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From: Jung, Soon-wook (genius00_at_[hidden])
Date: 2007-05-24 10:38:40


Hello, users?

Currently, I'm trying to compile XOOPIC (2D plasma simulation program, MPI
parallel operation available) in conjunction with MPI.

I had no problem with XOOPIC compilation in single-machine operation mode;
however, when MPI mode is turned enabled, it generated about four or more
page error messages.

Linux cluster that I'm using is supposed is under single-machine operation
due to some technical problems. (It means that only one node is currently
working.)

 

The error shown below doesn't appear to originate from XOOPIC, but rather
from MPI linkage.

(I've made a simple mpi-test c program, compiled with mpicc and run with
mpirun. It just worked fine.)

 

* I have MPI version 1.2.7p1

* gcc, g++ version 3.4.6 (both)

* OS: centOS

* Both MPICH & MPICH2 are installed in the machine. (/usr/local/mpich,
/usr/local/mpich2)

 

1. This is PATH & LD_LIBRARY_PATH

---------------------------------------------

Echo $PATH

/usr/kerberos/sbin:/usr/local/mpich/bin:/usr/local/mpich2/bin:/usr/local/pbs
/sbin:/usr/local/pbs/bin:/usr/local/maui/sbin:/usr/local/maui/bin:/usr/local
/bwatch:/usr/local/hpc/bin:/opt/intel/compiler/9.1/bin:/opt/absoft/bin:/usr/
local/ldap/bin:/usr/local/ldap/sbin:/usr/kerberos/bin:/usr/local/mpich/bin:/
usr/local/mpich2/bin:/usr/local/pbs/sbin:/usr/local/pbs/bin:/usr/local/maui/
sbin:/usr/local/maui/bin:/usr/local/bwatch:/usr/local/hpc/bin:/opt/intel/com
piler/9.1/bin:/opt/absoft/bin:/usr/local/ldap/bin:/usr/local/ldap/sbin:/usr/
local/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/local/ganglia/bin:/home/jooilyoo
n/bin:/usr/local/ganglia/bin:/usr/local/mpich:/usr/local/mpich2

 

Echo $LD_LIBRARY_PATH

/opt/intel/compiler/9.1/lib:/opt/intel/mkl/8.1.1/lib/em64t::/usr/local/mpich
/bin:/usr/local/mpich2/bin/:/usr/local/mpich:/usr/local/mpich2:/usr/local/mp
ich/lib:/usr/local/mpich2/lib

------------------------------------------------

 

 

2. Below is a message relevant to MPI during configuration. (It seems no
problem occurs.)

------------------------------------------------

checking for mpicxx... /usr/local/mpich/bin/mpicxx

checking for mpicc... /usr/local/mpich/bin/mpicc

------------------------------------------------

 

3. Below is a message in config.log

------------------------------------------------

configure:7702: checking for mpicxx

configure:7720: found /usr/local/mpich/bin/mpicxx

configure:7732: result: /usr/local/mpich/bin/mpicxx

configure:7833: checking for mpicc

configure:7851: found /usr/local/mpich/bin/mpicc

configure:7863: result: /usr/local/mpich/bin/mpicc

-------------------------------------------------

 

4. This is a error message when make is executed.

--------------------------------------------------

g++ -Wall -Wno-unused -g -DDEBUG -DUNIX -DMPI_VERSION -DMPI_DEBUG -o
xoopic main.o xgmain.o -L../otools -lotools -L../advisor -ladvisor
-L../physics -lphysics -lotools -ladvisor -Wl,-rpath,. -L/usr/lib -ltk8.4
-L/usr/lib -ltcl8.4 -L/usr/local/xgrafix/lib
-Wl,-rpath,/usr/local/xgrafix/lib -lXGC250 -L/usr/X11R6/lib64
-Wl,-rpath,/usr/X11R6/lib64 -lXpm -ldl -L/usr/lib -lz -Wl,-rpath,/usr/lib
-lm

 

main.o(.text+0x18d): In function `main':

/home/jooilyoon/xoopic2/xg/main.cpp:72: undefined reference to `MPI_Init'

main.o(.text+0x19c):/home/jooilyoon/xoopic2/xg/main.cpp:76: undefined
reference to `MPI_Comm_group'

main.o(.text+0x1b1):/home/jooilyoon/xoopic2/xg/main.cpp:77: undefined
reference to `MPI_Comm_create'

main.o(.text+0x1c1):/home/jooilyoon/xoopic2/xg/main.cpp:78: undefined
reference to `MPI_Comm_rank'

../otools/libotools.a(diagn.o)(.text+0x85de): In function
`Diagnostics::UpdatePreDiagnostics()':

/home/jooilyoon/xoopic2/otools/diagn.cpp:867: undefined reference to
`lam_mpi_sum'

../otools/libotools.a(diagn.o)(.text+0x85e3):/home/jooilyoon/xoopic2/otools/
diagn.cpp:867: undefined reference to `lam_mpi_float'

../otools/libotools.a(diagn.o)(.text+0x85ed):/home/jooilyoon/xoopic2/otools/
diagn.cpp:867: undefined reference to `MPI_Reduce'

../otools/libotools.a(diagn.o)(.gnu.linkonce.r._ZTVN3MPI2OpE+0x20):
undefined reference to `MPI::Op::Init(void (*)(void const*, void*, int,
MPI::Datatype const&), bool)'

../otools/libotools.a(diagn.o)(.gnu.linkonce.r._ZTVN3MPI2OpE+0x28):
undefined reference to `MPI::Op::Free()'

../otools/libotools.a(diagn.o)(.gnu.linkonce.t._ZN4PMPI8Datatype8Set_nameEPK
c+0x1d): In function `PMPI::Datatype::Set_name(char const*)':

/usr/include/mpi2cxx/datatype_inln.h:260: undefined reference to
`MPI_Type_set_name'

../otools/libotools.a(diagn.o)(.gnu.linkonce.t._ZN4PMPI8Datatype8Set_attrEiP
Kv+0x23): In function `PMPI::Datatype::Set_attr(int, void const*)':

/usr/include/mpi2cxx/datatype_inln.h:253: undefined reference to
`MPI_Type_set_attr'

../otools/libotools.a(diagn.o)(.gnu.linkonce.t._ZNK4PMPI8Datatype8Get_nameEP
cRi+0x25): In function `PMPI::Datatype::Get_name(char*, int&) const':

/usr/include/mpi2cxx/datatype_inln.h:246: undefined reference to
`MPI_Type_get_name'

../otools/libotools.a(diagn.o)(.gnu.linkonce.t._ZNK4PMPI8Datatype12Get_envel
opeERiS1_S1_S1_+0x3e): In function `PMPI::Datatype::Get_envelope(int&, int&,
int&, int&) const':

...........

(about a few pages of similar errors follow)

............

../otools/libotools.a(dump.o)(.text+0xd1a): In function `Quit':

/home/jooilyoon/xoopic2/otools/dump.cpp:375: undefined reference to
`MPI_Finalize'

collect2: ld returned 1 exit status

make[2]: *** [xoopic] Error 1

make[2]: Leaving directory `/home/jooilyoon/xoopic2/xg'

make[1]: *** [all-recursive] Error 1

make[1]: Leaving directory `/home/jooilyoon/xoopic2'

make: *** [all] Error 2

[root_at_node1 xoopic2]#

--------------------------------------------------------

 

All messages shown during configure, make, make install + config.log files
are compressed into mpi-output.tar, attached in this e-mail.

Can anybody please advise me on this problem? Any suggestion would be
sincerely appreciated.

Thanks.

 

Jung, Soon-Wook