[torqueusers] qsub problem

Divy Kanungo divyk at bgnet.bgsu.edu
Fri Feb 16 01:10:25 MST 2007


Hi,
We have a cluster of sixteen nodes controlled by Linux Server.We 
are currently using PBS torque (torque-1.0.1.p6) for job 
scheduling and mpich 1.2.5 for compiling parallel applications. 
We recently upgraded the Server from 2.6.5 to 2.6.17 and also 
gcc from 3.4.3 to gcc 4.1.1
The job file works fine for other programs. But I have a program 
which makes extensive use os standard library functions (std::) 
and that program is not giving error when I compile it outside 
the job file (i.e. mpiCC from command prompt) but when I do the 
same thing i.e. mpiCC issued inside job file. I get the 
following errors:

/usr/local/lib/libbg.so: undefined reference to 
`__gnu_cxx::__exchange_and_add(int volatile*, int)'
/usr/local/lib/libbg.so: undefined reference to 
`std::_Rb_tree_decrement(std::_Rb_tree_node_base*)'
/usr/local/lib/libbg.so: undefined reference to 
`std::_List_node_base::unhook()'
/usr/local/lib/libbg.so: undefined reference to 
`std::_List_node_base::hook(std::_List_node_base*)'
/usr/local/lib/libbg.so: undefined reference to 
`std::basic_string<char, std::char_traits<char>, 
std::allocator<char> >::_Re
p::_S_empty_rep_storage'
/usr/local/lib/libbg.so: undefined reference to 
`std::_Rb_tree_insert_and_rebalance(bool, 
std::_Rb_tree_node_base*, std::_Rb
_tree_node_base*, std::_Rb_tree_node_base&)'
/usr/local/lib/libbg.so: undefined reference to 
`std::_Rb_tree_rebalance_for_erase(std::_Rb_tree_node_base*, 
std::_Rb_tree_n
ode_base&)'
/usr/local/lib/libbg.so: undefined reference to 
`std::_Rb_tree_increment(std::_Rb_tree_node_base*)'
/usr/local/lib/libbg.so: undefined reference to 
`std::basic_stringbuf<char, std::char_traits<char>, 
std::allocator<char> >::
_M_sync(char*, unsigned, unsigned)'
collect2: ld returned 1 exit status
mpiexec: Error: resolve_exe: executable "./bgtwTest.out" is not 
executable.

real    0m0.002s
user    0m0.000s
sys     0m0.000s

the Jobfile I am using is as follows:
#PBS -N my_j
#PBS -l walltime=00:12:00
#PBS -l nodes=8
#PBS -j oe
#PBS -o appl.otxt

cd $HOME
mpiCC -lbgtw -o bgtwTest.out bgtwTest.cpp
time mpiexec -n 2 ./bgtwTest.out

I dont know what's wrong. How do I get rid of this problem. Any 
help is appreciated.

Divy.




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