[mpich-discuss] icc error with mpich2

[Dave Goodell]

This appears to be a repeat of your previous message.  Did you mean to send something else?

-Dave

On Aug 24, 2010, at 5:59 PM CDT, Siraj wrote:

> Hi,
> Thanks for the reply. Well i have changed the path of include directory by changing it from 
> /hpc/home/sislam/mpich2-1.2.1p1/include
> to
> /hpc/home/sislam/mpich2-1.2.1p1/src/include
> 
> and the problem is solved but why there are tow include directories in mich2-1.2.p1 folder. 
> 
> Actually this machine have one another old mpich but i have disable it and have installed the new mpich2  using command 
> 
> ./configure --prefix=/hpc/u2/sislam/mpich2-1.2.1p1''--with-atomic-primitives=no' 'CC=icc' 'F77=ifort'
> 
> and then i run make and make install. 
> 
> Now my code is compiled but when I run it using mpirun -np 8 cam command i get the following error after some time 
> 
> -------------------------------------
> Filename specifier for history file            1  = %c.cam2.h%t.%y-%m.nc
>  Filename specifier for history file            7  = %c.cam2.i.%y-%m-%d-%s.nc
>  Accumulation precision history file            1 =           8
>  Packing density history file            1 =           2
>  Number of time samples per file (MFILT) for history file            1  is
>            1
>  Accumulation precision history file            7 =           8
>  Packing density history file            7 =           1
>  Number of time samples per file (MFILT) for history file            7  is
>            1
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x60000000062baf34 src_=0x60000000062baf34 len_=4
> 
> internal ABORT - process 1
> Assertion failed in file helper_fns.c at line 335: 0
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x600000000623e1a0 src_=0x600000000623e1a0 len_=4
> 
> internal ABORT - process 4
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x600000000623c088 src_=0x600000000623c088 len_=4
> 
> internal ABORT - process 2
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x600000000623c0d8 src_=0x600000000623c0d8 len_=4
> 
> internal ABORT - process 6
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x600000000626c814 src_=0x600000000626c814 len_=4
> 
> internal ABORT - process 5
> memcpy argument memory ranges overlap, dst_=0x6000000006237d50 src_=0x6000000006237d50 len_=4
> 
> internal ABORT - process 0
> rank 4 in job 2  pg-hpc-altix-01_48099   caused collective abort of all ranks
>   exit status of rank 4: return code 1
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x600000000623c08c src_=0x600000000623c08c len_=4
> 
> internal ABORT - process 3
> Assertion failed in file helper_fns.c at line 335: 0
> memcpy argument memory ranges overlap, dst_=0x600000000623906c src_=0x600000000623906c len_=4
> 
> internal ABORT - process 7
> rank 3 in job 2  pg-hpc-altix-01_48099   caused collective abort of all ranks
>   exit status of rank 3: return code 1
> rank 1 in job 2  pg-hpc-altix-01_48099   caused collective abort of all ranks
>   exit status of rank 1: return code 1
> rank 0 in job 2  pg-hpc-altix-01_48099   caused collective abort of all ranks
>   exit status of rank 0: return code 1
> (seq_mct_drv) : Initialize lnd component
> CAM run failed
> 
> Siraj
> 
> ------------------------------------
> 
> 
> Message: 1
> Date: Mon, 23 Aug 2010 19:30:42 -0600 (GMT-06:00)
> From: chan at mcs.anl.gov
> Subject: Re: [mpich-discuss] icc error with mpich2
> To: mpich-discuss at mcs.anl.gov
> Message-ID:
>        <381714913.1224641282613442701.JavaMail.root at zimbra.anl.gov>
> Content-Type: text/plain; charset=utf-8
> 
> 
> ----- "Siraj" <sirajkhan78 at gmail.com> wrote:
> 
> 
> > /usr/include/mpi.h(30): error: invalid redeclaration of type name
> > "MPI_Request" (declared at line 264 of
> > "/hpc/home/sislam/mpich2-1.2.
> 1p1/include/mpi.h")
> >   typedef unsigned int          MPI_Request;
> 
> It looks like you have 2 mpi.h header files, one in /usr/include/mpi.h
> and one in /hpc/home/sislam/mpich2-1.2.1p1/include. You may have
> more than 1 MPI implementation on your machine.
> 
> > Note: I have compiled mpich using following command
> > ./configure --prefix=/hpc/u2/sislam/mpich2-1.2.1p1'
> > '--with-atomic-primitives=no' 'CC=icc' 'F77=ifort'
> 
> did you do "make" and "make install" after configure ?
> your mpich2 install directory, /hpc/u2/sislam/mpich2-1.2.1p1,
> is different from above 2 ?!
> 
> Can you try using the mpi wrappers, like mpicc and pif90,
> from /hpc/u2/sislam/mpich2-1.2.1p1/bin to compile and link
> your ccsm code ?  In general, one should use MPI wrappers provided
> by MPI implementation instead of using native compiler directly.
> MPI wrappers provided by MPICH2 is very careful about the include
> and link path orders, so it should avoid the problem that you see here.
> If not, let us know...
> 
> 
> A.Chan
> 
> 
> 
> Siraj
> 
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