<div>Thanks for your advice. But to be honest I do not know much about how our model uses MPI.</div>
<div>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.</div>
<div>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.</div>
<div> </div>
<div>Thanks very much.</div>
<div> </div>
<div>Rui<br></div>
<div class="gmail_quote">On Fri, Jul 16, 2010 at 9:29 AM, Anthony Chan <span dir="ltr"><<a href="mailto:chan@mcs.anl.gov">chan@mcs.anl.gov</a>></span> wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote"><br>You should use MPI compiler wrapper (mpicc, mpif90...) to compile/link<br>your app. If not, you need to link with all MPICH2 supported libraries<br>
by hand, e.g. -lpthread. Add -show to the MPI wrapper to see what the<br>supported libraries are.<br><br>A.Chan<br>
<div>
<div></div>
<div class="h5">----- "Rui Mei" <<a href="mailto:meir02ster@gmail.com">meir02ster@gmail.com</a>> wrote:<br><br>> Hi, all,<br>><br>> I sent a post on problems with installation of MPICH on SGI under my<br>
> local<br>> account one month ago. Thanks to your help, it is fixed now. I am able<br>> to<br>> install it with those commands:<br>><br>> ./configure --prefix=/u/home/rum06003/mpi --with-device=ch3:sock 2>&1<br>
> | tee<br>> c.txt<br>><br>> make 2>&1 | tee m.txt<br>><br>> make install 2>&1 | tee mi.txt.<br>><br>> Now the problem is that when I run our research model, it fails in<br>> the<br>
> configure process and part of the error message is as follows, related<br>> to<br>> MPI. But there was no error message during MPI installation. Thanks<br>> if<br>> someone can offer some advice on this issue.<br>
><br>> Rui<br>><br>> .intr.o -L/opt/i/netcdf/lib -lnetcdf -static-intel<br>> -L/u/home/rum06003/mpi2/lib -lmpich<br>> /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x13a2): In<br>> function<br>
> `MPIR_Get_contextid':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x13f2): In<br>> function<br>> `MPIR_Get_contextid':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x2ad2): In<br>> function<br>> `MPIR_Get_intercomm_contextid':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(commutil.o)(.text+0x2b22): In<br>
> function<br>> `MPIR_Get_intercomm_contextid':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4182): In<br>> function<br>> `MPIR_Err_return_comm':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x41d2): In<br>> function<br>> `MPIR_Err_return_comm':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x43d2): In<br>> function<br>> `MPIR_Err_return_win':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4422): In<br>
> function<br>> `MPIR_Err_return_win':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x47d2): In<br>> function<br>> `MPIR_Nest_decr_export':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4832): In<br>> function<br>> `MPIR_Nest_decr_export':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x48e2): In<br>> function<br>> `MPIR_Nest_incr_export':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(errutil.o)(.text+0x4942): In<br>
> function<br>> `MPIR_Nest_incr_export':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x522): In<br>> function<br>> `MPIR_Init_thread':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x562): In<br>> function<br>> `MPIR_Init_thread':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x6c2): In<br>> function<br>> `MPIR_Thread_CS_Finalize':<br>> : undefined reference to `pthread_key_delete'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x6f2): In<br>
> function<br>> `MPIR_Thread_CS_Finalize':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x752): In<br>> function<br>> `MPIR_Thread_CS_Finalize':<br>
> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x762): In<br>> function<br>> `MPIR_Thread_CS_Finalize':<br>> : undefined reference to `pthread_key_delete'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x7b2): In<br>> function<br>> `MPIR_Thread_CS_Finalize':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0x802): In<br>
> function<br>> `MPIR_Thread_CS_Init':<br>> : undefined reference to `pthread_key_create'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xb42): In<br>> function<br>> `PMPI_Init_thread':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xb92): In<br>> function<br>> `PMPI_Init_thread':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xc62): In<br>> function<br>> `PMPI_Init_thread':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xcb2): In<br>
> function<br>> `PMPI_Init_thread':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xcf2): In<br>> function<br>> `PMPI_Init_thread':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(initthread.o)(.text+0xd42): In<br>> function<br>> `PMPI_Init_thread':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x2a2): In<br>> function<br>> `PMPI_Recv':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x372): In<br>
> function<br>> `PMPI_Recv':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x3c2): In<br>> function<br>> `PMPI_Recv':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(recv.o)(.text+0x402): In<br>> function<br>> `PMPI_Recv':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x292): In<br>
> function<br>> `PMPI_Send':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x362): In<br>> function<br>> `PMPI_Send':<br>> : undefined reference to `pthread_getspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x3b2): In<br>> function<br>> `PMPI_Send':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(send.o)(.text+0x3f2): In<br>
> function<br>> `PMPI_Send':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(mpid_type_debug.o)(.text+0x17f2):<br>> In<br>> function `MPIDI_Datatype_printf':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(mpid_type_debug.o)(.text+0x1842):<br>> In<br>> function `MPIDI_Datatype_printf':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x2b22):<br>> In function `MPIDI_CH3_ReqHandler_AccumRespDerivedDTComplete':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x2b72):<br>
> In function `MPIDI_CH3_ReqHandler_AccumRespDerivedDTComplete':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x3402):<br>> In function `MPIDI_CH3_ReqHandler_PutAccumRespComplete':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_handle_recv_req.o)(.text+0x3452):<br>> In function `MPIDI_CH3_ReqHandler_PutAccumRespComplete':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0x2a62):<br>> In<br>> function `MPIDI_CH3_PktHandler_Accumulate':<br>> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0x2ab2):<br>
> In<br>> function `MPIDI_CH3_PktHandler_Accumulate':<br>> : undefined reference to `pthread_setspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0xc542):<br>> In<br>> function `MPIDI_Win_complete':<br>
> : undefined reference to `pthread_getspecific'<br>> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0xc592):<br>> In<br>> function `MPIDI_Win_complete':<br>> : undefined reference to `pthread_setspecific'<br>
> /u/home/rum06003/mpi2/lib/libmpich.a(ch3u_rma_sync.o)(.text+0xd732):<br>> In<br>> function `MPIDI_Win_post':<br>> : undefined reference to `pthread_getspecific'<br>> etc .................<br>><br>
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</blockquote></div><br>