To add to what George said -- it looks like you have multiple
different implementations of MPI installed on your machine (LAM/MPI,
MPICH, MPICH2, ...?). Ensure that you completely compile and run
your application with *one* implementation of MPI (they are not
binary compatible).
Keep in mind that each MPI implementation is a wholly separate
project and code base. This list can only provide help with Open MPI
(not LAM/MPI, MPICH, or MPICH2). Other MPI implementations have
their own support mailing lists.
On May 24, 2007, at 11:44 AM, George Bosilca wrote:
There are 2 problems. First, it look like you're using LAM and not
Open MPI as there are some lam_ missing symbols. Second, please use
mpicxx to link your application as it will add all the missing
libraries.
george.
On May 24, 2007, at 10:38 AM, Jung, Soon-wook wrote:
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
<ompi-output.tar>
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Cisco Systems
