
>
> I see, it's MPICH-1.
> May I ask why?
>
> Would a workaround perhaps be to build only mpif77 (no mpif90),
> replace 'use mpi' by '#include "mpif.h"' in the application code,
> and recompile it with mpif77?
>
> I wonder if -ff2c works at all with Fortran90.
> (See man page detail below.)
>
> Anyway, I remember that there were complaints of runtime
> errors (P4 errors) with mpich-1,
> reported on this and other mailing lists,
> when running on current Linux kernels.
> Even with simple codes like the cpi example.
> Using MPICH-1 may be an uphill battle.
>
> I hope this helps,
> Gus Correa
>
> >From man gfortran (4.1.2):
>
> -ff2c
> Generate code designed to be compatible with code
> generated by g77 and f2c.
>
> The calling conventions used by g77 (originally
> implemented in f2c) require functions that return type default
> "REAL" to actually return the C type
> "double", and functions that return type "COMPLEX" to
> return the values via an extra argument in the calling sequence that
> points to where to store the
> return value. Under the default GNU calling conventions,
> such functions simply return their results as they would in GNU C --
> default "REAL" functions
> return the C type "float", and "COMPLEX" functions return
> the GNU C type "complex". Additionally, this option implies the
> -fsecond-underscore option,
> unless -fno-second-underscore is explicitly requested.
>
> This does not affect the generation of code that
> interfaces with the libgfortran library.
>
> Caution: It is not a good idea to mix Fortran code
> compiled with "-ff2c" with code compiled with the default "-fno-f2c"
> calling conventions as, calling
> "COMPLEX" or default "REAL" functions between program
> parts which were compiled with different calling conventions will
> break at execution time.
>
> Caution: This will break code which passes intrinsic
> functions of type default "REAL" or "COMPLEX" as actual arguments,
> as the library implementations
> use the -fno-f2c calling conventions.
>
>
>
>
> Pavan Balaji wrote:
>
>
> Gus: He doesn't want to use MPICH2. He's using MPICH-1.
>
> -- Pavan
>
> On 09/13/2011 09:51 AM, Gus Correa wrote:
>
> Hi Akshar
>
> Maybe the F90FLAGS="-ff2c" flag is causing the problem?
> What if you remove it and use gfortran for F77 and FC?
>
>
> Also, my 'configure -help' (a bit old, MPICH2 1.3.2p1)
> mentions FC, not F90, as the environment variable to be set.
>
> For what it is worth, MPICH2 builds fine for us, with
> gcc, g++ and gfortran (for F77 and FC).
>
> My two cents,
> Gus Correa
>
> akshar bhosale wrote:
>
> Hi,
>
> If i specify F77 anf F90 as gfortran, it doesn't
> create mpif90 and
> mpif77 at all.
> Please see attached config log
> If i specify F90=gfortran and F90FLAGS="-ff2c", the it
> creates mpif90
> and mpif77 but is generating below issue.
> Kindly help.
> -akshar
>
> On Tue, Sep 13, 2011 at 9:46 AM, Rajeev
> Thakur<thakur at mcs.anl.gov <mailto:thakur at mcs.anl.gov>
> <mailto:thakur at mcs.anl.gov <mailto:thakur at mcs.anl.gov>>>
> wrote:
>
> In the configure step, if you specify both F77 and
> F90 as gfortran,
> it should work.
>
> Rajeev
>
> On Sep 12, 2011, at 9:49 PM, akshar bhosale wrote:
>
> > Hi,
> > thanks.
> > but, in case of mpicc, it can be ignored, but in
> case of mpif90,
> it is still an issue.
> > e.g. hello_mpi.f90 program
> > ####################
> > program main
> > use mpi
> > !
> > ! implicit none
> > !
> > integer error
> > integer id
> > integer p
> > real ( kind = 8 ) wtime
> > !
> > ! Initialize MPI.
> > !
> > call MPI_Init ( error )
> > !
> > ! Get the number of processes.
> > !
> > call MPI_Comm_size ( MPI_COMM_WORLD, p, error )
> >
> > !
> > ! Get the individual process ID.
> > !
> > call MPI_Comm_rank ( MPI_COMM_WORLD, id, error )
> > !
> > ! Print a message.
> > !
> > if ( id == 0 ) then
> >
> > wtime = MPI_Wtime ( )
> >
> > write ( *, '(a)' ) ' '
> > write ( *, '(a)' ) 'HELLO_MPI - Master process:'
> > write ( *, '(a)' ) ' FORTRAN90/MPI version'
> > write ( *, '(a)' ) ' '
> > write ( *, '(a)' ) ' An MPI test program.'
> > write ( *, '(a)' ) ' '
> > write ( *, '(a,i8)' ) ' The number of
> processes is ', p
> > write ( *, '(a)' ) ' '
> >
> > end if
> >
> > write ( *, '(a)' ) ' '
> > write ( *, '(a,i8,a)' ) ' Process ', id, '
> says "Hello, world!"'
> >
> > if ( id == 0 ) then
> >
> > write ( *, '(a)' ) ' '
> > write ( *, '(a)' ) 'HELLO_MPI - Master process:'
> > write ( *, '(a)' ) ' Normal end of
> execution: "Goodbye,
> world!".'
> >
> > wtime = MPI_Wtime ( ) - wtime
> > write ( *, '(a)' ) ' '
> > write ( *, '(a,g14.6,a)' ) ' Elapsed wall
> clock time = ',
> wtime, ' seconds.'
> >
> > end if
> > !
> > ! Shut down MPI.
> > !
> > call MPI_Finalize ( error )
> >
> > stop
> > end
> > ############################
> >
> > $ ../../../build/bin/mpif90 hello_mpi.f90
> >
> /scratch1/np_cs/trial1/build/__lib/libmpich.a(farg.o):
> In function
> `mpir_iargc__':
> > farg.f:(.text+0x6): undefined reference to
> `f__xargc'
> >
> /scratch1/np_cs/trial1/build/__lib/libmpich.a(farg.o):
> In function
> `mpir_getarg__':
> > farg.f:(.text+0x38): undefined reference to
> `getarg_'
> > collect2: ld returned 1 exit status
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Mon, Sep 12, 2011 at 9:42 AM, Rajeev Thakur
> <thakur at mcs.anl.gov
> <mailto:thakur at mcs.anl.gov><mailto:tha__kur at mcs.anl.gov
> <mailto:thakur at mcs.anl.gov>>> wrote:
> > Ignore that. Compile a real program as mpicc foo.c.
> >
> > On Sep 11, 2011, at 8:38 PM, akshar bhosale wrote:
> >
> > > Hi,
> > > thank you for reply.
> > >
> > > I tried to install it make it using following
> options now and i
> get following error with undefined reference to
> main. options given
> while configuring the same are :
> > > export F90=fortran;F90FLAGS="-ff2c".
> > > but error of undefined reference to main is
> observed in every
> executable like :
> > >
> > > ./mpicc -v
> > > mpicc for 1.2.7 (release) of : 2005/06/22
> 16:33:49
> > > Using built-in specs.
> > > Target: x86_64-redhat-linux
> > > Configured with: ../configure --prefix=/usr
> --mandir=/usr/share/man --infodir=/usr/share/info
> --enable-shared
> --enable-threads=posix --enable-checking=release
> --with-system-zlib
> --enable-__cxa_atexit --disable-libunwind-exceptions
> --enable-libgcj-multifile
> --enable-languages=c,c++,objc,__obj-c++,java,fortran,ada
> --enable-java-awt=gtk --disable-dssi --disable-plugin
>
> --with-java-home=/usr/lib/jvm/__java-1.4.2-gcj-1.4.2.0/jre
> --with-cpu=generic --host=x86_64-redhat-linux
> > > Thread model: posix
> > > gcc version 4.1.2 20080704 (Red Hat 4.1.2-50)
> > >
> /usr/libexec/gcc/x86_64-__redhat-linux/4.1.2/collect2
> --eh-frame-hdr -m elf_x86_64 --hash-style=gnu
> -dynamic-linker
> /lib64/ld-linux-x86-64.so.2
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64/__crt1.o
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64/__crti.o
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/crtbegin.o
> -L/scratch1/np_cs/trial2/__build/lib
> -L/opt/intel/mkl/10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t><http://10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t>>
> -L/opt/intel/mkl/10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t><http://10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t>>
> -L/usr/lib/gcc/x86_64-redhat-__linux/4.1.2
> -L/usr/lib/gcc/x86_64-redhat-__linux/4.1.2
>
> -L/usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64 -lmpich
> -lpthread -lrt -lgcc
> --as-needed -lgcc_s --no-as-needed -lc -lgcc
> --as-needed -lgcc_s
> --no-as-needed
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/crtend.o
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64/__crtn.o
> > >
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64/__crt1.o:
> In
> function `_start':
> > > (.text+0x20): undefined reference to `main'
> > > collect2: ld returned 1 exit status
> > >
> > > ./mpif90 -v
> > > mpif90 for 1.2.7 (release) of : 2005/06/22
> 16:33:49
> > > Driving: gfortran
> -L/scratch1/np_cs/trial2/__build/lib -v
> -lmpichf90 -lmpich -lpthread -lrt -lgfortranbegin
> -lgfortran -lm
> -shared-libgcc
> > > Using built-in specs.
> > > Target: x86_64-redhat-linux
> > > Configured with: ../configure --prefix=/usr
> --mandir=/usr/share/man --infodir=/usr/share/info
> --enable-shared
> --enable-threads=posix --enable-checking=release
> --with-system-zlib
> --enable-__cxa_atexit --disable-libunwind-exceptions
> --enable-libgcj-multifile
> --enable-languages=c,c++,objc,__obj-c++,java,fortran,ada
> --enable-java-awt=gtk --disable-dssi --disable-plugin
>
> --with-java-home=/usr/lib/jvm/__java-1.4.2-gcj-1.4.2.0/jre
> --with-cpu=generic --host=x86_64-redhat-linux
> > > Thread model: posix
> > > gcc version 4.1.2 20080704 (Red Hat 4.1.2-50)
> > >
> /usr/libexec/gcc/x86_64-__redhat-linux/4.1.2/collect2
> --eh-frame-hdr -m elf_x86_64 --hash-style=gnu
> -dynamic-linker
> /lib64/ld-linux-x86-64.so.2
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64/__crt1.o
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64/__crti.o
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/crtbegin.o
> -L/scratch1/np_cs/trial2/__build/lib
> -L/opt/intel/mkl/10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t><http://10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t>>
> -L/opt/intel/mkl/10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t><http://10.2.2.025/__lib/em64t
> <http://10.2.2.025/lib/em64t>>
> -L/usr/lib/gcc/x86_64-redhat-__linux/4.1.2
> -L/usr/lib/gcc/x86_64-redhat-__linux/4.1.2
>
> -L/usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64 -lmpichf90
> -lmpich -lpthread
> -lrt -lgfortranbegin -lgfortran -lm -lgcc_s -lgcc
> -lc -lgcc_s -lgcc
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/crtend.o
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/../../../../lib64/__crtn.o
> > >
>
> /usr/lib/gcc/x86_64-redhat-__linux/4.1.2/libgfortranbegin.__a(fmain.o):
> In function `main':
> > > (.text+0xa): undefined reference to `MAIN__'
> > > collect2: ld returned 1 exit status
> > >
> > > Am i missing somethin?
> > > thank you
> > > -akshar
> > >
> > > On Mon, Sep 12, 2011 at 1:24 AM, William Gropp
> <wgropp at illinois.edu
> <mailto:wgropp at illinois.edu><mailto:wg__ropp at illinois.edu
> <mailto:wgropp at illinois.edu>>> wrote:
> > > You can use gfortran for F77 and F90. If
> your requirement is
> to use gfortran for F77 and a different fortran for
> F90, then they
> will need to use consistent linker names, calling
> conventions, data
> sizes, and libraries. The config.log file will have
> details on why
> configure decided that the Fortran 77 and Fortran 90
> compilers were
> not compatible.
> > >
> > > Bill
> > >
> > >
> > > On Sep 9, 2011, at 4:28 PM, akshar bhosale wrote:
> > >
> > > hi,
> > > we have requirement of mpich-1.2.7 with
> gfortran. We have fiven
> flags as : CC=gcc;F90=fortran;F77=__gfortran; and
> tried to configure,
> it throws error as configure: error: Fortran 90 and
> Fortran 77
> compilers are not compatible..
> > > We have to do it using gfortran only. os is
> rhel5.1 64 bit
> > > what extran flags settings we have to do?
> > >
> > > -akshar
> > > _________________________________________________
> > > mpich-discuss mailing list
> mpich-discuss at mcs.anl.gov <mailto:mpich-discuss at mcs.anl.gov>
> <mailto:mpich-discuss at mcs.anl.__gov
> <mailto:mpich-discuss at mcs.anl.gov>>
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> > >
> https://lists.mcs.anl.gov/__mailman/listinfo/mpich-discuss
> <https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss>
> > >
> > > William Gropp
> > > Director, Parallel Computing Institute
> > > Deputy Director for Research
> > > Institute for Advanced Computing Applications
> and Technologies
> > > Paul and Cynthia Saylor Professor of Computer
> Science
> > > University of Illinois Urbana-Champaign
> > >
> > >
> > >
> > >
> > > _________________________________________________
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