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

[Rui Mei]

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 .................
> >
> > _______________________________________________
> > mpich-discuss mailing list
> > mpich-discuss at mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss
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