[mpich-discuss] a question about MPICH2 on SGI under local account

Fri Jul 16 09:07:52 CDT 2010

Instead of setting your native compiler, use MPI compiler wrapper.  With
the wrapper, you don't need to set MPI include and libraries and that
should simplify the build system of your model in most cases.

----- "Rui Mei" <meir02ster at gmail.com> wrote:

> Thanks for your advice. But to be honest I do not know much about how
> our
> model uses MPI.
> To make the model run, what I usually do related to MPI is to set MPI
> lib ,
> MPI include, and mpirun path right in the jobscript.
> I guess I need to modify the configure file according what you says.
> Any
> further advice on that? I can provide you files if needed.
> 
> Thanks very much.
> 
> Rui
> On Fri, Jul 16, 2010 at 9:29 AM, Anthony Chan <chan at mcs.anl.gov>
> wrote:
> 
> >
> > You should use MPI compiler wrapper (mpicc, mpif90...) to
> compile/link
> > your app.  If not, you need to link with all MPICH2 supported
> libraries
> > by hand, e.g. -lpthread.   Add -show to the MPI wrapper to see what
> the
> > supported libraries are.
> >
> > A.Chan
> >  ----- "Rui Mei" <meir02ster at gmail.com> wrote:
> >
> > > Hi, all,
> > >
> > > I sent a post on problems with installation of MPICH on SGI under
> my
> > > local
> > > account one month ago. Thanks to your help, it is fixed now. I am
> able
> > > to
> > > install it with those commands:
> > >
> > > ./configure --prefix=/u/home/rum06003/mpi --with-device=ch3:sock
> 2>&1
> > > | tee
> > > c.txt
> > >
> > > make 2>&1 | tee m.txt
> > >
> > > make install 2>&1 | tee mi.txt.
> > >
> > > Now the problem is that when I run our research model, it fails
> in
> > > the
> > > configure process and part of the error message is as follows,
> related
> > > to
> > > MPI. But there was no error message during MPI installation.
> Thanks
> > > if
> > > someone can offer some advice on this issue.
> > >
> > > Rui
> > >
> > > .intr.o -L/opt/i/netcdf/lib -lnetcdf -static-intel
> > > -L/u/home/rum06003/mpi2/lib -lmpich
> > > /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x13a2):
> In
> > > function
> > > `MPIR_Get_contextid':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x13f2):
> In
> > > function
> > > `MPIR_Get_contextid':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x2ad2):
> In
> > > function
> > > `MPIR_Get_intercomm_contextid':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x2b22):
> In
> > > function
> > > `MPIR_Get_intercomm_contextid':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4182): In
> > > function
> > > `MPIR_Err_return_comm':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x41d2): In
> > > function
> > > `MPIR_Err_return_comm':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x43d2): In
> > > function
> > > `MPIR_Err_return_win':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4422): In
> > > function
> > > `MPIR_Err_return_win':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x47d2): In
> > > function
> > > `MPIR_Nest_decr_export':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4832): In
> > > function
> > > `MPIR_Nest_decr_export':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x48e2): In
> > > function
> > > `MPIR_Nest_incr_export':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4942): In
> > > function
> > > `MPIR_Nest_incr_export':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x522):
> In
> > > function
> > > `MPIR_Init_thread':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x562):
> In
> > > function
> > > `MPIR_Init_thread':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x6c2):
> In
> > > function
> > > `MPIR_Thread_CS_Finalize':
> > > : undefined reference to `pthread_key_delete'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x6f2):
> In
> > > function
> > > `MPIR_Thread_CS_Finalize':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x752):
> In
> > > function
> > > `MPIR_Thread_CS_Finalize':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x762):
> In
> > > function
> > > `MPIR_Thread_CS_Finalize':
> > > : undefined reference to `pthread_key_delete'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x7b2):
> In
> > > function
> > > `MPIR_Thread_CS_Finalize':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x802):
> In
> > > function
> > > `MPIR_Thread_CS_Init':
> > > : undefined reference to `pthread_key_create'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xb42):
> In
> > > function
> > > `PMPI_Init_thread':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xb92):
> In
> > > function
> > > `PMPI_Init_thread':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xc62):
> In
> > > function
> > > `PMPI_Init_thread':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xcb2):
> In
> > > function
> > > `PMPI_Init_thread':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xcf2):
> In
> > > function
> > > `PMPI_Init_thread':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xd42):
> In
> > > function
> > > `PMPI_Init_thread':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x2a2): In
> > > function
> > > `PMPI_Recv':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x372): In
> > > function
> > > `PMPI_Recv':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x3c2): In
> > > function
> > > `PMPI_Recv':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x402): In
> > > function
> > > `PMPI_Recv':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x292): In
> > > function
> > > `PMPI_Send':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x362): In
> > > function
> > > `PMPI_Send':
> > > : undefined reference to `pthread_getspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x3b2): In
> > > function
> > > `PMPI_Send':
> > > : undefined reference to `pthread_setspecific'
> > > /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x3f2): In
> > > function
> > > `PMPI_Send':
> > > : undefined reference to `pthread_setspecific'
> > >
> /u/home/rum06003/mpi2/lib/libmpich.a(mpid_type_debug.o)(.text+0x17f2):
> > > In
> > > function `MPIDI_Datatype_printf':
> > > : undefined reference to `pthread_getspecific'
> > >
> /u/home/rum06003/mpi2/lib/libmpich.a(mpid_type_debug.o)(.text+0x1842):
> > > In
> > > function `MPIDI_Datatype_printf':
> > > : undefined reference to `pthread_setspecific'
> > >
> >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x2b22):
> > > In function `MPIDI_CH3_ReqHandler_AccumRespDerivedDTComplete':
> > > : undefined reference to `pthread_getspecific'
> > >
> >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x2b72):
> > > In function `MPIDI_CH3_ReqHandler_AccumRespDerivedDTComplete':
> > > : undefined reference to `pthread_setspecific'
> > >
> >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x3402):
> > > In function `MPIDI_CH3_ReqHandler_PutAccumRespComplete':
> > > : undefined reference to `pthread_getspecific'
> > >
> >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x3452):
> > > In function `MPIDI_CH3_ReqHandler_PutAccumRespComplete':
> > > : undefined reference to `pthread_setspecific'
> > >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0x2a62):
> > > In
> > > function `MPIDI_CH3_PktHandler_Accumulate':
> > > : undefined reference to `pthread_getspecific'
> > >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0x2ab2):
> > > In
> > > function `MPIDI_CH3_PktHandler_Accumulate':
> > > : undefined reference to `pthread_setspecific'
> > >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0xc542):
> > > In
> > > function `MPIDI_Win_complete':
> > > : undefined reference to `pthread_getspecific'
> > >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0xc592):
> > > In
> > > function `MPIDI_Win_complete':
> > > : undefined reference to `pthread_setspecific'
> > >
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0xd732):
> > > In
> > > function `MPIDI_Win_post':
> > > : undefined reference to `pthread_getspecific'
> > > etc .................
> > >
> > > _______________________________________________
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> >