[mpich-discuss] icc error with mpich2

[Siraj]

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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