problem building with openmpi

[Wei-keng Liao]

Hi, Jim

Compiling Fortran programs is painfully slow today :(

I have not got a chance to test OpenMPI 3.0.
I tested against OpenMPI 2.1.2 and it was fine.
2.1.2 also put mpi.mod in lib folder instead of include.
PnetCDF configure.ac does not look for mpi.mod explicitly.
It just tried compile a short program that uses mpi.mod.
Please send me the file config.log, if you would like me to take a look.

I have no idea why -lpbs appears there. I assume libtool finds it from
linker dependency list. Does this only happen when building static-only
library? Did you try build shared libraries and see the same problem?

Wei-keng

On Nov 6, 2017, at 11:57 AM, Jim Edwards wrote:

> It turns out that openmpi puts it's mpi.mod in the lib instead of include directory and the pnetcdf configure wasn't finding it.
> Once I fixed this and use mpi.mod instead of mpif.h that solved the problem, however then I run into another problem at the
> link step:  
> 
>  CCLD     ncmpivalid
> 
> ld: cannot find -lpbs
> 
> I haven't figured out where the requirement on a library pbs comes from or how to get rid of it?
> 
> 
> On Mon, Nov 6, 2017 at 9:36 AM, Jim Edwards <jedwards at ucar.edu> wrote:
> 
> On Mon, Nov 6, 2017 at 9:16 AM, Jim Edwards <jedwards at ucar.edu> wrote:
> I am trying to build with openmpi/3.0.0 and intel17 and hanging in the build
> of pnetcdf.f90.   
> 
> The make output at the time is:
> make[4]: Entering directory '/glade/u/home/jedwards/src/parallel-netcdf/src/binding/f90'
> 
>   FC       pnetcdf.lo
> 
> examining the process I see:
> 
> 
> /glade/u/apps/opt/intel/2017u1/compilers_and_libraries/linux/bin/intel64/ifort -I. -I. -debug minimal -g -O0 -c pnetcdf.f90 -o pnetcdf.o -I/glade/u/apps/ch/os/usr/include -L/glade/u/apps/opt/intel/2017u1/compilers_and_libraries/linux/lib/intel64_lin -L/glade/u/apps/ch/os/usr/lib64 -L/glade/u/apps/ch/os/lib64 -L/glade/u/apps/ch/os/usr/lib -L/glade/u/apps/ch/os/lib -L/glade/u/apps/ch/opt/openmpi/3.0.0/intel/17.0.1/lib -Wl,--disable-new-dtags -Wl,-rpath,/glade/u/apps/opt/intel/2017u1/compilers_and_libraries/linux/lib/intel64_lin -Wl,-rpath,/glade/u/apps/ch/os/usr/lib64 -Wl,-rpath,/glade/u/apps/ch/os/lib64 -Wl,-rpath,/glade/u/apps/ch/os/usr/lib -Wl,-rpath,/glade/u/apps/ch/os/lib -Wl,-rpath,/glade/u/apps/ch/opt/openmpi/3.0.0/intel/17.0.1/lib -lrt -ldl
> 
> 
> 
> ​Please ignore the following incorrect statement, I did this in another window where I still had the default mpt loaded instead of openmpi, if I do this with openmpi, it still hangs. ​
> 
> 
>  
> 
> If I remove all of the -L and -rpath flags and just do:
> 
>  /glade/u/apps/opt/intel/2017u1/compilers_and_libraries/linux/bin/intel64/ifort -I. -I. -debug minimal -g -O0 -c pnetcdf.f90 -o pnetcdf.o 
> 
> That completes right away, so the problem seems to have to do with libtool.   Also building with mpt instead of openmpi on the same system works.    
> 
> Any ideas?
> 
> -- 
> Jim Edwards
> 
> CESM Software Engineer
> National Center for Atmospheric Research
> Boulder, CO 
> 
> 
> 
> -- 
> Jim Edwards
> 
> CESM Software Engineer
> National Center for Atmospheric Research
> Boulder, CO 
> 
> 
> 
> -- 
> Jim Edwards
> 
> CESM Software Engineer
> National Center for Atmospheric Research
> Boulder, CO