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/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