Hello, users?

Currently, Im 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 Im 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 doesnt appear to originate from XOOPIC, but rather from MPI linkage.

(Ive 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/compiler/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/jooilyoon/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/mpich/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_nameEPKc+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_attrEiPKv+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_nameEPcRi+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_envelopeERiS1_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@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