[Q-e-developers] Compiling error on Cray XE6 (UNCLASSIFIED)

[Ivan Girotto]

Dear Miller,

the missing symbols are contained within the OpneMPI library (see 
below). This is because you are linking Blacs compiled for OpenMPI.

[igirotto at argo lib]$ pwd
/opt/openmpi/1.4.5/pgi/10.9/lib

[igirotto at argo lib]$ readelf -Ws libmpi.so | grep ompi_mpi_float
    992: 00000000002d22a0   512 OBJECT  GLOBAL DEFAULT   21 
ompi_mpi_float_int
   1880: 00000000002d08a0   512 OBJECT  GLOBAL DEFAULT   21 ompi_mpi_float
   6886: 00000000002d22a0   512 OBJECT  GLOBAL DEFAULT   21 
ompi_mpi_float_int
   7774: 00000000002d08a0   512 OBJECT  GLOBAL DEFAULT   21 ompi_mpi_float

Whether you are not using OpenMPI library you should either find the 
right version of Blacs for the MPI library you are using or switch using 
OpenMPI if it's available.
On the other hand, if you are certainly using OpenMPI to compile I guess 
something it's missing within the environment as suggested previously 
from Layla.

Ivan

-- 

Ivan Girotto - igirotto at ictp.it
High Performance Computing Specialist
Information&  Communication Technology Section
The Abdus Salam - www.ictp.it
International Centre for Theoretical Physics
Strada Costiera, 11 - 34151 Trieste - IT
Tel +39.040.2240.484
Fax +39.040.2240.249



On 16/08/2012 08:52, Layla Martin-Samos wrote:
> Dear Miller, it doest not look like an espresso-Makefile (make.sys) 
> related problem but more like an environment problem. Is in the lib 
> /opt/intel/Compiler/11.1/056/mkl/lib/em64/libmkl_blacs_openmpi_lp64.a
> that the compiler does not manage to link some mpi basic definitions. 
> It really looks like something in your Cray environment has not been 
> loaded correctly, or is not compatible.
>
> hope it helps
>
> Layla
>
>
> 2012/8/15 Miller, MJ ERDC-RDE-ITL-MS Contractor 
> <MJ.Miller at erdc.dren.mil <mailto:MJ.Miller at erdc.dren.mil>>
>
>     Classification: UNCLASSIFIED
>     Caveats: FOUO
>
>     QE:
>
>     I'm trying to troubleshoot a compilation problem on our Cray XE6.
>     The code seems to compile following the instructions given in the
>     README, but fails to link with the MPI libraries as far as I can
>     see. We are getting undefined reference errors that seem to
>     indicate at least a library path problem, but may be more
>     involved. Our efforts thus far have included setting environment
>     variables as described in the README file, and swapping compiler
>     and open_mpi versions. Here is a excerpt from the compile log
>     where things start to go wrong. Please take a look and reply if
>     you can help us.
>
>     make[2]: Entering directory
>     `/work/mjmiller/espresso-5.0--htakephi/PW/src'
>
>     test -n "" && ( cd ../.. ; make -w  || exit 1) || :
>
>     mpif90 -static-intel  -openmp -o pw.x \
>
>                pwscf.o  libpw.a ../../Modules/libqemod.a
>     ../../flib/ptools.a ../../flib/flib.a ../../clib/clib.a
>     ../../iotk/src/libiotk.a -lmkl_scalapack_lp64
>     -lmkl_blacs_openmpi_lp64   -lmkl_intel_lp64  -lmkl_intel_thread
>     -lmkl_core
>
>     /opt/intel/Compiler/11.1/056/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(igesd2d_.o):
>     In function `igesd2d_':
>
>     _igesd2d_.c:(.text+0x40): undefined reference to `ompi_mpi_int'
>
>     _igesd2d_.c:(.text+0x99): undefined reference to `ompi_mpi_byte'
>
>     /opt/intel/Compiler/11.1/056/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(sgesd2d_.o):
>     In function `sgesd2d_':
>
>     _sgesd2d_.c:(.text+0x40): undefined reference to `ompi_mpi_float'
>
>     _sgesd2d_.c:(.text+0x99): undefined reference to `ompi_mpi_byte'
>
>     /opt/intel/Compiler/11.1/056/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(dgesd2d_.o):
>     In function `dsendrecv_':
>
>     _dgesd2d_.c:(.text+0x8e): undefined reference to `ompi_mpi_double'
>
>     _dgesd2d_.c:(.text+0xab): undefined reference to `ompi_mpi_double'
>
>     _dgesd2d_.c:(.text+0x101): undefined reference to `ompi_mpi_double'
>
>     _dgesd2d_.c:(.text+0x125): undefined reference to `ompi_mpi_double'
>
>     /opt/intel/Compiler/11.1/056/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(dgesd2d_.o):
>     In function `dgesd2d_':
>
>     _dgesd2d_.c:(.text+0x21a): undefined reference to `ompi_mpi_double'
>
>     _dgesd2d_.c:(.text+0x273): undefined reference to `ompi_mpi_byte'
>
>     /opt/intel/Compiler/11.1/056/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(cgesd2d_.o):
>     In function `cgesd2d_':
>
>     _cgesd2d_.c:(.text+0x99): undefined reference to `ompi_mpi_byte'
>
>     /opt/intel/Compiler/11.1/056/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(zgesd2d_.o):
>     In function `zgesd2d_':
>
>     _zgesd2d_.c:(.text+0x99): undefined reference to `ompi_mpi_byte'
>
>     /opt/intel/Compiler/11.1/056/mkl/lib/em64t/libmkl_blacs_openmpi_lp64.a(strsd2d_.o):
>
>     Thanks,
>
>     MJ Miller, Ph.D.
>
>     ERDC-DSRC
>
>     Vicksburg, MS
>
>     601-634-7465 <tel:601-634-7465>
>
>
>     Classification: UNCLASSIFIED
>     Caveats: FOUO
>
>
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>
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