[CIG-SHORT] Problem installing nemesis

[Brad Aagaard]

Laura-

The config.log indicates that the mpich library is found, but there are 
unresolved symbols when linking with it (see except below). There are 
two ways to solve this. (1) Switch to using mpicc and mpiCC to compile C 
and C++ source code that uses MPI (i.e., nemesis and PyLith). You can 
set things in the command line to configure using CC=mpicc nd CXX=mpiCC. 
(2) Look at the output of "mpicc -v" and see what libraries are needed 
to link MPI programs and add these to the command line via 
LIBRARIES="-lmpich OTHER LIBRARIES GO HERE".

Excerpt from config.log:

configure:3149: gcc -o conftest -g -O2 
-I/home/alisic/opt/petsc-dev/linux_g++_debug/include 
-L/home/alisic/opt/petsc-dev/linux_g++_debug/lib conftest.c -lmpich   >&5
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `pthread_create'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `pthread_getspecific'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `pthread_key_delete'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `aio_read64'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `aio_error64'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `aio_suspend64'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `pthread_key_create'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `aio_write64'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `aio_return64'
/home/alisic/opt/petsc-dev/linux_g++_debug/lib/libmpich.so: undefined 
reference to `pthread_setspecific'
collect2: ld returned 1 exit status

Brad

Laura Alisic wrote:
> Hi,
> 
> I am in the process of installing PyLith 1.0.1 from source on a linux 
> machine (32-bit). So far I have installed all dependencies of PyLith, 
> apart from nemesis. During configuration of nemesis, it doesn't seem to 
> be able to find the MPI library, despite the fact it's being called in 
> the configure command I used. Also, it's set in my .cshrc file in 
> $LD_LIBRARY_PATH. 
> 
> My $LD_LIBRARY_PATH looks as follows:
> stapi% echo $LD_LIBRARY_PATH                                            
>                                              
> /home/alisic/Snac/build/lib:/home/alisic/StGermain/StGermain/build/lib:/home/alisic/opt/petsc-dev/lib/linux_g++_debug:/home/alisic/opt/petsc-dev/linux_g++_debug/lib
> 
> The MPI lib directory contains the following:
> stapi% ls /home/alisic/opt/petsc-dev/linux_g++_debug/lib
> libchaco.a         libmpich.a           libmpich.so@       
> libpetsccontrib.so*  libpetscmat.a     libpetscts.a
> libfmpich.a        libmpichcxx.a        libmpich.so.1@     libpetscdm.a  
>        libpetscmat.so*   libpetscts.so*
> libfmpich.so@      libmpichcxx.so@      libmpich.so.1.1*   
> libpetscdm.so*       libpetscsnes.a    libpetscvec.a
> libfmpich.so.1@    libmpichcxx.so.1@    libpetsc.a         
> libpetscksp.a        libpetscsnes.so*  libpetscvec.so*
> libfmpich.so.1.1*  libmpichcxx.so.1.1*  libpetsccontrib.a  
> libpetscksp.so*      libpetsc.so*      mpich2-ch3.pc
> 
> The config.log is attached. 
> 
> How could I go about solving this issue? I've been trying several 
> configure options without success.
> Any help would be greatly appreciated!
> 
> Thanks,
> Laura
> 
> 
> ===============================
>     Laura Alisic
>     ----------------
>     PhD Student in Geophysics
>     Seismological Laboratory
>     California Institute of Technology
>     alisic at gps.caltech.edu <mailto:alisic at gps.caltech.edu>
>     www.gps.caltech.edu/~alisic <http://www.gps.caltech.edu/~alisic>
> ===============================
> 
> 
> 
> ------------------------------------------------------------------------
> 
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