[FLASH-USERS] hdf5typeio error (?) for LaserSlab

[Marissa Adams]

Hi all,

I am getting the following error when trying to make an executable for the
*LaserSlab* example found in the documentation (
http://flash.uchicago.edu/~jbgallag/2012/flash4_ug/node34.html#SECTION08175000000000000000
-- I have written the exact same setup script noted in this section):

io_h5file_interface.o: In function `io_h5open_file_for_read_':
> /home/<username>/FLASH4.3/object/io_h5file_interface.c:273: undefined
> reference to `H5Pset_fapl_mpio'
> /home/<username>/FLASH4.3/object/io_h5file_interface.c:271: undefined
> reference to `H5Pset_fapl_mpio'
> io_h5file_interface.o: In function `io_h5init_file_':
> /home/<username>/FLASH4.3/object/io_h5file_interface.c:165: undefined
> reference to `H5Pset_fapl_mpio'
> /home/<username>/FLASH4.3/object/io_h5file_interface.c:163: undefined
> reference to `H5Pset_fapl_mpio'
> io_h5read_unknowns.o: In function `io_h5read_unknowns_':
> /home/<username>/FLASH4.3/object/io_h5read_unknowns.c:53: undefined
> reference to `H5Pset_dxpl_mpio'
> io_h5write_unknowns.o: In function `io_h5write_unknowns_':
> /home/<username>/FLASH4.3/object/io_h5write_unknowns.c:156: undefined
> reference to `H5Pset_dxpl_mpio'
> io_h5write_unknowns_sp.o: In function `io_h5write_unknowns_sp_':
> /home/<username>/FLASH4.3/object/io_h5write_unknowns_sp.c:237: undefined
> reference to `H5Pset_dxpl_mpio'
> make: *** [flash4] Error 1
>

​The HDF5 compiled in the* /opt/ *of the ​cluster I am on is not
parallelized. So I've compiled my own PHDF5 module in my home directory. I
have been able to successfully make with +hdf5typeio with the *Sedov*
problem, which yields nicely refined output.

On the other hand, I've tried to make a *LaserSlab* problem with +noio,
which was successful. However when running my executable I got a segfault
error, which I am not sure to be related to the problem needing
parallelized HDF5.

Looking at *io_h5file_interface.c*, there seems to be perhaps a commenting
issue (?):

 /* if we are splitting the output file ... */
>   /*  if(*io_outputSplitNum ==
> 1){
>      ierr = H5Pset_fapl_mpio(acc_template, MPI_COMM_WORLD,
> MPI_INFO_NULL);
>
> }else{
>
>   */ ierr = H5Pset_fapl_mpio(acc_template, io_comm, MPI_INFO_NULL);
>   /*} */
>

(similar set up at lines 273, 271, 165, 163)

Can someone help with this? Thanks for reading!

Best,
Marissa Adams




-- 
Marissa Adams                         E-mail: madams at pas.rochester.edu
Graduate Student                      Ph: (585) 402-5779
Department of Physics & Astronomy     Website:
http://www.pas.rochester.edu/~madams/
University of Rochester
478 Bausch & Lomb Hall
P.O. Box 270171
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