[mpich-discuss] mpich compilation issue
akshar bhosale
akshar.bhosale at gmail.com
Tue Sep 13 21:52:52 CDT 2011
Hi,
below post is similar to our issue but workaround suggested did not work..
http://translate.google.co.in/translate?hl=en&sl=zh-CN&u=http://www.chinaunix.net/jh/4/979115.html&ei=zsptTo7hPIrQrQfNi524BQ&sa=X&oi=translate&ct=result&resnum=7&ved=0CFQQ7gEwBg&prev=/search%3Fq%3Dpi3f90.f90%252Bundefined%2Breference%2Bto%2B%2560mpi_init_%2527%26hl%3Den%26client%3Dfirefox-a%26hs%3DDP3%26rls%3Dorg.mozilla:en-US:official%26prmd%3Divns
On Tue, Sep 13, 2011 at 10:39 PM, Gus Correa <gus at ldeo.columbia.edu> wrote:
> Hi Akshar
>
> It sounds as a bug in the program,
> which causes a deadlock, not a problem with MPICH2.
> Your error message:
>
> > MPID_Send(57): DEADLOCK: attempting to send a message to the local
> > process without a prior matching receive
> If you post the code, the list may help you.
>
>
> Gus Correa
>
>
> akshar bhosale wrote:
>
>> sorry for not answering why not mpich2.
>> We have tried to compile our code using mpich2, it compiles but while
>> running the executable generated, it runs and in between it comes out giving
>> some mpi send error. The code compiled with mpif90 (mpich-1.2.7p1) using
>> gfortran on other machine runs fine.
>> Error is as follows:
>>
>> #######
>> 3 aft MPI_SEND 2 7 2 0
>> 3 call MPI_SEND 2 8 2 0
>> 3 aft MPI_SEND 2 8 2 0
>> 3 call MPI_SEND 2 9 2 0
>> 3 aft MPI_SEND 2 9 2 0
>> 3 call MPI_SEND 2 10 2 0
>> 3 aft MPI_SEND 2 10 2 0
>> 3 call MPI_SEND 3 1 3 0
>> [cli_3]: aborting job:
>> Fatal error in MPI_Send: Other MPI error, error stack:
>> MPI_Send(175): MPI_Send(buf=0x2aaab2af2018, count=1, dtype=USER<vector>,
>> dest=3, tag=30003, MPI_COMM_WORLD) failed
>> MPID_Send(57): DEADLOCK: attempting to send a message to the local process
>> without a prior matching receive
>> ###############
>>
>> -akshar
>>
>> On Tue, Sep 13, 2011 at 10:02 PM, akshar bhosale <
>> akshar.bhosale at gmail.com <mailto:akshar.bhosale at gmail.**com<akshar.bhosale at gmail.com>>>
>> 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 <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 <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 <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 <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
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>> <mailto:mpich-discuss at mcs.anl.**gov<mpich-discuss at mcs.anl.gov>
>> >
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>> **>
>> > >
>> > > 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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