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Sat Oct 16 10:00:00 MDT 2004
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<< issues linking to the MPI library, http://bb.cgd.ucar.edu//viewtopic.php?t=30 >>
Postercathryn.meyer at yale.eduPostedFri Oct 15, 2004 2:24 pm MDT, http://bb.cgd.ucar.edu//viewtopic.php?p=78#78
Message: I am trying to compile CAM3.0 (patched version) on a linux cluster, however the MPI library is not linking properly. When I attempt to compile the model, I get the following error messages (I get more than what I have pasted below, I cut most of them out to save space):
<br />
<br />------------------------------------------------------------
<br />: multiple definition of `MAIN_'
<br />cam.o(.text+0x10): first defined here
<br />/usr/bin/ld: Warning: size of symbol `MAIN_' changed from 5339 to 49 in
<br />test_mpi.o
<br />STATICEcosysDynMod.o(.text+0x3a62): In function
<br />`staticecosysdynmod_readmonthlyvegetation_':
<br />: undefined reference to `mpi_bcast_'
<br />STATICEcosysDynMod.o(.text+0x3ac5): In function
<br />`staticecosysdynmod_readmonthlyvegetation_':
<br />: undefined reference to `mpi_bcast_'
<br />STATICEcosysDynMod.o(.text+0x3b28): In function
<br />`staticecosysdynmod_readmonthlyvegetation_':
<br />: undefined reference to `mpi_bcast_'
<br />
<b!
r />surfFileMod.o(.text+0x3d00): In function `surffilemod_surfrd_':
<br />: undefined reference to `mpi_bcast_'
<br />surfFileMod.o(.text+0x3d35): In function `surffilemod_surfrd_':
<br />: undefined reference to `mpi_bcast_'
<br />surfFileMod.o(.text+0x3d6a): In function `surffilemod_surfrd_':
<br />: undefined reference to `mpi_bcast_'
<br />surfFileMod.o(.text+0x3da4): In function `surffilemod_surfrd_':
<br />: undefined reference to `mpi_bcast_'
<br />surfFileMod.o(.text+0x3dde): In function `surffilemod_surfrd_':
<br />: undefined reference to `mpi_bcast_'
<br />surfFileMod.o(.text+0x3e13): more undefined references to `mpi_bcast_'
<br />follow
<br />swap_comm.o(.text+0x35): In function `swap_comm_swap_comm_init_':
<br />rrier_':
<br />
<br />wrap_mpi.o(.text+0x1fd9): In function `mpiallgatherint_':
<br />: undefined reference to `mpi_allgather_'
<br />gmake: *** Error 2
<br />---------------------------------------------------------------
<br />
<br />Any thoughts?
<b!
r />
<br />Cathy
------------------------------
PosterjmccaaPostedFri Oct 15, 2004 2:55 pm MDT, http://bb.cgd.ucar.edu//viewtopic.php?p=79#79
Message: We'll need more information to help:
<br />What version of mpi are you using?
<br />What compilers (c and fortran, exact versions) are you using?
<br />What configure command did you issue to configure the model?
<br />
<br />If you've modified the configure script or your Makefile, please describe those changes as well.
<br />
<br />Jim
------------------------------
Postercathryn.meyer at yale.eduPostedFri Oct 15, 2004 3:19 pm MDT, http://bb.cgd.ucar.edu//viewtopic.php?p=80#80
Message: Here is all the cluster info for you:
<br />
<br />pgf77 5.2-2
<br />pgcc 5.2-2
<br />
<br />Linux bulldoga.wss.yale.edu 2.4.20-31.9smp #1 SMP Tue Apr 13 17:40:10 EDT 2004 i686 i686 i386 GNU/Linux
<br />
<br />Dual cpus of the following type:
<br />vendor_id : GenuineIntel
<br /> cpu family : 15
<br /> model : 2
<br /> model name : Intel(R) Xeon(TM) CPU 2.60GHz
<br /> stepping : 9
<br /> cpu MHz : 2599.961
<br /> cache size : 512 KB
<br /> physical id : 0
<br /> siblings : 1
<br /> fdiv_bug : no
<br /> hlt_bug : no
<br /> f00f_bug : no
<br /> coma_bug : no
<br /> fpu : yes
<br /> fpu_exception : yes
<br /> cpuid level : 2
<br /> wp : yes
<br /> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca
<br /> cmov
<br /> pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm
<br /> bogomips : 5190.45
<br />
<br /> 80 IBM Blade !
Server HS20 nodes
<br /> 2GB RAM per node
<br /> Networking: GB Ethernet
<br />
<br /> MPICH mpich-1.2.5-ch_p4
<br />-----------------------------------------------------------------------------------------
<br />
<br />Also, I did not change the Makefile, and the configure command I used was:
<br />
<br />CAMROOT/models/atm/cam/bld/configure -i
<br />
<br />This gave me the following error:
<br />
<br />testing MPI library... **** FAILED ****
<br />Issued the command:
<br />gmake test_mpi 2>&1
<br />
<br />The output was:
<br />cat: Srcfiles: No such file or directory
<br />Makefile:1030: /home/ccm33/Depends: No such file or directory
<br />/home/ccm33/cam1/models/atm/cam/bld/mkSrcfiles > /home/ccm33/Srcfiles
<br />/home/ccm33/cam1/models/atm/cam/bld/mkDepends Filepath Srcfiles > /home/ccm33/De
<br />pends
<br />pgf90 -c -I. -I/home/ccm33/cam1/models/atm/cam/src/physics/cam1 -I/home/ccm33/ca
<br />m1/models/atm/ca!
m/src/dynamics/eul -I/home/ccm33/cam1/models/atm/cam/src/cont!
rol
<br
/> -I/home/ccm33/cam1/models/csm_share/shr -I/home/ccm33/cam1/models/atm/cam/src/u
<br />tils -I/home/ccm33/cam1/models/utils/timing -I/home/ccm33/cam1/models/atm/cam/sr
<br />c/advection/slt -I/home/ccm33/cam1/models/atm/cam/src/ocnsice/dom -I/home/ccm33/
<br />cam1/models/lnd/clm2/src/main -I/home/ccm33/cam1/models/lnd/clm2/src/biogeophys
<br />-I/home/ccm33/cam1/models/lnd/clm2/src/biogeochem -I/home/ccm33/cam1/models/lnd/
<br />clm2/src/mksrfdata -I/home/ccm33/cam1/models/lnd/clm2/src/riverroute -I/home/ccm
<br />33/cam1/models/ice/csim4 -I/home/ccm33/netcdf-3.5.1/include -I/usr/local/cluster
<br />/mpi/include -I/home/ccm33/esmf/mod/modO/linux_pgi -I/home/ccm33/netcdf-3.5.1/l
<br />ib -r8 -i4 -DCAM -DNO_SHR_VMATH -DHIDE_SHR_MSG -DLINUX -Mdalign -Mextend -DPGF9
<br />0 -byteswapio -O2 test_mpi.F
<br />pgf90 -o test_mpi test_mpi.o -L/usr/local/cluster/mpi/lib -lmpich
<br />test_mpi.o(.text+0x2c): In function `MAIN_':
<br />: undefined reference to `mpi_init_'
<br />gm!
ake: *** Error 2
<br />--------------------------------------------------------------------------------------------------
<br />
<br />Cathy
------------------------------
Postercathryn.meyer at yale.eduPostedFri Oct 15, 2004 7:42 pm MDT, http://bb.cgd.ucar.edu//viewtopic.php?p=81#81
Message: I seem to have gotten past the above error and now the model configures okay but then when I go to compile it (using the gmake command) I get the error: "Can't find include file mpif.h (test_mpi.F :3)". Although the file mpif.h is in the directory specified correctly as the mpi include directory. Any thoughts as to why the compiler can't see this file?
<br />
<br />Cathy
------------------------------
PosterjmccaaPostedFri Oct 15, 2004 8:15 pm MDT, http://bb.cgd.ucar.edu//viewtopic.php?p=82#82
Message: Cathy,
<br />
<br />Because you used configure interactively, I really can't tell what's going on unless you send a log of your configure session. Is there something you're trying to accomplish that can't be done on the command line?
<br />
<br />The most likely cause of the mpif.h error is that the line in your generated Makefile that starts with INC_MPI doesn't actually point to a directory that contains mpif.h. For instance, on my system, i get the following line:
<br />INC_MPI := /usr/local/mpich-1.2.5-pgi-hpf-cc-5.1-3/include
<br />and in that directory is the mpif.h file that I can list as follows:
<br />>> ls /usr/local/mpich-1.2.5-pgi-hpf-cc-5.1-3/include/mpif.h
<br />-rw-r--r-- 1 root root 10009 Apr 13 2004 /usr/local/mpich-1.2.5-pgi-hpf-cc-5.1-3/include/mpif.h
<br />
<br />Jim
------------------------------
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