[Paraview] Compiling Paraview errors on Oak Ridge HPC Titan

[Burlen Loring]

You may be missing a gni library? use nm on the .a files to figure out 
if it has the missing symbols. Also with static linking the order you 
list the libraries matters. in your case you'll need to list the gni 
library(ies) before the mpich libarary on the link line. You could check 
if that's your problem by running "make VERBOSE=1" and examining the 
order that's used. You could potentiall force the linker to not care 
about library order by enclosing mpi and it's dependencies in 
--start-group , --end-group linker options...

It's a little more work but in my experience things will go smoother for 
you if you avoid the CC wrappers when building ParaView. also pgi is 
used relatively rarely compared to gcc so you're asking for problems. 
Fine if you're prepared to dig in a deal with them, but if you want it 
just to work, then use gcc.

to avoid cc wrappers one thing you need to do is find mpi and its 
dependencies. if you run "CC --verbose" you can see the link options 
used by CC. You want to extract just the ones you need and no others. 
then since you want static linking you might need determine the order of 
the libraries. to give you some ideas about what you're after, I'll 
attach result of this process from NERSC's Cray XC30 Edison, but watch 
out I used dynamic linking so it's not exactly what you need.

hope this will help

On 06/07/2013 07:02 AM, Hong Yi wrote:
>
> I've been working on building ParaView on Oak Ridge HPC Titan (Cray 
> HPC system) for its coprocessing/catalyst libraries to be linked to 
> PHASTA simulation code running on Titan for in-situ coprocessing as 
> well as live monitoring via pvserver which are already built and can 
> run successfully on Oak Ridge visualization cluster Lens. There are 
> some "undefined references" errors while building ParaView on Titan 
> which I already contacted Titan HPC support specialist but we are 
> currently out of ideas on what to try next to fix these compilation 
> errors. So I am hoping to get some ideas from people on this list who 
> might have experienced such issues and might have some fresh ideas to 
> help us move forward.
>
> Specifically, we have to build ParaView on titan with 
> "BUILD_SHARED_LIB" off so it can be statically linked to PHASTA 
> simulation code and run on the Titan compute nodes. I set "apron" as 
> MPIEXEC, set Cray pgi  wrapper compilers CC, cc, ftn as 
> MPI_CXX_COMPILER, MPI_C_COMPILER, and MPI_FORTRAN_COMPILER, set 
> Cray_mpich2/5.6.3 as MPI libraries to link to.  First, I tried to use 
> gnu compilers as CMAKE compilers and was able to configure and then 
> build ParaView, but got the following "undefined references" errors in 
> libmpich.a such as the following when it was about 51% built:
>
> ------------------------------------
>
> Linking CXX executable ../../../bin/vtkpython
>
> /opt/cray/mpt/5.6.3/gni/mpich2-pgi/119/lib/libmpich.a(gni_poll.o): In 
> function `MPID_nem_gni_process_async_mhndl_ack':
>
> gni_poll.c:(.text+0x3d): undefined reference to `GNI_SmsgRelease'
>
> gni_poll.c:(.text+0x58): undefined reference to `gni_err_str'
>
> --------------------------------
>
> Then as suggested by HPC support specialist, I changed to use cray pgi 
> wrapper compilers CC, cc, ftn as corresponding CMAKE compilers (rather 
> than use gnu compilers as I initially did), however, I got the 
> following "undefined references" errors when it was about 19% built:
>
> --------------------------------
>
> /ccs/proj/nfi010/ParaView/ParaView-3.98.1-source/VTK/Utilities/KWSys/vtksys/SystemTools.cxx:1768: 
> warning: Using 'getpwnam' in statically linked applications requires 
> at runtime the shared libraries from the glibc version used for linking
>
> /opt/pgi/12.10.0/linux86-64/12.10/lib/libCmpz.a(eh_util.o): In 
> function `std::uncaught_exception(void)':
>
> eh_util.c:(.text+0x307): undefined reference to 
> `__zceh_uncaught_exception'
>
> /usr/bin/ld: link errors found, deleting executable 
> `../../../bin/vtkHashSource-pv3.98'
>
> child process exit status 1: /sw/xk6/altd/bin/ld
>
> make[2]: *** [bin/vtkHashSource-pv3.98] Error 2
>
> make[1]: *** 
> [VTK/Utilities/HashSource/CMakeFiles/vtkHashSource.dir/all] Error 2
>
> make: *** [all] Error 2
>
> ---------------------------------------
>
> Not sure why pgi compiler is trying to use glibc which then leads to 
> the undefined reference error as shown above with libCmpz.a. This 
> problem does not happen if we use gnu compilers for CMake compilers 
> but we got another set of undefined references in libmpich.a as 
> described above.
>
> Anybody has any ideas on what is wrong here and what we should try 
> next to resolve these "undefined references" errors?
>
> Many thanks for any suggestions you can provide!
>
> Hong
>
>
>
> _______________________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://www.paraview.org/mailman/listinfo/paraview

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.paraview.org/pipermail/paraview/attachments/20130607/2f12681b/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: config-pv3-mesa.sh
Type: application/x-shellscript
Size: 2393 bytes
Desc: not available
URL: <http://www.paraview.org/pipermail/paraview/attachments/20130607/2f12681b/attachment.bin>